Mercurial > repos > yating-l > rename_scaffolds
comparison rename.py @ 0:65c9ce351343 draft
planemo upload commit af6c4dc7f6d6795f2b2db7299eb14ae1d5622ac1
| author | yating-l |
|---|---|
| date | Fri, 20 Jan 2017 17:06:52 -0500 |
| parents | |
| children | 0d13e4410c3d |
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| -1:000000000000 | 0:65c9ce351343 |
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| 1 """ | |
| 2 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 | |
| 3 """ | |
| 4 import sys | |
| 5 from collections import OrderedDict | |
| 6 | |
| 7 def rename(inputfile, outputfile, indexfile): | |
| 8 namemap = OrderedDict() | |
| 9 with open(outputfile, 'w') as out: | |
| 10 with open(inputfile, 'r') as rf: | |
| 11 lines = rf.readlines() | |
| 12 i = 1 | |
| 13 for line in lines: | |
| 14 if ">" in line: | |
| 15 oldname = line[1:].rstrip() | |
| 16 newname = "scaffold_" + str(i) | |
| 17 line = ">" + newname | |
| 18 i = i+1 | |
| 19 namemap[oldname] = newname | |
| 20 #TODO: Add line breaks to chromosome sequences that are in a single line | |
| 21 #else: | |
| 22 #if (len(line) > 50): | |
| 23 #for | |
| 24 out.write(line.rstrip() + "\n") | |
| 25 with open(indexfile, 'w') as index: | |
| 26 for k in namemap: | |
| 27 index.write(k + "\t" + namemap[k] + "\n") | |
| 28 | |
| 29 def main(): | |
| 30 inputfile = str(sys.argv[1]) | |
| 31 outputfile = str(sys.argv[2]) | |
| 32 indexfile = str(sys.argv[3]) | |
| 33 rename(inputfile, outputfile, indexfile) | |
| 34 | |
| 35 if __name__ == "__main__": | |
| 36 main() | |
| 37 | |
| 38 |