How to Import external HI-C map data?¶
1. From a matrix coordinate format text file¶
As shown below in example, in this format, first and second column is location on chromosome and third column is the respective value:
20000000 20000000 2692.0
20000000 20100000 885.0
20100000 20100000 6493.0
20000000 20200000 15.0
20100000 20200000 52.0
20200000 20200000 2.0
20000000 20300000 18.0
20100000 20300000 40.0
.
.
.
.
.
.
Hi-C maps data with the above format are available with this article and can be downlaoded here.
At first, we import gcMapExplorer.lib module
All neccessary modules are avaiable in gcMapExplorer.lib module
In [1]:
from gcMapExplorer import lib as gmlib
This module has methods to read and save ccmap file as shown below in the exmaple.
We read Hi-C file as follows:
In [2]:
cooReader = gmlib.importer.CooMatrixHandler('./data/CooMatrixFormat/chr15_100kb.RAWobserved')
See also
Function gcMapExplorer.lib.importer.CooMatrixHandler()
for more details.
Now, save the Hi-C map as ccmap:
We save imported Hi-C map in output
directory as
chr15_100kb_Raw_from_text.ccmap
file. To reduce the storage memory,
map file is compressed in gzip format.
In [3]:
cooReader.save_ccmaps('output/CooMatrix/chr15_100kb_Raw_from_text.ccmap', xlabels='chr15')
del cooReader # Delete object and generated any temporary files
INFO:CooMatrixHandler: Reading file: [./data/CooMatrixFormat/chr15_100kb.RAWobserved]...
INFO:CooMatrixHandler: ... Finished reading file: [./data/CooMatrixFormat/chr15_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 318258
INFO:genMapFromLists:Minimum base-pair: 20000000 and Maximum base-pair: 102500000 are present in input data
INFO:genMapFromLists:Shape of overall map: (1026, 1026)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr15_100kb_Raw_from_text.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr15_100kb_Raw_from_text.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr15_100kb_Raw_from_text.npbin] ...
INFO:save_ccmap: Finished!!!
See also
- Function
gcMapExplorer.lib.importer.CooMatrixHandler.save_ccmaps()
for more details. - Function
gcMapExplorer.lib.ccmap.save_ccmap()
for more details.
Importing from a tar archive
If a Hi-C map data file is present inside a tar archive, the map file can be directly imported as follows:
In [4]:
tarfile = 'data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz' # Input Tar archive
mapfile = '100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved' # Map file in archive
cooReader = gmlib.importer.CooMatrixHandler(mapfile, tarfile)
where, data/100kb_resolution_intrachromosomal.tar.gz
is input tar
archive and
100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved
is a map file inside the archive.
Now, save the Hi-C map as ccmap: as already shown above.
In [5]:
cooReader.save_ccmaps('output/CooMatrix/chr15_100kb_raw_from_archive.ccmap', xlabels='chr15')
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 318258
INFO:genMapFromLists:Minimum base-pair: 20000000 and Maximum base-pair: 102500000 are present in input data
INFO:genMapFromLists:Shape of overall map: (1026, 1026)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr15_100kb_raw_from_archive.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr15_100kb_raw_from_archive.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr15_100kb_raw_from_archive.npbin] ...
INFO:save_ccmap: Finished!!!
Convert several files from a tar archive¶
100kb_resolution_intrachromosomal.tar.gz
file contains six Hi-C map
data files. Through a for
loop, these files can be imported and
saved. Path to these files in the tar archive are as follows:
100kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_100kb.RAWobserved
100kb_resolution_intrachromosomal/chr5/MAPQGE30/chr5_100kb.RAWobserved
100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved
100kb_resolution_intrachromosomal/chr20/MAPQGE30/chr20_100kb.RAWobserved
100kb_resolution_intrachromosomal/chr21/MAPQGE30/chr21_100kb.RAWobserved
100kb_resolution_intrachromosomal/chr22/MAPQGE30/chr22_100kb.RAWobserved
These file names have a pattern, and we utilize this pattern to form a
name inside for
loop.
In [6]:
tarfile = 'data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz'
chroms = [1, 5, 15, 20, 21, 22] # List of chromosomes
# Loop for each chromosome
inputFileList = []
outputFileList = []
xlabels = []
for chrom in chroms:
mapfile = '100kb_resolution_intrachromosomal/chr{0}/MAPQGE30/chr{0}_100kb.RAWobserved' .format(chrom)
inputFileList.append(mapfile)
output_file = 'output/CooMatrix/chr{0}_100kb_RawObserved.ccmap' .format(chrom) # Output file name
outputFileList.append(output_file)
xlabels.append( 'chr{0}'.format(chrom) )
cooReader = gmlib.importer.CooMatrixHandler(inputFileList, tarfile)
cooReader.save_ccmaps(outputFileList, xlabels=xlabels)
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 2435300
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 249200000 are present in input data
INFO:genMapFromLists:Shape of overall map: (2493, 2493)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr1_100kb_RawObserved.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr1_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr1_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr5/MAPQGE30/chr5_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr5/MAPQGE30/chr5_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 1533205
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 180800000 are present in input data
INFO:genMapFromLists:Shape of overall map: (1809, 1809)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr5_100kb_RawObserved.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr5_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr5_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 318258
INFO:genMapFromLists:Minimum base-pair: 20000000 and Maximum base-pair: 102500000 are present in input data
INFO:genMapFromLists:Shape of overall map: (1026, 1026)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr15_100kb_RawObserved.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr15_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr15_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr20/MAPQGE30/chr20_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr20/MAPQGE30/chr20_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 179488
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 62900000 are present in input data
INFO:genMapFromLists:Shape of overall map: (630, 630)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr20_100kb_RawObserved.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr20_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr20_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr21/MAPQGE30/chr21_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr21/MAPQGE30/chr21_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 60664
INFO:genMapFromLists:Minimum base-pair: 9400000 and Maximum base-pair: 48100000 are present in input data
INFO:genMapFromLists:Shape of overall map: (482, 482)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr21_100kb_RawObserved.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr21_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr21_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr22/MAPQGE30/chr22_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr22/MAPQGE30/chr22_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 59429
INFO:genMapFromLists:Minimum base-pair: 16000000 and Maximum base-pair: 51200000 are present in input data
INFO:genMapFromLists:Shape of overall map: (513, 513)
INFO:save_ccmap: Saving ccmap to file [output/CooMatrix/chr22_100kb_RawObserved.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr22_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/CooMatrix/chr22_100kb_RawObserved.npbin] ...
