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

planemo upload commit af6c4dc7f6d6795f2b2db7299eb14ae1d5622ac1

"""
Call rename to rename scaffolds in reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file
"""
import sys
from collections import OrderedDict

def rename(inputfile, outputfile, indexfile):
    namemap = OrderedDict()
    with open(outputfile, 'w') as out:
        with open(inputfile, 'r') as rf:
            lines = rf.readlines()
            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])
    rename(inputfile, outputfile, indexfile)

if __name__ == "__main__":
    main()