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get_cmap_subsets.py
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get_cmap_subsets.py
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import sys
def main():
if len(sys.argv) != 3:
sys.stderr.write("Usage: program.py cmap_file subset_file\n")
sys.stderr.write("Subset file must be in this format: contig start end (tab-delimited)\n")
sys.exit(1)
subset_file = open(sys.argv[2],'r')
subsets = {}
for line in subset_file:
line = line.strip().split('\t')
if line[0] not in subsets:
subsets[line[0]] = [(float(line[1]), float(line[2]))]
else:
subsets[line[0]].append((float(line[1]), float(line[2])))
subset_file.close()
cmap_file = open(sys.argv[1],'r')
#CMapId ContigLength NumSites SiteID LabelChannel Position StdDev Coverage Occurrence
cmaps = {}
for line in cmap_file:
if line.startswith("#"):
print line.strip()
continue
line = line.strip().split('\t')
if line[0] not in cmaps:
cmaps[line[0]] = [(int(line[4]), float(line[5]))]
else:
cmaps[line[0]].append((int(line[4]), float(line[5])))
cmap_file.close()
pos = []
cur_subset = {'id':None,'end':None}
labels = []
for contig in subsets:
i=0
for start,end in subsets[contig]:
i+=1
for j, (label,position) in enumerate(cmaps[contig],start=1):
if not pos:
if position>=start:
pos.append(position)
labels.append(label)
else:
if position==end or j==len(cmaps[contig]):
pos.append(position)
labels.append(label)
finish(labels, pos, contig, i)
pos, labels = [], []
break
elif position>end:
finish(labels, pos, contig, i)
pos, labels = [], []
break
else:
pos.append(position)
labels.append(label)
def finish(labels, pos, contig, i):
if not labels[-1]==0:
pos.append(pos[-1]+100)
labels.append(0)
total_nicks = len(pos)-1
total_length = pos[-1]-pos[0]+100
for j in range(len(pos)):
print "%s000%d\t%.1f\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d" % (contig, i, total_length, total_nicks, j+1, labels[j], pos[j]-pos[0]+100, labels[j], labels[j], labels[j])
if __name__=="__main__":main()