INFO:save_ccmap: Finished!!!
Now, in output
directory, all files from archive are saved. These
files can be used either with browser to visualize or for further
analysis.
Convert to gcmap
file¶
The contact map files can be converted to gcmap
format file.
See also
- Function
gcMapExplorer.lib.importer.CooMatrixHandler.save_gcmap()
for more details.
In [7]:
tarfile = 'data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz'
chroms = [1, 5, 15, 20, 21, 22] # List of chromosomes
# Loop for each chromosome
inputFileList = []
outputFileList = []
xlabels = []
for chrom in chroms:
mapfile = '100kb_resolution_intrachromosomal/chr{0}/MAPQGE30/chr{0}_100kb.RAWobserved' .format(chrom)
inputFileList.append(mapfile)
output_file = 'output/CooMatrix/chr{0}_100kb_RawObserved.ccmap' .format(chrom) # Output file name
outputFileList.append(output_file)
xlabels.append( 'chr{0}'.format(chrom) )
cooReader = gmlib.importer.CooMatrixHandler(inputFileList, tarfile)
cooReader.save_gcmap('output/CooMatrix/rawObserved_100kb.gcmap', xlabels=xlabels, coarsingMethod='sum', compression='lzf')
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 2435300
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 249200000 are present in input data
INFO:genMapFromLists:Shape of overall map: (2493, 2493)
INFO:addCCMap2GCMap: Opened file [output/CooMatrix/rawObserved_100kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/CooMatrix/rawObserved_100kb.gcmap] for [chr1] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr1] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr1] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr1] ...
INFO:addCCMap2GCMap: Closed file [output/CooMatrix/rawObserved_100kb.gcmap]...
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr5/MAPQGE30/chr5_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr5/MAPQGE30/chr5_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 1533205
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 180800000 are present in input data
INFO:genMapFromLists:Shape of overall map: (1809, 1809)
INFO:addCCMap2GCMap: Opened file [output/CooMatrix/rawObserved_100kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/CooMatrix/rawObserved_100kb.gcmap] for [chr5] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr5] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr5] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr5] ...
INFO:addCCMap2GCMap: Closed file [output/CooMatrix/rawObserved_100kb.gcmap]...
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 318258
INFO:genMapFromLists:Minimum base-pair: 20000000 and Maximum base-pair: 102500000 are present in input data
INFO:genMapFromLists:Shape of overall map: (1026, 1026)
INFO:addCCMap2GCMap: Opened file [output/CooMatrix/rawObserved_100kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/CooMatrix/rawObserved_100kb.gcmap] for [chr15] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr15] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr15] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr15] ...
INFO:addCCMap2GCMap: Closed file [output/CooMatrix/rawObserved_100kb.gcmap]...
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr20/MAPQGE30/chr20_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr20/MAPQGE30/chr20_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 179488
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 62900000 are present in input data
INFO:genMapFromLists:Shape of overall map: (630, 630)
INFO:addCCMap2GCMap: Opened file [output/CooMatrix/rawObserved_100kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/CooMatrix/rawObserved_100kb.gcmap] for [chr20] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr20] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr20] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr20] ...
INFO:addCCMap2GCMap: Closed file [output/CooMatrix/rawObserved_100kb.gcmap]...
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr21/MAPQGE30/chr21_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr21/MAPQGE30/chr21_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 60664
INFO:genMapFromLists:Minimum base-pair: 9400000 and Maximum base-pair: 48100000 are present in input data
INFO:genMapFromLists:Shape of overall map: (482, 482)
INFO:addCCMap2GCMap: Opened file [output/CooMatrix/rawObserved_100kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/CooMatrix/rawObserved_100kb.gcmap] for [chr21] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr21] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr21] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr21] ...
INFO:addCCMap2GCMap: Closed file [output/CooMatrix/rawObserved_100kb.gcmap]...
INFO:CooMatrixHandler: Extracting-Reading [100kb_resolution_intrachromosomal/chr22/MAPQGE30/chr22_100kb.RAWobserved] from [data/CooMatrixFormat/100kb_resolution_intrachromosomal.tar.gz]...
INFO:CooMatrixHandler: ...Finished extracting and reading [100kb_resolution_intrachromosomal/chr22/MAPQGE30/chr22_100kb.RAWobserved]
INFO:genMapFromLists: Total number of data in input file: 59429
INFO:genMapFromLists:Minimum base-pair: 16000000 and Maximum base-pair: 51200000 are present in input data
INFO:genMapFromLists:Shape of overall map: (513, 513)
INFO:addCCMap2GCMap: Opened file [output/CooMatrix/rawObserved_100kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/CooMatrix/rawObserved_100kb.gcmap] for [chr22] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr22] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr22] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr22] ...
INFO:addCCMap2GCMap: Closed file [output/CooMatrix/rawObserved_100kb.gcmap]...
2. From HOMER Hi-C interaction matrix format¶
HOMER package contains modules to analyze genome wide interaction data. It creates Hi-C matrix in a specific format as shown in this link.
