Mercurial > repos > devteam > tabular_to_fastq
annotate tabular_to_fastq.py @ 4:1f75d46e55f5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author | devteam |
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date | Fri, 01 Nov 2019 13:22:35 -0400 |
parents | 643018aa1435 |
children | e8ca9af08774 |
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643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 # Dan Blankenberg |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 from __future__ import print_function |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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3 |
0 | 4 import sys |
5 | |
3
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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6 |
0 | 7 def main(): |
8 input_filename = sys.argv[1] | |
9 output_filename = sys.argv[2] | |
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643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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10 identifier_col = int(sys.argv[3]) - 1 |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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11 sequence_col = int(sys.argv[4]) - 1 |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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12 quality_col = int(sys.argv[5]) - 1 |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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13 |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
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14 max_col = max(identifier_col, sequence_col, quality_col) |
0 | 15 num_reads = None |
16 skipped_lines = 0 | |
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643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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17 out = open(output_filename, 'w') |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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18 for num_reads, line in enumerate(open(input_filename)): |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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19 fields = line.rstrip('\n\r').split('\t') |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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20 if len(fields) > max_col: |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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21 out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col])) |
0 | 22 else: |
23 skipped_lines += 1 | |
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643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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24 |
0 | 25 out.close() |
26 if num_reads is None: | |
3
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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27 print("Input was empty.") |
0 | 28 else: |
3
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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29 print("%i tabular lines were written as FASTQ reads. Be sure to use the FASTQ Groomer tool on this output before further analysis." % (num_reads + 1 - skipped_lines)) |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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30 |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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31 |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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diff
changeset
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32 if __name__ == "__main__": |
643018aa1435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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33 main() |