Mercurial > repos > iuc > extract_genomic_dna
annotate extract_genomic_dna.py @ 11:80414c33a59a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
author | iuc |
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date | Thu, 21 Nov 2024 07:20:29 +0000 |
parents | e400dcbc60d0 |
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rev | line source |
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8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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1 #!/usr/bin/env python |
7
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
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2 from __future__ import print_function |
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents:
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3 |
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8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
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4 import argparse |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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5 import os |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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6 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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7 import bx.seq.nib |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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8 import bx.seq.twobit |
3
b71579ad576c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31
iuc
parents:
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9 from bx.intervals.io import Comment, Header |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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10 |
8
e400dcbc60d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
iuc
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11 import extract_genomic_dna_utils as egdu # noqa: I100,I202 |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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12 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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13 parser = argparse.ArgumentParser() |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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14 parser.add_argument("--input_format", dest="input_format", help="Input dataset format") |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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15 parser.add_argument("--input", dest="input", help="Input dataset") |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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16 parser.add_argument("--genome", dest="genome", help="Input dataset genome build") |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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17 parser.add_argument( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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18 "--interpret_features", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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19 dest="interpret_features", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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20 default=None, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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21 help="Interpret features if input format is gff", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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22 ) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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23 parser.add_argument("--columns", dest="columns", help="Columns to use in input file") |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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24 parser.add_argument( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
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25 "--reference_genome_source", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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26 dest="reference_genome_source", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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27 help="Source of reference genome file", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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28 ) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
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29 parser.add_argument( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
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30 "--reference_genome", dest="reference_genome", help="Reference genome file" |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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31 ) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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32 parser.add_argument("--output_format", dest="output_format", help="Output format") |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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33 parser.add_argument( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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34 "--fasta_header_type", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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35 dest="fasta_header_type", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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36 default=None, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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37 help="Fasta header format", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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38 ) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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39 parser.add_argument( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
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40 "--fasta_header_delimiter", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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41 dest="fasta_header_delimiter", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
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42 default=None, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
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43 help="Fasta header field delimiter", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
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44 ) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
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45 parser.add_argument("--output", dest="output", help="Output dataset") |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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46 args = parser.parse_args() |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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47 |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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48 input_is_gff = args.input_format == "gff" |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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49 interpret_features = input_is_gff and args.interpret_features == "yes" |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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50 if len(args.columns.split(",")) == 5: |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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51 # Bed file. |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
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52 chrom_col, start_col, end_col, strand_col, name_col = egdu.parse_cols_arg( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
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53 args.columns |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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54 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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55 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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56 # Gff file. |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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57 chrom_col, start_col, end_col, strand_col = egdu.parse_cols_arg(args.columns) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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58 name_col = False |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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59 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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60 if args.reference_genome_source == "history": |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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61 seq_path = egdu.convert_to_twobit(args.reference_genome) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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62 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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63 seq_path = args.reference_genome |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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64 seq_dir = os.path.split(seq_path)[0] |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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65 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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66 includes_strand_col = strand_col >= 0 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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67 strand = None |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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68 nibs = {} |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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69 skipped_lines = 0 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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70 first_invalid_line = 0 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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71 invalid_lines = [] |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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72 warnings = [] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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73 warning = "" |
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8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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74 twobitfile = None |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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75 line_count = 1 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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76 file_iterator = open(args.input) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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77 if interpret_features: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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78 file_iterator = egdu.GFFReaderWrapper(file_iterator, fix_strand=False) |
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80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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79 out = open(args.output, "wt") |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
80 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
81 for feature in file_iterator: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
82 # Ignore comments, headers. |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
83 if isinstance(feature, (Header, Comment)): |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
84 line_count += 1 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
85 continue |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
86 name = "" |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
87 if interpret_features: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
88 # Processing features. |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
89 egdu.convert_gff_coords_to_bed(feature) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
90 chrom = feature.chrom |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
91 start = feature.start |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
92 end = feature.end |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
93 strand = feature.strand |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
94 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
95 # Processing lines, either interval or GFF format. |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
96 line = feature.rstrip("\r\n") |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
97 if line and not line.startswith("#"): |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
98 fields = line.split("\t") |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
99 try: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
100 chrom = fields[chrom_col] |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
101 start = int(fields[start_col]) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
102 end = int(fields[end_col]) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
103 if name_col: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
104 name = fields[name_col] |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
105 if input_is_gff: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
106 start, end = egdu.convert_gff_coords_to_bed([start, end]) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
107 if includes_strand_col: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
108 strand = fields[strand_col] |
7
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents:
5
diff
changeset
|
109 except Exception: |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
110 warning = "Invalid chrom, start or end column values. " |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
111 warnings.append(warning) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
112 if not invalid_lines: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
113 invalid_lines = egdu.get_lines(feature) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
114 first_invalid_line = line_count |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
115 skipped_lines += len(invalid_lines) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
116 continue |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
117 if start > end: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