Covert to ccmap¶
An example input file human_INL_sample1_matrix_1Mb_raw.txt
is
present in data/HomerFormat
directory. Below, we read it and convert
it to .ccmap
formats. The input file contains several chromosomes,
therefore, several .ccmap
files will be generated for each
respective chromosome.
Ouput .ccmap
files with suffix='_sample1'
will be saved in
output/homer
directory.
See also
Class gcMapExplorer.lib.importer.HomerInputHandler()
for more details.
In [8]:
# Initialize
homer_reader = gmlib.importer.HomerInputHandler('data/HomerFormat/human_INL_sample1_matrix_1Mb_raw.txt')
# Convert and save
homer_reader.save_ccmaps('output/homer', suffix='_sample1')
# Delete all temporary files, neccessary, automatically deleted
del homer_reader
INFO:HomerInputHandler: Getting chromosome list and resolution from Input Files ...
INFO:HomerInputHandler: Resolution: 1mb
INFO:HomerInputHandler: Following chromsomes found in input files:
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrMT
chrX
chrY
INFO:HomerInputHandler: Reading [data/HomerFormat/human_INL_sample1_matrix_1Mb_raw.txt] file ...
INFO:HomerInputHandler: ... Finished reading [data/HomerFormat/human_INL_sample1_matrix_1Mb_raw.txt] file ...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr1_os2op88v.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr1_os2op88v.tmp]
INFO:genMapFromLists: Total number of data in input file: 40344
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 249000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (250, 250)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr1_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr1_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr1_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr2_s2naz0mw.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr2_s2naz0mw.tmp]
INFO:genMapFromLists: Total number of data in input file: 46886
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 243000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (244, 244)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr2_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr2_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr2_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr3_2wk51mvy.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr3_2wk51mvy.tmp]
INFO:genMapFromLists: Total number of data in input file: 33308
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 197000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (198, 198)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr3_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr3_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr3_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr4_r259nr74.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr4_r259nr74.tmp]
INFO:genMapFromLists: Total number of data in input file: 29054
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 191000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (192, 192)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr4_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr4_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr4_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr5_iw9vukuv.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr5_iw9vukuv.tmp]
INFO:genMapFromLists: Total number of data in input file: 26286
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 180000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (181, 181)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr5_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr5_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr5_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr6_r9501e3v.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr6_r9501e3v.tmp]
INFO:genMapFromLists: Total number of data in input file: 25032
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 171000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (172, 172)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr6_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr6_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr6_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr7_9fjq0vyg.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr7_9fjq0vyg.tmp]
INFO:genMapFromLists: Total number of data in input file: 20748
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 159000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (160, 160)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr7_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr7_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr7_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr8_f6aj3qtd.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr8_f6aj3qtd.tmp]
INFO:genMapFromLists: Total number of data in input file: 18371
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 146000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (147, 147)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr8_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr8_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr8_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr9_aeb9ztst.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr9_aeb9ztst.tmp]
INFO:genMapFromLists: Total number of data in input file: 11414
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 141000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (142, 142)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr9_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr9_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr9_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr10_38y06zud.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr10_38y06zud.tmp]
INFO:genMapFromLists: Total number of data in input file: 15560
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 135000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (136, 136)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr10_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr10_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr10_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr11_ftyreanw.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr11_ftyreanw.tmp]
INFO:genMapFromLists: Total number of data in input file: 15429
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 134000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (135, 135)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr11_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr11_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr11_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr12_dd_54_jc.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr12_dd_54_jc.tmp]
INFO:genMapFromLists: Total number of data in input file: 14928
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 133000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (134, 134)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr12_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr12_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr12_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr13_lprd76h8.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr13_lprd76h8.tmp]
INFO:genMapFromLists: Total number of data in input file: 8675
INFO:genMapFromLists:Minimum base-pair: 19000000 and Maximum base-pair: 115000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (116, 116)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr13_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr13_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr13_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr14_gpy0w_ia.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr14_gpy0w_ia.tmp]
INFO:genMapFromLists: Total number of data in input file: 7245
INFO:genMapFromLists:Minimum base-pair: 19000000 and Maximum base-pair: 107000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (108, 108)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr14_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr14_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr14_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr15_jlzwvcxg.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr15_jlzwvcxg.tmp]
