annotate trim_reference.py @ 2:fa7086274673 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 044b7c1696bf6fef1c8ebf5143c0a841831e92fa
author iuc
date Fri, 15 Mar 2024 16:14:58 +0000
parents 554aa2a63f04
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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2
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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3 from __future__ import print_function
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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4
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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5 import argparse
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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6 import sys
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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7
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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8 if __name__ == '__main__':
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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9 parser = argparse.ArgumentParser()
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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10 parser.add_argument('input_file', type=argparse.FileType())
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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11 parser.add_argument('output_file', type=argparse.FileType('w'), nargs='?', default=sys.stdout)
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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12 args = parser.parse_args()
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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13 lines = args.input_file.readlines()
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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14 i = len(lines) - 1
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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15 trimmed = False
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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16 # step backwards through the lines, removing all As until we find a non-A nucleotide
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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17 while not trimmed:
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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18 line = lines[i].upper().rstrip()
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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19 for j in range(len(line) - 1, -1, -1):
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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20 # walk backwards through the line, checking for a non-A (and non-space) character
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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21 if line[j] not in ['A', ' ']:
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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22 lines[i] = line[:j + 1] + '\n'
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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23 trimmed = True
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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24 break
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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25 else:
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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26 # we processed the whole line - all As - so we don't include this line in the output
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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27 i -= 1
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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28 args.output_file.write(''.join(lines[:i + 1]))