118 warning = "Invalid interval, start '%d' > end '%d'. " % (start, end) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
119 warnings.append(warning) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
120 if not invalid_lines: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
121 invalid_lines = egdu.get_lines(feature) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
122 first_invalid_line = line_count |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
123 skipped_lines += len(invalid_lines) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
124 continue |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
125 if strand not in ["+", "-"]: |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
126 strand = "+" |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
127 sequence = "" |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
128 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
129 continue |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
130 # Open sequence file and get sequence for feature/interval. |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
131 if os.path.exists("%s/%s.nib" % (seq_dir, chrom)): |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
132 if chrom in nibs: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
133 nib = nibs[chrom] |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
134 else: |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
135 nibs[chrom] = nib = bx.seq.nib.NibFile( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
136 open("%s/%s.nib" % (seq_path, chrom)) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
137 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
138 try: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
139 sequence = nib.get(start, end - start) |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
140 except Exception: |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
141 warning = ( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
142 "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
143 % (start, end - start, args.genome) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
144 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
145 warnings.append(warning) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
146 if not invalid_lines: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
147 invalid_lines = egdu.get_lines(feature) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
148 first_invalid_line = line_count |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
149 skipped_lines += len(invalid_lines) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
150 continue |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
151 elif os.path.isfile(seq_path): |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
152 if not (twobitfile): |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
153 twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path)) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
154 try: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
155 if interpret_features: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
156 # Create sequence from intervals within a feature. |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
157 sequence = "" |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
158 for interval in feature.intervals: |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
159 sequence += twobitfile[interval.chrom][ |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
160 interval.start: interval.end |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
161 ] |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
162 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
163 sequence = twobitfile[chrom][start:end] |
7
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents:
5
diff
changeset
|
164 except Exception: |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
165 warning = ( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
166 "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
167 % (start, end - start, chrom) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
168 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
169 warnings.append(warning) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
170 if not invalid_lines: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
171 invalid_lines = egdu.get_lines(feature) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
172 first_invalid_line = line_count |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
173 skipped_lines += len(invalid_lines) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
174 continue |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
175 else: |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
176 warning = "Chromosome by name '%s' was not found for build '%s'. " % ( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
177 chrom, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
178 args.genome, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
179 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
180 warnings.append(warning) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
181 if not invalid_lines: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
182 invalid_lines = egdu.get_lines(feature) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
183 first_invalid_line = line_count |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
184 skipped_lines += len(invalid_lines) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
185 continue |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
186 if sequence == "": |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
187 warning = ( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
188 "Chrom: '%s', start: '%d', end: '%d' is either invalid or not present in build '%s'. " |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
189 % (chrom, start, end, args.genome) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
190 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
191 warnings.append(warning) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
192 if not invalid_lines: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
193 invalid_lines = egdu.get_lines(feature) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
194 first_invalid_line = line_count |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
195 skipped_lines += len(invalid_lines) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
196 continue |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
197 if includes_strand_col and strand == "-": |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
198 sequence = egdu.reverse_complement(sequence) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
199 if args.output_format == "fasta": |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
200 if input_is_gff: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
201 start, end = egdu.convert_bed_coords_to_gff([start, end]) |
2
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
changeset
|
202 if args.fasta_header_type == "bedtools_getfasta_default": |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
203 out.write( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
204 ">%s\n" |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
205 % egdu.get_bedtools_getfasta_default_header( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
206 str(chrom), str(start), str(end), strand, includes_strand_col |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
207 ) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
208 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
209 else: |
2
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
changeset
|
210 # args.fasta_header_type == "char_delimited": |
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
changeset
|
211 fields = [args.genome, str(chrom), str(start), str(end), strand] |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
212 field_delimiter = egdu.get_fasta_header_delimiter( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
213 args.fasta_header_delimiter |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
214 ) |
2
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
changeset
|
215 meta_data = field_delimiter.join(fields) |
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
changeset
|
216 if name.strip(): |
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
changeset
|
217 out.write(">%s %s\n" % (meta_data, name)) |
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
changeset
|
218 else: |
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents:
0
diff
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|
219 out.write(">%s\n" % meta_data) |
7
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents:
5
diff
changeset
|
220 c = 0 |
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents:
5
diff
changeset
|
221 sequence_length = len(sequence) |
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents:
5
diff
changeset
|
222 while c < sequence_length: |
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents:
5
diff
changeset
|
223 b = min(c + 50, sequence_length) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
224 out.write("%s\n" % str(sequence[c:b])) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
225 c = b |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
226 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
227 # output_format == "interval". |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff
changeset
|
228 if interpret_features: |
11
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
229 meta_data = "\t".join( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
230 [ |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
231 feature.chrom, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
232 "galaxy_extract_genomic_dna", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
233 "interval", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
234 str(feature.start), |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
235 str(feature.end), |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
236 feature.score, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
237 feature.strand, |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
238 ".", |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
239 egdu.gff_attributes_to_str(feature.attributes, "GTF"), |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
parents:
8
diff
changeset
|
240 ] |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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241 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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242 else: |
2
702970e4a134
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
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243 # Here fields was set up around line 73. |
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8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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244 meta_data = "\t".join(fields) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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245 if input_is_gff: |
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80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
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246 format_str = '%s seq "%s";\n' |
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8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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247 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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248 format_str = "%s\t%s\n" |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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249 out.write(format_str % (meta_data, str(sequence))) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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250 # Update line count. |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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251 if isinstance(feature, egdu.GFFFeature): |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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252 line_count += len(feature.intervals) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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253 else: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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254 line_count += 1 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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255 out.close() |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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256 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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257 if warnings: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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258 warn_msg = "%d warnings, 1st is: " % len(warnings) |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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259 warn_msg += warnings[0] |
7
3088e7e70888
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
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260 print(warn_msg) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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261 if skipped_lines: |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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262 # Error message includes up to the first 10 skipped lines. |
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80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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263 print( |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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264 'Skipped %d invalid lines, 1st is #%d, "%s"' |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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265 % (skipped_lines, first_invalid_line, "\n".join(invalid_lines[:10])) |
80414c33a59a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296
iuc
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266 ) |
0
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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267 |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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268 if args.reference_genome_source == "history": |
8dd8e89c0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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269 os.remove(seq_path) |