Mercurial > repos > yating-l > regtools_junctions_extract

annotate validator.py @ 2:cf258ca024ff draft

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planemo upload commit ca69686dfafcabb815c93fd46d3c4dfe57459e39-dirty
author yating-l
date Mon, 19 Dec 2016 14:49:37 -0500
parents 2626c5b4c665
children 24fc8a8efe19
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 import sys
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2
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3 """
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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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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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8 # Store the lines that have been removed
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9 removedLines = []
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10 scoreLines = []
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11 # 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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12 with open(revised_file, 'w') as tmp:
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13 with open(bedfile, 'r') as f:
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14 lines = f.readlines()
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15 i = 1
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16 for line in lines:
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17 fields = line.split()
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18 strand = fields[5]
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19 score = fields[4]
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20 if (int(fields[4]) > 1000):
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21 scoreLines.append("line" + str(i) + ":" + line)
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22 fields[4] = '1000'
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23 if (strand == '+' or strand == '-'):
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24 tmp.write('\t'.join(map(str, fields)))
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25 tmp.write("\n")
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26 else:
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27 removedLines.append("line" + str(i) + ": " + line)
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28 i = i+1
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29
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30 return removedLines, scoreLines
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31
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32 def main():
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33 inputfile = str(sys.argv[1])
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34 outputfile = str(sys.argv[2])
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35 removed, changed = checkAndFixBed(inputfile, outputfile)
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36 if (removed != []):
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37 print "\nRemoved invalid lines: \n"
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38 print "\n".join(removed)
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39 if (changed != []):
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40 print "\nThe following lines have scores > 1000, so they are changed to 1000:\n"
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41 print "\n".join(changed)
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42
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43 if __name__ == "__main__":
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44 main()