Produces the coverage of different samples that lies in a specific directory, by yielding the following data:
- mean depth of coverage per locus,
- % of locus size covered by at least 1-fold
- % of locus size covered by at least 10-fold.
The input files must be in 'yyyy.depth.gz' or 'yyyy.depth' format.
Only works in python2.x
$ python getCoverage.py -h
Example of a depth file (chromosome position coverage):
1 1 0
1 2 0
1 3 0
1 4 0
1 5 0
1 6 0
1 7 0
Example of a directory to process data:
/home/xpto/depth_my_project/
|- depth
|- sample_1.depth.gz
|- sample_2.depth.gz
|- sample_3.depth.gz
|- another_sample_3.depth.gz
|- reference
|- ref_h3.fasta
$ cd /home/xpto/depth_my_project
$ python <installed path>/getCoverage.py -i 'depth/*.depth.gz' -r reference/ref_h3.fasta -o out_result.csv
$ python <installed path>/getCoverage.py -i 'depth/*.depth.gz' -r reference/ref_h3.fasta -o out_result.csv -c 0,9,15
Only works in python2.x