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annotate trimmer.py @ 0:dec27ea206c3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:00:48 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
1 #!/usr/bin/env python
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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2
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 import sys
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 import optparse
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 def stop_err( msg ):
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 sys.stderr.write( msg )
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 sys.exit()
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 def main():
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 usage = """%prog [options]
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 options (listed below) default to 'None' if omitted
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 """
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 parser = optparse.OptionParser(usage=usage)
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 parser.add_option(
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 '-a','--ascii',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 dest='ascii',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 action='store_true',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 default = False,
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 help='Use ascii codes to defined ignored beginnings instead of raw characters')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 parser.add_option(
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 '-q','--fastq',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 dest='fastq',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 action='store_true',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 default = False,
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 help='The input data in fastq format. It selected the script skips every even line since they contain sequence ids')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 parser.add_option(
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 '-i','--ignore',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 dest='ignore',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 help='A comma separated list on ignored beginnings (e.g., ">,@"), or its ascii codes (e.g., "60,42") if option -a is enabled')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 parser.add_option(
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 '-s','--start',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 dest='start',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 default = '0',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40 help='Trim from beginning to here (1-based)')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 parser.add_option(
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 '-e','--end',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 dest='end',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 default = '0',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 help='Trim from here to the ned (1-based)')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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48 parser.add_option(
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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49 '-f','--file',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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50 dest='input_txt',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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51 default = False,
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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52 help='Name of file to be chopped. STDIN is default')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54 parser.add_option(
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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55 '-c','--column',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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56 dest='col',
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57 default = '0',
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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58 help='Column to chop. If 0 = chop the whole line')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59
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60
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61 options, args = parser.parse_args()
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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62 invalid_starts = []
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63
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64 if options.input_txt:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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65 infile = open ( options.input_txt, 'r')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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66 else:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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67 infile = sys.stdin
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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68
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69 if options.ignore and options.ignore != "None":
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70 invalid_starts = options.ignore.split(',')
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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71
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72 if options.ascii and options.ignore and options.ignore != "None":
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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73 for i, item in enumerate( invalid_starts ):
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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74 invalid_starts[i] = chr( int( item ) )
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75
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76 col = int( options.col )
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77
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78 for i, line in enumerate( infile ):
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 line = line.rstrip( '\r\n' )
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 if line:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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81
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82 if options.fastq and i % 2 == 0:
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83 print line
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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84 continue
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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85
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86
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87 if line[0] not in invalid_starts:
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88 if col == 0:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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89 if int( options.end ) > 0:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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90 line = line[ int( options.start )-1 : int( options.end ) ]
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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91 else:
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92 line = line[ int( options.start )-1 : ]
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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93 else:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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94 fields = line.split( '\t' )
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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95 if col-1 > len( fields ):
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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96 stop_err('Column %d does not exist. Check input parameters\n' % col)
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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97
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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98 if int( options.end ) > 0:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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99 fields[col - 1] = fields[col - 1][ int( options.start )-1 : int( options.end ) ]
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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100 else:
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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101 fields[col - 1] = fields[col - 1][ int( options.start )-1 : ]
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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102 line = '\t'.join(fields)
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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103 print line
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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104
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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105 if __name__ == "__main__": main()
dec27ea206c3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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106