INFO:genMapFromLists: Total number of data in input file: 6249
INFO:genMapFromLists:Minimum base-pair: 20000000 and Maximum base-pair: 102000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (103, 103)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr15_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr15_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr15_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr16_o789hlat.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr16_o789hlat.tmp]
INFO:genMapFromLists: Total number of data in input file: 5629
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 90000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (91, 91)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr16_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr16_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr16_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr17_pbw8e3tc.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr17_pbw8e3tc.tmp]
INFO:genMapFromLists: Total number of data in input file: 5650
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 81000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (82, 82)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr17_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr17_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr17_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr18_9zacbp4b.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr18_9zacbp4b.tmp]
INFO:genMapFromLists: Total number of data in input file: 5581
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 78000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (79, 79)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr18_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr18_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr18_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr19_da1h_3r7.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr19_da1h_3r7.tmp]
INFO:genMapFromLists: Total number of data in input file: 3012
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 59000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (60, 60)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr19_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr19_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr19_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr20_sftox467.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr20_sftox467.tmp]
INFO:genMapFromLists: Total number of data in input file: 3563
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 62000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (63, 63)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr20_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr20_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr20_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr21_ian0ewc5.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr21_ian0ewc5.tmp]
INFO:genMapFromLists: Total number of data in input file: 1266
INFO:genMapFromLists:Minimum base-pair: 9000000 and Maximum base-pair: 48000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (49, 49)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr21_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr21_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr21_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr22_wi3r03j3.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr22_wi3r03j3.tmp]
INFO:genMapFromLists: Total number of data in input file: 1222
INFO:genMapFromLists:Minimum base-pair: 16000000 and Maximum base-pair: 51000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (52, 52)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr22_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr22_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr22_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrMT_fw97q5wp.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrMT_fw97q5wp.tmp]
INFO:genMapFromLists: Total number of data in input file: 1
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 0 are present in input data
INFO:genMapFromLists:Shape of overall map: (1, 1)
INFO:save_ccmap: Saving ccmap to file [output/homer/chrMT_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrMT_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrMT_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrX_e1hpf37f.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrX_e1hpf37f.tmp]
INFO:genMapFromLists: Total number of data in input file: 20634
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 155000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (156, 156)
INFO:save_ccmap: Saving ccmap to file [output/homer/chrX_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrX_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrX_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrY_ixqiqv7f.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrY_ixqiqv7f.tmp]
INFO:genMapFromLists: Total number of data in input file: 18
INFO:genMapFromLists:Minimum base-pair: 3000000 and Maximum base-pair: 59000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (60, 60)
INFO:save_ccmap: Saving ccmap to file [output/homer/chrY_1mb__sample1.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrY_1mb__sample1.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrY_1mb__sample1.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:HomerInputHandler: Saved ['output/homer/chr1_1mb__sample1.ccmap', 'output/homer/chr2_1mb__sample1.ccmap', 'output/homer/chr3_1mb__sample1.ccmap', 'output/homer/chr4_1mb__sample1.ccmap', 'output/homer/chr5_1mb__sample1.ccmap', 'output/homer/chr6_1mb__sample1.ccmap', 'output/homer/chr7_1mb__sample1.ccmap', 'output/homer/chr8_1mb__sample1.ccmap', 'output/homer/chr9_1mb__sample1.ccmap', 'output/homer/chr10_1mb__sample1.ccmap', 'output/homer/chr11_1mb__sample1.ccmap', 'output/homer/chr12_1mb__sample1.ccmap', 'output/homer/chr13_1mb__sample1.ccmap', 'output/homer/chr14_1mb__sample1.ccmap', 'output/homer/chr15_1mb__sample1.ccmap', 'output/homer/chr16_1mb__sample1.ccmap', 'output/homer/chr17_1mb__sample1.ccmap', 'output/homer/chr18_1mb__sample1.ccmap', 'output/homer/chr19_1mb__sample1.ccmap', 'output/homer/chr20_1mb__sample1.ccmap', 'output/homer/chr21_1mb__sample1.ccmap', 'output/homer/chr22_1mb__sample1.ccmap', 'output/homer/chrMT_1mb__sample1.ccmap', 'output/homer/chrX_1mb__sample1.ccmap', 'output/homer/chrY_1mb__sample1.ccmap'] files.
Convert from zip file to ccmap file¶
An example input zip file human_INL.zip
is present in
data/HomerFormat
directory. This zip file contains two text files.
Below, we read, combine and convert them to .ccmap
formats. The
input file contains several chromosomes, therefore, several .ccmap
files will be generated for each respective chromosome.
Ouput .ccmap
files with suffix='_combined'
will be saved in
output/homer
directory.
In [9]:
# Name of input ZIP file
inputCompressedFile = 'data/HomerFormat/human_INL.zip'
# List of files inside zip archive
files = ['human_INL_sample1_matrix_1Mb_raw.txt', 'human_INL_sample2_matrix_1Mb_raw.txt']
# Initialize
homer_reader = gmlib.importer.HomerInputHandler(files, inputCompressedFile)
homer_reader.save_ccmaps('output/homer', suffix='_combined')
# Delete all temporary files, not neccessary, automatically deleted after
del homer_reader
INFO:HomerInputHandler: Getting chromosome list and resolution from Input Files ...
INFO:HomerInputHandler: Resolution: 1mb
INFO:HomerInputHandler: Following chromsomes found in input files:
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrMT
chrX
chrY
INFO:HomerInputHandler: Reading [human_INL_sample1_matrix_1Mb_raw.txt] file ...
INFO:HomerInputHandler: ... Finished reading [human_INL_sample1_matrix_1Mb_raw.txt] file ...
INFO:HomerInputHandler: Reading [human_INL_sample2_matrix_1Mb_raw.txt] file ...
