def buildCoverageStats(infile, outfile):
'''Generate coverage statistics for regions of interest from a
bed file using Picard'''
# TS check whether this is always required or specific to current baits
# file
# baits file requires modification to make picard accept it
# this is performed before CalculateHsMetrics
to_cluster = USECLUSTER
baits = PARAMS["roi_baits"]
modified_baits = infile + "_temp_baits_final.bed"
regions = PARAMS["roi_regions"]
statement = '''samtools view -H %(infile)s > %(infile)s_temp_header.txt;
awk 'NR>2' %(baits)s |
awk -F '\\t' 'BEGIN { OFS="\\t" } {print $1,$2,$3,"+",$4;}'
> %(infile)s_temp_baits.bed;
cat %(infile)s_temp_header.txt %(infile)s_temp_baits.bed
> %(modified_baits)s; checkpoint ;
rm -rf %(infile)s_temp_baits.bed %(infile)s_temp_header.txt
'''
P.run()
PipelineMappingQC.buildPicardCoverageStats(infile, outfile, modified_baits,
modified_baits)
IOTools.zapFile(modified_baits)
def buildCoverageStats(infile, outfile):
'''Generate coverage statistics for regions of interest from a
bed file using Picard'''
# TS check whether this is always required or specific to current baits file
# baits file requires modification to make picard accept it
# this is performed before CalculateHsMetrics
to_cluster = USECLUSTER
baits = PARAMS["roi_baits"]
modified_baits = infile + "_temp_baits_final.bed"
regions = PARAMS["roi_regions"]
statement = '''samtools view -H %(infile)s > %(infile)s_temp_header.txt;
awk 'NR>2' %(baits)s |
awk -F '\\t' 'BEGIN { OFS="\\t" } {print $1,$2,$3,"+",$4;}'
> %(infile)s_temp_baits.bed;
cat %(infile)s_temp_header.txt %(infile)s_temp_baits.bed
> %(modified_baits)s; checkpoint ;
rm -rf %(infile)s_temp_baits.bed %(infile)s_temp_header.txt
'''
P.run()
PipelineMappingQC.buildPicardCoverageStats(
infile, outfile, modified_baits, modified_baits)
IOTools.zapFile(modified_baits)
