Mercurial > repos > iuc > extract_genomic_dna

annotate extract_genomic_dna.py @ 5:c8467246b57e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author iuc
date Sat, 21 Jan 2017 14:41:27 -0500
parents b71579ad576c
children 3088e7e70888
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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 changeset
1 #!/usr/bin/env python
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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2 import argparse
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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3 import os
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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4
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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5 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
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6 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: 2
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7 from bx.intervals.io import Comment, Header
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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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8
5
c8467246b57e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
iuc
parents: 3
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9 import extract_genomic_dna_utils as egdu # noqa: I100
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8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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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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11 parser = argparse.ArgumentParser()
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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12 parser.add_argument('--input_format', dest='input_format', help="Input dataset format")
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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13 parser.add_argument('--input', dest='input', help="Input dataset")
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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14 parser.add_argument('--genome', dest='genome', help="Input dataset genome build")
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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15 parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff")
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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16 parser.add_argument('--columns', dest='columns', help="Columns to use in input file")
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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17 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file")
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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18 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file")
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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19 parser.add_argument('--output_format', dest='output_format', help="Output format")
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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20 parser.add_argument('--fasta_header_type', dest='fasta_header_type', default=None, help="Fasta header format")
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
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21 parser.add_argument('--fasta_header_delimiter', dest='fasta_header_delimiter', default=None, help="Fasta header field delimiter")
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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22 parser.add_argument('--output', dest='output', help="Output dataset")
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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23 args = parser.parse_args()
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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24
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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25 input_is_gff = args.input_format == 'gff'
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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26 interpret_features = input_is_gff and args.interpret_features == "yes"
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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27 if len(args.columns.split(',')) == 5:
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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28 # Bed file.
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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29 chrom_col, start_col, end_col, strand_col, name_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
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30 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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31 # Gff file.
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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32 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
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33 name_col = False
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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34
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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35 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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36 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
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37 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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38 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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39 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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40
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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41 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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42 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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43 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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44 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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45 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
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46 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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47 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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48 warning = ''
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 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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50 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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51 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
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52 if interpret_features:
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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53 file_iterator = egdu.GFFReaderWrapper(file_iterator, fix_strand=False)
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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54 out = open(args.output, 'wt')
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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55
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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56 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'
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57 # Ignore comments, headers.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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58 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
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59 line_count += 1
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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60 continue
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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61 name = ""
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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62 if interpret_features:
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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63 # Processing features.
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 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
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65 chrom = feature.chrom
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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66 start = feature.start
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 end = feature.end
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 strand = feature.strand
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 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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70 # Processing lines, either interval or GFF format.
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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71 line = feature.rstrip('\r\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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72 if line and not line.startswith("#"):
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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73 fields = line.split('\t')
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 try:
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 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
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76 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
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77 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
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78 if name_col:
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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79 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:
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80 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:
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81 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
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82 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
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83 strand = fields[strand_col]
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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diff changeset
84 except:
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 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
86 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
87 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
88 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
89 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
90 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
91 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
92 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
93 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
94 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
95 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
96 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
97 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
98 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
99 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
100 if strand not in ['+', '-']:
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 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
102 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
103 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
104 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
105 # 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
106 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
107 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
108 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
109 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
110 nibs[chrom] = nib = bx.seq.nib.NibFile(open("%s/%s.nib" % (seq_path, 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
111 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
112 sequence = nib.get(start, end - start)
3
b71579ad576c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31
iuc
parents: 2
diff changeset
113 except Exception as e:
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
114 warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (start, end - start, args.genome)
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 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
116 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
117 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
118 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
119 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
120 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
121 elif os.path.isfile(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
122 if not(twobitfile):
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 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
124 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
125 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
126 # Create sequence from intervals within a 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
127 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
128 for interval in feature.intervals:
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 sequence += twobitfile[interval.chrom][interval.start:interval.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
130 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
131 sequence = twobitfile[chrom][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
132 except:
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 warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " % (start, end - start, 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 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
135 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
136 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
137 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
138 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
139 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
140 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
141 warning = "Chromosome by name '%s' was not found for build '%s'. " % (chrom, args.genome)
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
142 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
143 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
144 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
145 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
146 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
147 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
148 if 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
149 warning = "Chrom: '%s', start: '%d', end: '%d' is either invalid or not present in build '%s'. " % (chrom, start, end, args.genome)
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 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
151 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
152 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
153 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
154 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
155 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
156 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
157 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
158 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
159 l = len(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
160 c = 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
161 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
162 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
163 if args.fasta_header_type == "bedtools_getfasta_default":
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 0
diff changeset
164 out.write(">%s\n" % egdu.get_bedtools_getfasta_default_header(str(chrom),
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 0
diff changeset
165 str(start),
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 0
diff changeset
166 str(end),
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 0
diff changeset
167 strand,
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 0
diff changeset
168 includes_strand_col))
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 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
170 # 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
171 fields = [args.genome, str(chrom), str(start), str(end), strand]
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172 field_delimiter = egdu.get_fasta_header_delimiter(args.fasta_header_delimiter)
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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173 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
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174 if name.strip():
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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175 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
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176 else:
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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177 out.write(">%s\n" % meta_data)
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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178 while c < l:
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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179 b = min(c + 50, l)
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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180 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
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181 c = b
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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182 else:
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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183 # output_format == "interval".
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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184 if interpret_features:
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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185 meta_data = "\t".join([feature.chrom,
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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186 "galaxy_extract_genomic_dna",
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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187 "interval",
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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188 str(feature.start),
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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189 str(feature.end),
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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190 feature.score,
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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191 feature.strand,
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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192 ".",
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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193 egdu.gff_attributes_to_str(feature.attributes, "GTF")])
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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194 else:
2
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195 # Here fields was set up around line 73.
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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196 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'
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197 if input_is_gff:
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198 format_str = "%s seq \"%s\";\n"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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199 else:
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iuc
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200 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'
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201 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'
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parents:
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202 # Update line count.
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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203 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
parents:
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204 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'
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205 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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206 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:
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207 out.close()
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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208
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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209 if warnings:
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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210 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
parents:
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211 warn_msg += warnings[0]
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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parents:
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212 print warn_msg
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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213 if skipped_lines:
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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214 # Error message includes up to the first 10 skipped lines.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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215 print 'Skipped %d invalid lines, 1st is #%d, "%s"' % (skipped_lines, first_invalid_line, '\n'.join(invalid_lines[:10]))
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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parents:
diff changeset
216
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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diff changeset
217 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'
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diff changeset
218 os.remove(seq_path)