comparison rename.py @ 1:148e353417e7 draft default tip

planemo upload commit af6c4dc7f6d6795f2b2db7299eb14ae1d5622ac1

0:1a0e39acb62f

            i = 1
            for line in lines:
                if ">" in line:
                    oldname = line[1:].rstrip()
                    newname = "scaffold_" + str(i)
                    line = ">" + newname + "\n"
                    i = i+1
                    namemap[oldname] = newname
                out.write(line)
    with open(indexfile, 'w') as index:
        for k in namemap:
            index.write(k + "=>" + namemap[k] + "\n")

def main():
    inputfile = str(sys.argv[1])
    outputfile = str(sys.argv[2])
    indexfile = str(sys.argv[3])

1:148e353417e7

            i = 1
            for line in lines:
                if ">" in line:
                    oldname = line[1:].rstrip()
                    newname = "scaffold_" + str(i)
                    line = ">" + newname
                    i = i+1
                    namemap[oldname] = newname
                #TODO: Add line breaks to chromosome sequences that are in a single line
                #else:
                    #if (len(line) > 50):
                        #for 
                out.write(line.rstrip() + "\n")
    with open(indexfile, 'w') as index:
        for k in namemap:
            index.write(k + "\t" + namemap[k] + "\n")

def main():
    inputfile = str(sys.argv[1])
    outputfile = str(sys.argv[2])
    indexfile = str(sys.argv[3])