Mercurial > repos > yating-l > regtools_junctions_extract

annotate validator.py @ 0:2626c5b4c665 draft

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planemo upload commit db634d933827ebc78981c7a0aa18205a85fa42e6-dirty
author yating-l
date Mon, 19 Dec 2016 13:07:32 -0500
parents
children cf258ca024ff
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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yating-l
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1 import sys
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2
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3 """
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yating-l
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4 Call checkAndFixBed, check the integrity of bed file. If the strand is not "+" or "-" truncate that line and report to users
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yating-l
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5 create a column and move the score column to that column.
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6 """
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7 def checkAndFixBed(bedfile, revised_file):
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yating-l
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8 # Store the lines that have been removed
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9 removedLines = []
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10 # Remove the lines with invalid strand, create a score column to store the original scores and change scores in the original score column all to 1000
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11 with open(revised_file, 'w') as tmp:
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yating-l
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12 with open(bedfile, 'r') as f:
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yating-l
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13 lines = f.readlines()
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14 i = 1
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15 for line in lines:
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16 fields = line.split()
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17 strand = fields[5]
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18 score = fields[4]
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19 fields[4] = '1000'
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20 fields.append(score)
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21 if (strand == '+' or strand == '-'):
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22 tmp.write('\t'.join(map(str, fields)))
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23 tmp.write("\n")
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24 else:
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25 removedLines.append("line" + str(i) + ": " + line)
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26 i = i+1
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27
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28 return removedLines
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29
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30 def main():
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31 inputfile = str(sys.argv[1])
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32 outputfile = str(sys.argv[2])
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33 removed = checkAndFixBed(inputfile, outputfile)
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34 if (removed != []):
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35 print "\nRemoved invalid lines: \n"
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36 print "\n".join(removed)
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37
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38 if __name__ == "__main__":
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39 main()