coo2cmap - convert COO sparse matrix format to ccmap or gcmapΒΆ
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
NOTE that, above location is real value. However, with -idx/--index
option, these two same column will be considered as index value. index should
always start from zero for absolute beginning of chromosome.e.g. for 10kb,
0-10000 should have index of zero, 10000-20000 have index of one. If this
is file format,resolution should be provided with -r/--resolution
option.
- Usage:
usage: gcMapExplorer coo2cmap [-h] [-i input.txt] [-ic input.tar.gz] [-mt intra] [-r 10kb] [-idx] [-ccm 10kb_RawObserved] [-od OUTDIR] [-gcm inOut.gcmap] [-cmeth lzf] [-dmeth sum] [-wd /home/rajendra/deskForWork/scratch]
Optional arguments:
-h, --help show this help message and exit
-i input.txt, --input input.txt
Meta input file containing input contact map files list with respective
xlabel and ylabel. xlabel should be always provided. In case of intra-
chromosomal map, only xlabel is sufficient because both x and y axis are of
same chromosome. However for inter-chromosomal map, both xlabel and ylabel
should be provided. Example format:
100kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_100kb.RAWobserved chr1
100kb_resolution_intrachromosomal/chr5/MAPQGE30/chr5_100kb.RAWobserved chr5
100kb_resolution_intrachromosomal/chr15/MAPQGE30/chr15_100kb.RAWobserved chr15
100kb_resolution_intrachromosomal/chr20/MAPQGE30/chr20_100kb.RAWobserved chr20
100kb_resolution_intrachromosomal/chr21/MAPQGE30/chr21_100kb.RAWobserved chr21
100kb_resolution_intrachromosomal/chr22/MAPQGE30/chr22_100kb.RAWobserved chr22
-ic input.tar.gz, --input-compressed input.tar.gz
Input compressed archive file containing all the listed contact maps.
Presently, only "tar.gz" and "zip" compressed files are supported.
If -i/--input is not provided, all files from compressed file will be tried for
processing.
-mt intra, --mapType intra
Type of listed contact maps: "intra" or "inter" chromosomal map.
-r 10kb, --resolution 10kb
Resolution of all maps. It is an optional argument. Note that, if this
option is not provided, resolution will be automatically determined from the
contact map file. However, in case of -idx/--index option, resolution
should be provided as resolution cannot be determined from input contact map
file.
-idx, --index It determines whether contact map files have real coordinate of chromosome
or index number. If this option is enabled, -r/--resolution option should be
provided.
-ccm 10kb_RawObserved, --ccmap 10kb_RawObserved
Use this to convert all contact maps to ccmap format files. Provide suffix
of ccmap file names with this option and it will enable the conversion.
Output ccmap file name is generated automatically as follows;
if xlabel is not equal to ylabel: <xlabel>_<ylabel>_<suffix>.ccmap
else: <xlabel>_<suffix>.ccmap
Note that -od/--out-dir option is also required because all ccmaps will be
saved in this directory.
-od OUTDIR, --out-dir OUTDIR
Directory where all ccmap files will be saved.
-gcm inOut.gcmap, --gcmap inOut.gcmap
Provide gcmap file to convert all contact maps into one gcmap file.
File name should contain full path because -od/--out-dir is not considered
for this conversion.
-cmeth lzf, --compression-method lzf
Data compression method in gcmap file.
-dmeth sum, --downsample-method sum
Downsampling method to coarsen the resolution in gcmap file. The option is
intended to use with -gcm/--gcmap option. Three accepted methods are
sum : sum of values,
mean : Average of values and
max : Maximum of values.
This option generates all coarser maps where resolutions will be coarsened by
a factor of two, consecutively. e.g.: In case of 10 kb input resolution,
downsampled maps of "20kb", "40kb", "80kb", "160kb", "320kb" etc. will be
generated until, map size is less than 500.
-wd /home/rajendra/deskForWork/scratch, --work-dir /home/rajendra/deskForWork/scratch
Directory where temporary files will be stored.