bc2cmap -Bin-Contact files pair to ccmap or gcmap

In this format, two separate files are available. One file contains bins information and other contains contact frequency.

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
.
.
.

Both BIN and CONTACT files are necessary for the conversion.

Usage:

usage: gcMapExplorer bc2cmap [-h] [-ib nm_none_160000.bins]
                             [-ic nm_none_160000.n_contact] [-ccm RawObserved]
                             [-od OUTDIR] [-gcm inOut.gcmap] [-cmeth lzf]
                             [-dmeth sum]
                             [-wd /home/rajendra/deskForWork/scratch]

Optional arguments:

-h, --help            show this hel
p message and exit
-ib nm_none_160000.bins, --input-bin nm_none_160000.bins
                       Input BIN file as shown above.

-ic nm_none_160000.n_contact, --input-contact nm_none_160000.n_contact
                       Input CONTACT file as shown above.

-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.