Mercurial > repos > jowong > add_sample_as_first_line
annotate add_sample_name_as_first_line.py @ 0:231b21337c43 draft
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
author | jowong |
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date | Thu, 27 Sep 2018 17:05:18 -0400 |
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children | 492848eff35d |
rev | line source |
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0
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
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changeset
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1 import sys |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
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2 import argparse |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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3 import re |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
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4 |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
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5 def Parser(): |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
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6 the_parser = argparse.ArgumentParser(description="add sample name as first line of a tab file") |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
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7 the_parser.add_argument('--input', required=True, action="store", type=str, help="input tab file") |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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8 the_parser.add_argument('--output', required=True, action="store", type=str, help="output file") |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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9 the_parser.add_argument('--sample', required=True, action="store", type=str, help="sample name to add as the first line of input file") |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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10 args = the_parser.parse_args() |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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11 return args |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
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12 |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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13 args=Parser() |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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14 |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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15 sample_name = re.sub('[_12]*.fastq.gz', '', args.sample.rstrip().lstrip()) |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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16 |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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17 with open(args.input) as input: |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
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18 with open(args.output, 'w') as output: |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
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19 output.write(sample_name+"\n") |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
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20 for line in input: |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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21 output.write(line) |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
changeset
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22 |
231b21337c43
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
jowong
parents:
diff
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23 |