Skip to content

Commit

Permalink
removed dynamic version number of GIT logs. Replaced by addional inpu…
Browse files Browse the repository at this point in the history 
…t option for foldername
  • Loading branch information
@melferink
melferink committed Oct 4, 2016
1 parent 642edc3 commit 7978860
Showing 1 changed file with 31 additions and 39 deletions.
70 changes: 31 additions & 39 deletions ExonCov.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -549,8 +549,9 @@ def take_action(self, action, dest, opt, value, values, parser):
long_commands = ('categories')
short_commands = {'cat':'categories'}
parser = OptionParser(option_class=MultipleOption, usage='usage: %prog ', version='%s' % (PROG))
parser.add_option("-o", default="Exoncov_v3", dest="exoncov_folder", metavar="[PATH]", help="full name of output folder [default = Exoncov_v3]")
parser.add_option('-d',default="dedup.bam$", type ="string",dest='search_pattern',metavar='[FILE]', help="Search pattern for BAM file(s)(dedup.bam$[default]|dedup.realigned.bam$)")
parser.add_option('-i',action="extend", type="string",dest='input_file',metavar='[FILE]', help="Input BAM file(s)[default = off]")
parser.add_option('-d',default="dedup.bam$", type ="string",dest='search_pattern',metavar='[FILE]', help="Search pattern for BAM file(s)(dedup.bam$[default]|dedup.realigned.bam$)")
parser.add_option("-a", default="02:00:00", dest="timeslot", metavar="[INT]", help="timeslot used for qsub [default = 02:00:00]")
parser.add_option("--queue", default="all.q", dest="queue", metavar="[STRING]", help="sge queue [default = all.q]")
parser.add_option("-c", default="off", dest="max_mem", metavar="[INT]", help="memory reserved for qsub [default = off (=threads*10G)]")
Expand All @@ -567,8 +568,7 @@ def take_action(self, action, dest, opt, value, values, parser):
parser.add_option("-k", default=7, dest="transcript_column", metavar="[INT]", help="column in BED file that contains the transcripts [default = 7]")
parser.add_option("-q", default=10, dest="bq", metavar="[INT]", help="minimum base quality used [default = 10]")
parser.add_option("-m", default=20, dest="mq", metavar="[INT]", help="minimum mapping quality used [default = 20]")
parser.add_option("-x", default="/hpc/cog_bioinf/data/mapping/diagnostiek/Dx_resources/", dest="Dx_resources_folder", metavar="[string]", help="path to Dx_resource_folder [default = /hpc/cog_bioinf/data/mapping/diagnostiek/Dx_resources/]")

#parser.add_option("-x", default="/hpc/cog_bioinf/data/mapping/diagnostiek/Dx_resources/", dest="Dx_resources_folder", metavar="[string]", help="path to Dx_resource_folder [default = /hpc/cog_bioinf/data/mapping/diagnostiek/Dx_resources/]")

if len(sys.argv) == 1:
parser.parse_args(['--help'])
Expand Down Expand Up @@ -597,7 +597,8 @@ def take_action(self, action, dest, opt, value, values, parser):
mq=str(opt.mq)
timeslot=str(opt.timeslot)
queue=str(opt.queue)
Dx_resources_folder=str(opt.Dx_resources_folder)
#Dx_resources_folder=str(opt.Dx_resources_folder)
exoncov_folder=str(opt.exoncov_folder)

if opt.input_file:
input_file=opt.input_file
Expand Down Expand Up @@ -658,50 +659,41 @@ def take_action(self, action, dest, opt, value, values, parser):

