SegDupAnnotation/CombinedMasked.py at master · ChaissonLab/SegDupAnnotation · GitHub

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#!/usr/bin/env python
import sys
fileList=sys.argv[1]
outputFile=sys.argv[2]

chroms={}

ifl=open(fileList)
inFiles=ifl.readlines()

for line in inFiles:


    tmp=open(line.rstrip())
    header=tmp.readline()[1:]
    vals=header.split("/")
    pre="/".join(vals[:-1])
    suf=int(vals[-1])
    print(suf)
    tmp.close()

    if pre not in chroms:
        chroms[pre] = {}
    chroms[pre][suf] = line.rstrip()

outFile=open(outputFile,'w')


for pre in chroms:
    outFile.write(">" + pre + "\n")
    nParts=max(chroms[pre].keys())
    seq=""
    for i in range(0,nParts+1):
        partFile=open(chroms[pre][i])
        print("appending " + str(pre) + " " + str(i))
        partFile.readline()
        seq+="".join([l.strip() for l in partFile.readlines()])
    print("chrom " + pre + " has length " + str(len(seq)))

    last=int(len(seq)/60)
    chromSeq="\n".join([seq[j*60:(j+1)*60] for j in range(0,last) ])
    if len(seq) % 60 != 0:
        chromSeq += "\n" + seq[last*60:]
    chromSeq += "\n"

    outFile.write(chromSeq)