pairCoo2cmap - paired COO sparse matrix to ccmap or gcmapΒΆ

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.

This type of format appeared with this publication (GEO datasets).

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]

Optional arguments:

-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;

                      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.