INFO:HomerInputHandler: ... Finished reading [human_INL_sample2_matrix_1Mb_raw.txt] file ...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr1_i_ryor9d.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr1_i_ryor9d.tmp]
INFO:genMapFromLists: Total number of data in input file: 73792
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 249000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (250, 250)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr1_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr1_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr1_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr2_hxgi95kq.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr2_hxgi95kq.tmp]
INFO:genMapFromLists: Total number of data in input file: 84760
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 243000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (244, 244)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr2_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr2_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr2_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr3_prx9c7j6.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr3_prx9c7j6.tmp]
INFO:genMapFromLists: Total number of data in input file: 61102
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 197000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (198, 198)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr3_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr3_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr3_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr4_5xdu3keu.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr4_5xdu3keu.tmp]
INFO:genMapFromLists: Total number of data in input file: 52272
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 191000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (192, 192)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr4_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr4_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr4_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr5_3_erl3q3.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr5_3_erl3q3.tmp]
INFO:genMapFromLists: Total number of data in input file: 47594
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 180000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (181, 181)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr5_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr5_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr5_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr6_csbsm15l.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr6_csbsm15l.tmp]
INFO:genMapFromLists: Total number of data in input file: 46347
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 171000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (172, 172)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr6_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr6_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr6_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr7_jgvfl8tf.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr7_jgvfl8tf.tmp]
INFO:genMapFromLists: Total number of data in input file: 38192
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 159000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (160, 160)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr7_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr7_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr7_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr8_s_mm4_31.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr8_s_mm4_31.tmp]
INFO:genMapFromLists: Total number of data in input file: 34554
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 146000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (147, 147)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr8_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr8_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr8_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr9_w4hdr7ju.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr9_w4hdr7ju.tmp]
INFO:genMapFromLists: Total number of data in input file: 21457
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 141000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (142, 142)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr9_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr9_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr9_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr10_df0_3_ht.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr10_df0_3_ht.tmp]
INFO:genMapFromLists: Total number of data in input file: 29188
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 135000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (136, 136)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr10_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr10_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr10_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr11_7zjn_yhb.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr11_7zjn_yhb.tmp]
INFO:genMapFromLists: Total number of data in input file: 28920
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 134000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (135, 135)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr11_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr11_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr11_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr12_lli6w590.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr12_lli6w590.tmp]
INFO:genMapFromLists: Total number of data in input file: 27766
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 133000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (134, 134)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr12_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr12_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr12_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr13_g4hwjtpc.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr13_g4hwjtpc.tmp]
INFO:genMapFromLists: Total number of data in input file: 16584
INFO:genMapFromLists:Minimum base-pair: 19000000 and Maximum base-pair: 115000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (116, 116)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr13_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr13_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr13_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr14_dbnjda45.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr14_dbnjda45.tmp]
INFO:genMapFromLists: Total number of data in input file: 13904
INFO:genMapFromLists:Minimum base-pair: 19000000 and Maximum base-pair: 107000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (108, 108)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr14_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr14_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr14_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr15_jt6woss1.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr15_jt6woss1.tmp]
INFO:genMapFromLists: Total number of data in input file: 12006
INFO:genMapFromLists:Minimum base-pair: 20000000 and Maximum base-pair: 102000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (103, 103)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr15_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr15_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr15_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr16_a5qfcg7h.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr16_a5qfcg7h.tmp]
INFO:genMapFromLists: Total number of data in input file: 10808
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 90000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (91, 91)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr16_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr16_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr16_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr17_g_x4qxnl.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr17_g_x4qxnl.tmp]
INFO:genMapFromLists: Total number of data in input file: 10918
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 81000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (82, 82)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr17_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr17_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr17_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr18_j200eps4.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr18_j200eps4.tmp]
INFO:genMapFromLists: Total number of data in input file: 10852
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 78000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (79, 79)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr18_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr18_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr18_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr19_ct81mtsl.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr19_ct81mtsl.tmp]
INFO:genMapFromLists: Total number of data in input file: 5892
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 59000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (60, 60)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr19_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr19_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr19_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr20_cqoy4i8p.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr20_cqoy4i8p.tmp]
INFO:genMapFromLists: Total number of data in input file: 6974
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 62000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (63, 63)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr20_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr20_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr20_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr21_caryb9ul.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr21_caryb9ul.tmp]
INFO:genMapFromLists: Total number of data in input file: 2474
INFO:genMapFromLists:Minimum base-pair: 9000000 and Maximum base-pair: 48000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (49, 49)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr21_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr21_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr21_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr22_wcokl12m.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr22_wcokl12m.tmp]
INFO:genMapFromLists: Total number of data in input file: 2436
INFO:genMapFromLists:Minimum base-pair: 16000000 and Maximum base-pair: 51000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (52, 52)
INFO:save_ccmap: Saving ccmap to file [output/homer/chr22_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr22_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chr22_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrMT_gvc3k3gz.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrMT_gvc3k3gz.tmp]
INFO:genMapFromLists: Total number of data in input file: 2
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 0 are present in input data
INFO:genMapFromLists:Shape of overall map: (1, 1)
INFO:save_ccmap: Saving ccmap to file [output/homer/chrMT_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrMT_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrMT_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrX_c688spaz.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrX_c688spaz.tmp]
INFO:genMapFromLists: Total number of data in input file: 37926
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 155000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (156, 156)
INFO:save_ccmap: Saving ccmap to file [output/homer/chrX_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrX_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrX_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrY_tdt_hzhm.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrY_tdt_hzhm.tmp]
INFO:genMapFromLists: Total number of data in input file: 29
INFO:genMapFromLists:Minimum base-pair: 3000000 and Maximum base-pair: 59000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (60, 60)
INFO:save_ccmap: Saving ccmap to file [output/homer/chrY_1mb__combined.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrY_1mb__combined.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/homer/chrY_1mb__combined.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:HomerInputHandler: Saved ['output/homer/chr1_1mb__combined.ccmap', 'output/homer/chr2_1mb__combined.ccmap', 'output/homer/chr3_1mb__combined.ccmap', 'output/homer/chr4_1mb__combined.ccmap', 'output/homer/chr5_1mb__combined.ccmap', 'output/homer/chr6_1mb__combined.ccmap', 'output/homer/chr7_1mb__combined.ccmap', 'output/homer/chr8_1mb__combined.ccmap', 'output/homer/chr9_1mb__combined.ccmap', 'output/homer/chr10_1mb__combined.ccmap', 'output/homer/chr11_1mb__combined.ccmap', 'output/homer/chr12_1mb__combined.ccmap', 'output/homer/chr13_1mb__combined.ccmap', 'output/homer/chr14_1mb__combined.ccmap', 'output/homer/chr15_1mb__combined.ccmap', 'output/homer/chr16_1mb__combined.ccmap', 'output/homer/chr17_1mb__combined.ccmap', 'output/homer/chr18_1mb__combined.ccmap', 'output/homer/chr19_1mb__combined.ccmap', 'output/homer/chr20_1mb__combined.ccmap', 'output/homer/chr21_1mb__combined.ccmap', 'output/homer/chr22_1mb__combined.ccmap', 'output/homer/chrMT_1mb__combined.ccmap', 'output/homer/chrX_1mb__combined.ccmap', 'output/homer/chrY_1mb__combined.ccmap'] files.
