def formatProbeCoordinates(infile, outfile): '''Format the restriction fragments containing probes to include 1000bp exclusion sites on each side of each probe and report any collisions in probe fragments and exclusions. Collisions are reported for a sanity control check: probe collisions shouldn't occur and exclusion collisions can happen but they are not wrong, nor do they affect the analysis''' job_memory = "0.5G" (probe_collisions, exclus_collisions) = pipelineCaptCPerl.formatProbeFragments(infile, outfile) E.debug(probe_collisions) E.debug(exclus_collisions)
# import PipelineCaptureC as Capt_C # import CGAT.IOTools as IOTools # Import for full make (local directory changed to data files in debug opts) #import sys #sys.path.insert(0, '/home/mbp15ja/dev/Capture_C/Capture_C') #import pipeline_capt_c_perl as Pipe_Capt_C_Perl import pipelineCaptCPerl if __name__ == "__main__": probe_collisions, exclus_collisions = pipelineCaptCPerl.formatProbeFragments('/mnt/fastdata/mbp15ja/capturec-pilot/capture_c_pipeline_perl/digest.dir/dedup_probe_fragments.bed.gz', '/mnt/fastdata/mbp15ja/capturec-pilot/oligo_coord_dedup.txt') print(probe_collisions) print(exclus_collisions) # bam = '/fastdata/mbp15ja/capturec-pilot/capture_c_sudlab_pe_raw2/dedupped.dir/IGF0003828.bwa.bam' # probes = '/fastdata/mbp15ja/capturec-pilot/capture_c_sudlab_pe_raw2/probe_fragments.bed.gz' # outfile = '/fastdata/mbp15ja/capturec-pilot/IGF0003828.bwa.anomolies.tsv.gz' # Capt_C.quantifyAnomolies(bam, probes, outfile) # for line in IOTools.openFile('/fastdata/mbp15ja/capturec-pilot/capture_c_sudlab_pe_raw2/probe_fragments.bed.gz'): # print(line.split("\t")[3]) # Capt_C.fetchProbeFragments('/fastdata/mbp15ja/capturec-pilot/capture_c_sudlab_pe_raw2/probes.bed.gz', # '/fastdata/mbp15ja/capturec-pilot/capture_c_sudlab_pe_raw2/digest.dir/fragments.bed.gz', # '/fastdata/mbp15ja/capturec-pilot/probe_fragments.bed.gz', # '/fastdata/mbp15ja/capturec-pilot/lookup_out') # # Capt_C.sites2fragments('/fastdata/mbp15ja/capturec-pilot/capture_c_sudlab_pe_raw/digest.dir/digest.bed.gz',