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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import os
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5
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6 parser = argparse.ArgumentParser(description='Call bamtobed with parameters')
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7 parser.add_argument('-i', '--inputBAM', required=True, help='input BAM file')
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8 parser.add_argument('-o', '--outputBED', required=True, help='output BED file')
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9 parser.add_argument('-oot', '--otherOutputType', required=True, help='Y or N')
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10 parser.add_argument('-f', '--outputFormat', required=False, help='output file format')
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11 parser.add_argument('-sc', '--scoreCalculation', required=True, help='calculation for BED score')
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12 parser.add_argument('-tag', '--tag', required=False, help='another tag')
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13 parser.add_argument('-spt', '--splitD', required=False, help='split : with “N” CIGAR and “D” operation', action="store_true")
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14 parser.add_argument('-cgr', '--cigar', required=False, help='cigar string', action="store_true")
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15
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16 args = parser.parse_args()
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17
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18 # Displays the other output format if selected.
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19 if args.otherOutputType == "Y":
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20 print('format output chosen : ' + args.outputFormat)
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21
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22 # Construction of the command line calling the tool.
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23 myCommandLine = ('bedtools bamtobed'+' -i ' + args.inputBAM)
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24
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25 # Other output format options.
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26 if args.otherOutputType == "Y":
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27 if args.outputFormat == "BEDPE":
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28 myCommandLine += (' -bedpe ')
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29 elif args.outputFormat == "BED12":
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30 myCommandLine += (' -bed12 ')
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31
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32 # Score calculation options.
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33 if args.scoreCalculation == "ed":
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34 myCommandLine += (' -ed ')
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35 elif args.scoreCalculation == "tag":
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36 myCommandLine += (' -tag ' + args.tag)
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37
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38 # Split option.
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39 if args.splitD:
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40 myCommandLine += (' -splitD ')
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41 print('Splitted BAM')
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42
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43 # CIGAR option.
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44 if args.cigar:
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45 myCommandLine += (' -cigar ')
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46 print('CIGAR string column added')
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47
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48 myCommandLine += (' > ' + args.outputBED)
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49
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50 # Running of the command line.
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51 os.system(myCommandLine)
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52
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53
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54
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