Convert to gcmap¶
An example input file human_INL_sample1_matrix_1Mb_raw.txt
is
present in data/HomerFormat
directory. Below, we read it and convert
it to .gcmap
format. The input file contains several chromosomes,
and all contact maps will be added to gcmap
file.
Ouput human_INL_sample1_matrix_1Mb_raw.gcmap
files will be saved in
output/homer
directory.
In [10]:
# Initialize
homer_reader = gmlib.importer.HomerInputHandler('data/HomerFormat/human_INL_sample1_matrix_1Mb_raw.txt')
# Convert and save
homer_reader.save_gcmap('output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap',
coarsingMethod='sum', compression='lzf')
# Delete all temporary files, neccessary, automatically deleted
del homer_reader
INFO:HomerInputHandler: Getting chromosome list and resolution from Input Files ...
INFO:HomerInputHandler: Resolution: 1mb
INFO:HomerInputHandler: Following chromsomes found in input files:
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrMT
chrX
chrY
INFO:HomerInputHandler: Reading [data/HomerFormat/human_INL_sample1_matrix_1Mb_raw.txt] file ...
INFO:HomerInputHandler: ... Finished reading [data/HomerFormat/human_INL_sample1_matrix_1Mb_raw.txt] file ...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr1_mieka0wf.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr1_mieka0wf.tmp]
INFO:genMapFromLists: Total number of data in input file: 40344
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 249000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (250, 250)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr1] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr1] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr1] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr1] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr2_okklfl0b.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr2_okklfl0b.tmp]
INFO:genMapFromLists: Total number of data in input file: 46886
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 243000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (244, 244)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr2] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr2] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr2] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr2] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr3_oma3j6zf.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr3_oma3j6zf.tmp]
INFO:genMapFromLists: Total number of data in input file: 33308
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 197000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (198, 198)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr3] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr3] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr3] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr3] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr4_dp4j9gbn.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr4_dp4j9gbn.tmp]
INFO:genMapFromLists: Total number of data in input file: 29054
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 191000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (192, 192)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr4] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr4] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr4] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr4] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr5_3kjhgkcg.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr5_3kjhgkcg.tmp]
INFO:genMapFromLists: Total number of data in input file: 26286
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 180000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (181, 181)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr5] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr5] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr5] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr5] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr6_fqd2yomx.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr6_fqd2yomx.tmp]
INFO:genMapFromLists: Total number of data in input file: 25032
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 171000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (172, 172)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr6] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr6] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr6] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr6] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr7_kett40qt.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr7_kett40qt.tmp]
INFO:genMapFromLists: Total number of data in input file: 20748
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 159000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (160, 160)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr7] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr7] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr7] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr7] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr8_91ozz3u5.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr8_91ozz3u5.tmp]
INFO:genMapFromLists: Total number of data in input file: 18371
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 146000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (147, 147)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr8] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr8] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr8] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr8] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr9_6pw9sy7n.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr9_6pw9sy7n.tmp]
INFO:genMapFromLists: Total number of data in input file: 11414
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 141000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (142, 142)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr9] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr9] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr9] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr9] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr10_5alusogc.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr10_5alusogc.tmp]
INFO:genMapFromLists: Total number of data in input file: 15560
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 135000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (136, 136)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr10] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr10] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr10] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr10] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr11_h8niwp57.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr11_h8niwp57.tmp]
INFO:genMapFromLists: Total number of data in input file: 15429
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 134000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (135, 135)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr11] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr11] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr11] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr11] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr12_m49jetry.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr12_m49jetry.tmp]
INFO:genMapFromLists: Total number of data in input file: 14928
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 133000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (134, 134)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr12] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr12] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr12] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr12] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr13_r_9jh_ix.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr13_r_9jh_ix.tmp]
INFO:genMapFromLists: Total number of data in input file: 8675
INFO:genMapFromLists:Minimum base-pair: 19000000 and Maximum base-pair: 115000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (116, 116)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr13] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr13] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr13] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr13] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr14_nwt8hc33.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr14_nwt8hc33.tmp]
INFO:genMapFromLists: Total number of data in input file: 7245
INFO:genMapFromLists:Minimum base-pair: 19000000 and Maximum base-pair: 107000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (108, 108)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr14] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr14] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr14] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr14] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr15_qmrbk20l.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr15_qmrbk20l.tmp]
INFO:genMapFromLists: Total number of data in input file: 6249
INFO:genMapFromLists:Minimum base-pair: 20000000 and Maximum base-pair: 102000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (103, 103)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr15] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr15] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr15] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr15] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr16_pz3f626f.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr16_pz3f626f.tmp]
INFO:genMapFromLists: Total number of data in input file: 5629
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 90000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (91, 91)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr16] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr16] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr16] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr16] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr17_x0hhj02j.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr17_x0hhj02j.tmp]
INFO:genMapFromLists: Total number of data in input file: 5650
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 81000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (82, 82)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr17] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr17] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr17] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr17] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr18_nw13h912.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr18_nw13h912.tmp]
INFO:genMapFromLists: Total number of data in input file: 5581
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 78000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (79, 79)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr18] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr18] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr18] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr18] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr19_7b9xez8u.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr19_7b9xez8u.tmp]
INFO:genMapFromLists: Total number of data in input file: 3012
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 59000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (60, 60)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr19] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr19] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr19] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr19] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr20_gyrjop7e.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr20_gyrjop7e.tmp]
INFO:genMapFromLists: Total number of data in input file: 3563
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 62000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (63, 63)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr20] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr20] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr20] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr20] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr21_bp85hvdg.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr21_bp85hvdg.tmp]
INFO:genMapFromLists: Total number of data in input file: 1266
INFO:genMapFromLists:Minimum base-pair: 9000000 and Maximum base-pair: 48000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (49, 49)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr21] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr21] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr21] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr21] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chr22_wstacf6u.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chr22_wstacf6u.tmp]
INFO:genMapFromLists: Total number of data in input file: 1222
INFO:genMapFromLists:Minimum base-pair: 16000000 and Maximum base-pair: 51000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (52, 52)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chr22] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr22] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr22] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr22] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrMT_2aig8exv.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrMT_2aig8exv.tmp]
INFO:genMapFromLists: Total number of data in input file: 1
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 0 are present in input data
INFO:genMapFromLists:Shape of overall map: (1, 1)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chrMT] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chrMT] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chrMT] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chrMT] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrX_oxiy6jsb.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrX_oxiy6jsb.tmp]
INFO:genMapFromLists: Total number of data in input file: 20634
INFO:genMapFromLists:Minimum base-pair: 0 and Maximum base-pair: 155000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (156, 156)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chrX] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chrX] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chrX] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chrX] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
INFO:CooMatrixHandler: Reading file: [/home/rajendra/deskForWork/scratch/chrY_l7jxumt7.tmp]...
