Scripts to generate a valid input format for the method SMRegions

[koszulordie]

The script to generate a valid input format for SMRegions needs to be updated.

[koszulordie]

When setting up the scripts to put the regions in genomic coordinates, we identified two problems:

• The format for the region identifier domain_id and source databases source, which uses semicolons (;) as separator, created an unexpected conflict with the awk script that sends data chunks to transvar panno. The problem was solved by replacing semicolons with underscores (_).
• A small subset of the regions failed at transvar panno: the total number of regions dropped from 71695 to 71225; we need to check what is going on with this small set of regions.

[koszulordie]

I confirmed that there are some regions that failed mapping with transvar panno.

Example region that can be mapped successfully

/home/fmuinos/bbgdomains/scripts/Smregions_scripts/panno.sh ENST00000263100 SM00409 34 202 /workspace/projects/intogen_plus/containers/containers_25/transvar.simg /workspace/projects/intogen_plus/containers/datasets_25/transvar /workspace/projects/intogen_plus/containers/datasets_25/regions/cds_biomart.tsv

19 58352290 58353168 - ENST00000263100:SM00409:34:202 ENST00000263100:SM00409:34:202 ENSP00000263100

Example region that failed

/home/fmuinos/bbgdomains/scripts/Smregions_scripts/panno.sh ENST0000026491 PF13426_TIGR00229_cd0013 284 375 /workspace/projects/intogen_plus/containers/containers_25/transvar.simg /workspace/projects/intogen_plus/containers/datasets_25/transvar /workspace/projects/intogen_plus/containers/datasets_25/regions/cds_biomart.tsv

- ENST0000026491:PF13426_TIGR00229_cd0013:284:375 ENST0000026491:PF13426_TIGR00229_cd0013:284:375 ENSP00000264914