Mercurial > repos > dave > genebed_maf_to_fasta

comparison interval_maf_to_merged_fasta.py @ 0:be26293ade92 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
author dave
date Fri, 24 Jul 2020 12:35:57 -0400
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-1:000000000000 0:be26293ade92
1 #!/usr/bin/env python
2 """
3 Reads an interval or gene BED and a MAF Source.
4 Produces a FASTA file containing the aligned intervals/gene sequences, based upon the provided coordinates
5
6 Alignment blocks are layered ontop of each other based upon score.
7
8 usage: %prog maf_file [options]
9 -d, --dbkey=d: Database key, ie hg17
10 -c, --chromCol=c: Column of Chr
11 -s, --startCol=s: Column of Start
12 -e, --endCol=e: Column of End
13 -S, --strandCol=S: Column of Strand
14 -G, --geneBED: Input is a Gene BED file, process and join exons as one region
15 -t, --mafSourceType=t: Type of MAF source to use
16 -m, --mafSource=m: Path of source MAF file, if not using cached version
17 -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
18 -i, --interval_file=i: Input interval file
19 -o, --output_file=o: Output MAF file
20 -p, --species=p: Species to include in output
21 -O, --overwrite_with_gaps=O: Overwrite bases found in a lower-scoring block with gaps interior to the sequence for a species.
22 -z, --mafIndexFileDir=z: Directory of local maf_index.loc file
23
24 usage: %prog dbkey_of_BED comma_separated_list_of_additional_dbkeys_to_extract comma_separated_list_of_indexed_maf_files input_gene_bed_file output_fasta_file cached|user GALAXY_DATA_INDEX_DIR
25 """
26 # Dan Blankenberg
27 from __future__ import print_function
28
29 import sys
30
31 import bx.intervals.io
32 from bx.cookbook import doc_optparse
33
34 from galaxy.tools.util import maf_utilities
35
36
37 def stop_err(msg):
38 sys.exit(msg)
39
40
41 def __main__():
42 # Parse Command Line
43 options, args = doc_optparse.parse(__doc__)
44 mincols = 0
45 strand_col = -1
46
47 if options.dbkey:
48 primary_species = options.dbkey
49 else:
50 primary_species = None
51 if primary_species in [None, "?", "None"]:
52 stop_err("You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file.")
53
54 include_primary = True
55 secondary_species = maf_utilities.parse_species_option(options.species)
56 if secondary_species:
57 species = list(secondary_species) # make copy of species list
58 if primary_species in secondary_species:
59 secondary_species.remove(primary_species)
60 else:
61 include_primary = False
62 else:
63 species = None
64
65 if options.interval_file:
66 interval_file = options.interval_file
67 else:
68 stop_err("Input interval file has not been specified.")
69
70 if options.output_file:
71 output_file = options.output_file
72 else:
73 stop_err("Output file has not been specified.")
74
75 if not options.geneBED:
76 if options.chromCol:
77 chr_col = int(options.chromCol) - 1
78 else:
79 stop_err("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.")
80
81 if options.startCol:
82 start_col = int(options.startCol) - 1
83 else:
84 stop_err("Start column not set, click the pencil icon in the history item to set the metadata attributes.")
85
86 if options.endCol:
87 end_col = int(options.endCol) - 1
88 else:
89 stop_err("End column not set, click the pencil icon in the history item to set the metadata attributes.")
90
91 if options.strandCol:
92 strand_col = int(options.strandCol) - 1
93
94 mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir
95
96 overwrite_with_gaps = True
97 if options.overwrite_with_gaps and options.overwrite_with_gaps.lower() == 'false':
98 overwrite_with_gaps = False
99
100 # Finish parsing command line
101
102 # get index for mafs based on type
103 index = index_filename = None
104 # using specified uid for locally cached
105 if options.mafSourceType.lower() in ["cached"]:
106 index = maf_utilities.maf_index_by_uid(options.mafSource, mafIndexFile)
107 if index is None:
108 stop_err("The MAF source specified (%s) appears to be invalid." % (options.mafSource))
109 elif options.mafSourceType.lower() in ["user"]:
110 # index maf for use here, need to remove index_file when finished
111 index, index_filename = maf_utilities.open_or_build_maf_index(options.mafSource, options.mafIndex, species=[primary_species])
112 if index is None:
113 stop_err("Your MAF file appears to be malformed.")
114 else:
115 stop_err("Invalid MAF source type specified.")
116
117 # open output file
118 output = open(output_file, "w")
119
120 if options.geneBED:
121 region_enumerator = maf_utilities.line_enumerator(open(interval_file, "r").readlines())
122 else:
123 region_enumerator = enumerate(bx.intervals.io.NiceReaderWrapper(
124 open(interval_file, 'r'), chrom_col=chr_col, start_col=start_col,
125 end_col=end_col, strand_col=strand_col, fix_strand=True,
126 return_header=False, return_comments=False))
127
128 # Step through intervals
129 regions_extracted = 0
130 line_count = 0
131 for line_count, line in region_enumerator:
132 try:
133 if options.geneBED: # Process as Gene BED
134 try:
135 starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed(line)
136 # create spliced alignment object
137 alignment = maf_utilities.get_spliced_region_alignment(
138 index, primary_species, fields[0], starts, ends,
139 strand='+', species=species, mincols=mincols,
140 overwrite_with_gaps=overwrite_with_gaps)
141 primary_name = secondary_name = fields[3]
142 alignment_strand = fields[5]
143 except Exception as e:
144 print("Error loading exon positions from input line %i: %s" % (line_count, e))
145 continue
146 else: # Process as standard intervals
147 try:
148 # create spliced alignment object
149 alignment = maf_utilities.get_region_alignment(
150 index, primary_species, line.chrom, line.start,
151 line.end, strand='+', species=species, mincols=mincols,
152 overwrite_with_gaps=overwrite_with_gaps)
153 primary_name = "%s(%s):%s-%s" % (line.chrom, line.strand, line.start, line.end)
154 secondary_name = ""
155 alignment_strand = line.strand
156 except Exception as e:
157 print("Error loading region positions from input line %i: %s" % (line_count, e))
158 continue
159
160 # Write alignment to output file
161 # Output primary species first, if requested
162 if include_primary:
163 output.write(">%s.%s\n" % (primary_species, primary_name))
164 if alignment_strand == "-":
165 output.write(alignment.get_sequence_reverse_complement(primary_species))
166 else:
167 output.write(alignment.get_sequence(primary_species))
168 output.write("\n")
169 # Output all remainging species
170 for spec in secondary_species or alignment.get_species_names(skip=primary_species):
171 if secondary_name:
172 output.write(">%s.%s\n" % (spec, secondary_name))
173 else:
174 output.write(">%s\n" % (spec))
175 if alignment_strand == "-":
176 output.write(alignment.get_sequence_reverse_complement(spec))
177 else:
178 output.write(alignment.get_sequence(spec))
179 output.write("\n")
180
181 output.write("\n")
182 regions_extracted += 1
183 except Exception as e:
184 print("Unexpected error from input line %i: %s" % (line_count, e))
185 raise
186
187 # close output file
188 output.close()
189
190 # remove index file if created during run
191 maf_utilities.remove_temp_index_file(index_filename)
192
193 # Print message about success for user
194 if regions_extracted > 0:
195 print("%i regions were processed successfully." % (regions_extracted))
196 else:
197 print("No regions were processed successfully.")
198 if line_count > 0 and options.geneBED:
199 print("This tool requires your input file to conform to the 12 column BED standard.")
200
201
202 if __name__ == "__main__":
203 __main__()