## Cleanup/move files into relevant folders

"""
try:
Dx_resources_v=commands.getoutput("git --git-dir="+str(Dx_resources_folder)+".git describe --tags")
except:
Dx_resources_v="v3"
"""

if (os.path.exists(str(wkdir)+"/Exoncov_"+str(Dx_resources_v))):
os.system("rm "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+" -r")
os.mkdir(str(wkdir)+"/Exoncov_"+str(Dx_resources_v))
if (os.path.exists(str(wkdir)+"/"+str(exoncov_folder))):
os.system("rm "+str(wkdir)+"/"+str(exoncov_folder)+" -r")
os.mkdir(str(wkdir)+"/"+str(exoncov_folder))
else:
os.mkdir(str(wkdir)+"/Exoncov_"+str(Dx_resources_v))
if not (os.path.exists(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Exons")):
os.mkdir(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Exons")
if not (os.path.exists(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/All_transcripts")):
os.mkdir(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/All_transcripts")
if not (os.path.exists(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Preferred_transcripts")):
os.mkdir(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Preferred_transcripts")
if not (os.path.exists(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Gene_panel_coverage_sample")):
os.mkdir(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Gene_panel_coverage_sample")
if not (os.path.exists(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/SH")):
os.mkdir(str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/SH")

os.system("mv *preferred_transcripts_coverage.tsv "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Preferred_transcripts")
os.system("mv *transcript_coverage.tsv "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/All_transcripts")
os.system("mv *gene_panel_coverage_all.tsv "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Gene_panel_coverage_sample")
os.system("mv *coverage_*.tsv "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/")
os.system("mv *error* "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/")
os.system("mv Depth_job*sh* "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/SH/")
os.system("mv Hold_job_exoncov_depth*sh* "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/SH/")
os.mkdir(str(wkdir)+"/"+str(exoncov_folder))
if not (os.path.exists(str(wkdir)+"/"+str(exoncov_folder)+"/Exons")):
os.mkdir(str(wkdir)+"/"+str(exoncov_folder)+"/Exons")
if not (os.path.exists(str(wkdir)+"/"+str(exoncov_folder)+"/All_transcripts")):
os.mkdir(str(wkdir)+"/"+str(exoncov_folder)+"/All_transcripts")
if not (os.path.exists(str(wkdir)+"/"+str(exoncov_folder)+"/Preferred_transcripts")):
os.mkdir(str(wkdir)+"/"+str(exoncov_folder)+"/Preferred_transcripts")
if not (os.path.exists(str(wkdir)+"/"+str(exoncov_folder)+"/Gene_panel_coverage_sample")):
os.mkdir(str(wkdir)+"/"+str(exoncov_folder)+"/Gene_panel_coverage_sample")
if not (os.path.exists(str(wkdir)+"/"+str(exoncov_folder)+"/SH")):
os.mkdir(str(wkdir)+"/"+str(exoncov_folder)+"/SH")

os.system("mv *preferred_transcripts_coverage.tsv "+str(wkdir)+"/"+str(exoncov_folder)+"/Preferred_transcripts")
os.system("mv *transcript_coverage.tsv "+str(wkdir)+"/"+str(exoncov_folder)+"/All_transcripts")
os.system("mv *gene_panel_coverage_all.tsv "+str(wkdir)+"/"+str(exoncov_folder)+"/Gene_panel_coverage_sample")
os.system("mv *coverage_*.tsv "+str(wkdir)+"/"+str(exoncov_folder)+"/")
os.system("mv *error* "+str(wkdir)+"/"+str(exoncov_folder)+"/")
os.system("mv Depth_job*sh* "+str(wkdir)+"/"+str(exoncov_folder)+"/SH/")
os.system("mv Hold_job_exoncov_depth*sh* "+str(wkdir)+"/"+str(exoncov_folder)+"/SH/")

for file in html_files:
os.system("mv "+str(file)+" "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/")
os.system("mv "+str(file)+" "+str(wkdir)+"/"+str(exoncov_folder)+"/")

for file in exoncov_files:
os.system("mv "+str(file)+" "+str(wkdir)+"/Exoncov_"+str(Dx_resources_v)+"/Exons")
os.system("mv "+str(file)+" "+str(wkdir)+"/"+str(exoncov_folder)+"/Exons")

sys.exit("\n################\nScript completed\n################")











0 comments on commit 7978860

Please sign in to comment.