Mercurial > repos > portiahollyoak > gff_feature_colours

annotate add_colour.py @ 0:f562c252b285 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
author portiahollyoak
date Thu, 26 May 2016 10:48:35 -0400
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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1 #!/usr/bin/env python
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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2 # coding: utf-8
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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4 import argparse
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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5 import doctest # This will test if the functions are working
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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8 parser = argparse.ArgumentParser()
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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9 parser.add_argument("--input", help="GFF file")
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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10 parser.add_argument("--features", nargs='+', help='Features')
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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11 parser.add_argument("--colours",nargs='+', help='Colours for each feature')
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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12 parser.add_argument("--output", help="GFF file with colours")
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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13 args = parser.parse_args()
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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16 with open(args.output, "w") as output:
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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17 with open(args.input) as input_file_handle:
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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18 dictionary = dict(zip(args.features, args.colours))
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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19 for line in input_file_handle:
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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20 columns = line.strip().split("\t")
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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21 if columns[2] in dictionary:
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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22 columns[8] = columns[8] + "Colour={colour};\n".format(colour = dictionary[columns[2]])
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
portiahollyoak
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23 output.write("\t".join(columns))