Mercurial > repos > yating-l > rename_scaffolds

annotate rename.py @ 2:8fdd3e06e1ec draft

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planemo upload commit eb7c6866b218a41d9b22255ee6afb83551a5ff40
author yating-l
date Mon, 25 Jun 2018 15:29:18 -0400
parents 0d13e4410c3d
children 9529a207d704
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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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7 def rename(inputfile, outputfile, writer):
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8 with open(outputfile, 'w') as out:
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9 with open(inputfile, 'r') as rf:
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10 lines = rf.readlines()
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11 i = 1
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12 for line in lines:
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13 if ">" in line:
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14 oldname = line[1:].rstrip()
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15 newname = "scaffold_" + str(i)
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16 line = ">" + newname + "\n"
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17 i = i+1
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18 writer.writerow([oldname, newname])
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19 out.write(line)
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21 def main():
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22 inputfile = str(sys.argv[1])
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23 outputfile = str(sys.argv[2])
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24 indexfile = str(sys.argv[3])
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25 csvfile = open(indexfile, 'w')
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26 writer = csv.writer(csvfile)
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27 rename(inputfile, outputfile, writer)
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29 if __name__ == "__main__":
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30 main()
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