pairCoo2cmap - paired COO sparse matrix to ccmap or gcmap¶
This format is very similar to COO format with an additional information of chromosome. Therefore, maps for all chromosome could be contained in a single file.
Following file format can be read as a text file, where first and second column is location on chromosome and third column is the value:
chr4 60000 75000 chr4 60000 75000 0.1163470887070292 chr4 60000 75000 chr4 105000 120000 0.01292745430078102 chr4 60000 75000 chr4 435000 450000 0.01292745430078102 chr4 75000 90000 chr4 75000 90000 0.05170981720312409 chr4 75000 90000 chr4 345000 360000 0.01292745430078102 chr4 90000 105000 chr4 90000 105000 0.01292745430078102 . . . . . .
usage: gcMapExplorer pairCoo2cmap [-h] [-i maps.txt] [-ccm RawObserved] [-od OUTDIR] [-gcm inOut.gcmap] [-cmeth lzf] [-dmeth sum] [-wd /home/rajendra/deskForWork/scratch]
-h, --help show this help message and exit -i maps.txt, --input maps.txt Input file name. -ccm RawObserved, --ccmap RawObserved Use this to convert all contact maps to ccmaps file. Provide suffix of ccmap file names with this option and it will enable the conversion. Output ccmap file name is generated automatically as follows; <chromosome>_<resolution>_<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 thi conversion. -cmeth lzf, --compression-method lzf Data compression method for 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.