INFO:CooMatrixHandler: ... Finished reading file: [/home/rajendra/deskForWork/scratch/chrY_l7jxumt7.tmp]
INFO:genMapFromLists: Total number of data in input file: 18
INFO:genMapFromLists:Minimum base-pair: 3000000 and Maximum base-pair: 59000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (60, 60)
INFO:addCCMap2GCMap: Opened file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap] for [chrY] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chrY] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chrY] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chrY] ...
INFO:addCCMap2GCMap: Closed file [output/homer/human_INL_sample1_matrix_1Mb_raw.gcmap]...
3. From Bin-Contact format¶
These types of files are present in following GEO data: * http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61471 * http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34453
This format contains a pair of file: * bin file:
cbin chr from.coord to.coord count
1 2L 0 160000 747
2 2L 160000 320000 893
3 2L 320000 480000 1056
4 2L 480000 640000 1060
5 2L 640000 800000 978
6 2L 800000 960000 926
.
.
.
Contact file in list format
cbin1 cbin2 expected_count observed_count 1 1 40.245201 21339 1 2 83.747499 5661 1 3 92.12501 1546 1 4 93.401273 864 1 5 87.265472 442 . . .
Convert to ccmap¶
A pair of example input files nm_none_160000.bins
and
nm_none_160000.n_contact
is present in data/binContactFormat
directory. Below, we read it and convert it to .ccmap
formats. The
input file contains several chromosomes, therefore, several .ccmap
files will be generated for each respective chromosome.
Ouput .ccmap
files will be saved in output/binContact
directory.
See also
Class gcMapExplorer.lib.importer.BinsNContactFilesHandler()
for more details.
In [11]:
# File names
binFile = 'data/binContactFormat/nm_none_160000.bins'
contactFile = 'data/binContactFormat/nm_none_160000.n_contact'
# Initialize
binContactReader = gmlib.importer.BinsNContactFilesHandler(binFile, contactFile)
# Save ccmaps
binContactReader.save_ccmaps('output/binContact')
INFO:BinsNContactFilesHandler: Chromosome Size:
3L : 24640000
3R : 28000000
4 : 1280000
X : 22560000
2R : 21280000
2L : 23040000
INFO:BinsNContactFilesHandler: Chromosome Bins info:
3L: {'min': 278, 'max': 431}
3R: {'min': 432, 'max': 606}
4: {'min': 607, 'max': 614}
X: {'min': 615, 'max': 755}
2R: {'min': 145, 'max': 277}
2L: {'min': 1, 'max': 144}
INFO:BinsNContactFilesHandler: Generating temporary numpy array file [/home/rajendra/deskForWork/scratch/3L_fn2jgej2.npy] for 3L ...
INFO:BinsNContactFilesHandler: Finished.
INFO:BinsNContactFilesHandler: Generating temporary numpy array file [/home/rajendra/deskForWork/scratch/3R_hv4s3fha.npy] for 3R ...
INFO:BinsNContactFilesHandler: Finished.
INFO:BinsNContactFilesHandler: Generating temporary numpy array file [/home/rajendra/deskForWork/scratch/4_ez637xad.npy] for 4 ...
INFO:BinsNContactFilesHandler: Finished.
INFO:BinsNContactFilesHandler: Generating temporary numpy array file [/home/rajendra/deskForWork/scratch/X_f5he1gzh.npy] for X ...
INFO:BinsNContactFilesHandler: Finished.
INFO:BinsNContactFilesHandler: Generating temporary numpy array file [/home/rajendra/deskForWork/scratch/2R_q082jbqo.npy] for 2R ...
INFO:BinsNContactFilesHandler: Finished.
INFO:BinsNContactFilesHandler: Generating temporary numpy array file [/home/rajendra/deskForWork/scratch/2L_mlze04az.npy] for 2L ...
INFO:BinsNContactFilesHandler: Finished.
INFO:BinsNContactFilesHandler: Reading contact file ...
INFO:BinsNContactFilesHandler: Generating Hi-C Map for [2L] ...
INFO:genMapFromLists: Total number of data in input file: 20737
INFO:genMapFromLists:Minimum base-pair: 160000 and Maximum base-pair: 23040000 are present in input data
INFO:genMapFromLists:Shape of overall map: (145, 145)
INFO:BinsNContactFilesHandler: Finished
INFO:BinsNContactFilesHandler: Generating Hi-C Map for [2R] ...
