Mercurial > repos > yating-l > rename_scaffolds

annotate rename.py @ 0:65c9ce351343 draft

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