Mercurial > repos > yating-l > rename_scaffolds

annotate rename.py @ 1:0d13e4410c3d draft

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planemo upload commit 68b7e251486853b77396932b588c20f389c366d2
author yating-l
date Mon, 18 Jun 2018 18:36:00 -0400
parents 65c9ce351343
children 8fdd3e06e1ec
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 import csv
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6 from collections import OrderedDict
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7
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8 def rename(inputfile, outputfile, writer):
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9 namemap = OrderedDict()
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10 with open(outputfile, 'w') as out:
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11 with open(inputfile, 'r') as rf:
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12 lines = rf.readlines()
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13 i = 1
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14 for line in lines:
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15 if ">" in line:
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16 oldname = line[1:].rstrip()
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17 newname = "scaffold_" + str(i)
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18 line = ">" + newname
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19 i = i+1
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20 writer.writerow([oldname, newname])
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21 #TODO: Add line breaks to chromosome sequences that are in a single line
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22 out.write(line.rstrip() + "\n")
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24 def main():
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25 inputfile = str(sys.argv[1])
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26 outputfile = str(sys.argv[2])
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27 indexfile = str(sys.argv[3])
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28 csvfile = open(indexfile, 'w')
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29 fieldnames = ['Original sequence name', 'Renamed sequence name']
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30 writer = csv.writer(csvfile)
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31 writer.writerow(fieldnames)
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32 rename(inputfile, outputfile, writer)
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34 if __name__ == "__main__":
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35 main()
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