INFO:genMapFromLists: Total number of data in input file: 17689
INFO:genMapFromLists:Minimum base-pair: 160000 and Maximum base-pair: 21280000 are present in input data
INFO:genMapFromLists:Shape of overall map: (134, 134)
INFO:BinsNContactFilesHandler: Finished
INFO:BinsNContactFilesHandler: Generating Hi-C Map for [3L] ...
INFO:genMapFromLists: Total number of data in input file: 23716
INFO:genMapFromLists:Minimum base-pair: 160000 and Maximum base-pair: 24640000 are present in input data
INFO:genMapFromLists:Shape of overall map: (155, 155)
INFO:BinsNContactFilesHandler: Finished
INFO:BinsNContactFilesHandler: Generating Hi-C Map for [3R] ...
INFO:genMapFromLists: Total number of data in input file: 30625
INFO:genMapFromLists:Minimum base-pair: 160000 and Maximum base-pair: 28000000 are present in input data
INFO:genMapFromLists:Shape of overall map: (176, 176)
INFO:BinsNContactFilesHandler: Finished
INFO:BinsNContactFilesHandler: Generating Hi-C Map for [4] ...
INFO:genMapFromLists: Total number of data in input file: 64
INFO:genMapFromLists:Minimum base-pair: 160000 and Maximum base-pair: 1280000 are present in input data
INFO:genMapFromLists:Shape of overall map: (9, 9)
INFO:BinsNContactFilesHandler: Finished
INFO:BinsNContactFilesHandler: Generating Hi-C Map for [X] ...
INFO:genMapFromLists: Total number of data in input file: 19880
INFO:genMapFromLists:Minimum base-pair: 160000 and Maximum base-pair: 22560000 are present in input data
INFO:genMapFromLists:Shape of overall map: (142, 142)
INFO:BinsNContactFilesHandler: Finished
INFO:BinsNContactFilesHandler: Finished reading contact file.
INFO:BinsNContactFilesHandler: Hi-C Maps Summary:
Chromosome Size Max. Min.
3L (155, 155) 25431.0 3.0
3R (176, 176) 22142.0 11.0
4 (9, 9) 18961.0 1182.0
X (142, 142) 11447.0 1.0
2R (134, 134) 20234.0 1.0
2L (145, 145) 24438.0 6.0
INFO:save_ccmap: Saving ccmap to file [output/binContact/chr3L_160kb.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr3L_160kb.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr3L_160kb.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:save_ccmap: Saving ccmap to file [output/binContact/chr3R_160kb.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr3R_160kb.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr3R_160kb.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:save_ccmap: Saving ccmap to file [output/binContact/chr4_160kb.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr4_160kb.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr4_160kb.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:save_ccmap: Saving ccmap to file [output/binContact/chrX_160kb.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chrX_160kb.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chrX_160kb.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:save_ccmap: Saving ccmap to file [output/binContact/chr2R_160kb.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr2R_160kb.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr2R_160kb.npbin] ...
INFO:save_ccmap: Finished!!!
INFO:save_ccmap: Saving ccmap to file [output/binContact/chr2L_160kb.ccmap] and [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr2L_160kb.npbin] ...
INFO:save_ccmap: Compressing [/home/rajendra/workspace/genome_3d_organization/tutorials_modules/output/binContact/chr2L_160kb.npbin] ...
INFO:save_ccmap: Finished!!!
Convert to gcmap¶
A pair of example input files nm_none_160000.bins
and
nm_none_160000.n_contact
is present in data/binContactFormat
directory. Below, we read it and convert it to .gcmap
formats. The
input file contains several chromosomes, all contact map will be added
to the output gcmap
.
Ouput raw_160kb.gcmap
files will be saved in output/binContact
directory.
In [12]:
# Save gcmap
binContactReader.save_gcmap('output/binContact/raw_160kb.gcmap', coarsingMethod='sum', compression='lzf')
INFO:addCCMap2GCMap: Opened file [output/binContact/raw_160kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/binContact/raw_160kb.gcmap] for [chr3L] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr3L] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr3L] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr3L] ...
INFO:addCCMap2GCMap: Closed file [output/binContact/raw_160kb.gcmap]...
INFO:addCCMap2GCMap: Opened file [output/binContact/raw_160kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/binContact/raw_160kb.gcmap] for [chr3R] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr3R] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr3R] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr3R] ...
INFO:addCCMap2GCMap: Closed file [output/binContact/raw_160kb.gcmap]...
INFO:addCCMap2GCMap: Opened file [output/binContact/raw_160kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/binContact/raw_160kb.gcmap] for [chr4] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr4] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr4] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr4] ...
INFO:addCCMap2GCMap: Closed file [output/binContact/raw_160kb.gcmap]...
INFO:addCCMap2GCMap: Opened file [output/binContact/raw_160kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/binContact/raw_160kb.gcmap] for [chrX] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chrX] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chrX] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chrX] ...
INFO:addCCMap2GCMap: Closed file [output/binContact/raw_160kb.gcmap]...
INFO:addCCMap2GCMap: Opened file [output/binContact/raw_160kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/binContact/raw_160kb.gcmap] for [chr2R] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr2R] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr2R] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr2R] ...
INFO:addCCMap2GCMap: Closed file [output/binContact/raw_160kb.gcmap]...
INFO:addCCMap2GCMap: Opened file [output/binContact/raw_160kb.gcmap] for reading writing..
INFO:addCCMap2GCMap: Adding data to [output/binContact/raw_160kb.gcmap] for [chr2L] ...
INFO:addCCMap2GCMap: ...Finished adding data for [chr2L] ...
INFO:addCCMap2GCMap: Generating downsampled maps for [chr2L] ...
INFO:addCCMap2GCMap: ... Finished downsampling for [chr2L] ...
INFO:addCCMap2GCMap: Closed file [output/binContact/raw_160kb.gcmap]...