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author dave
date Fri, 10 Jul 2020 16:05:40 -0400
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1 #!/usr/bin/env python
2 """
3 Reads a list of intervals and a maf. Produces a new maf containing the
4 blocks or parts of blocks in the original that overlapped the intervals.
5
6 If a MAF file, not UID, is provided the MAF file is indexed before being processed.
7
8 NOTE: If two intervals overlap the same block it will be written twice.
9
10 usage: %prog maf_file [options]
11 -d, --dbkey=d: Database key, ie hg17
12 -c, --chromCol=c: Column of Chr
13 -s, --startCol=s: Column of Start
14 -e, --endCol=e: Column of End
15 -S, --strandCol=S: Column of Strand
16 -t, --mafType=t: Type of MAF source to use
17 -m, --mafFile=m: Path of source MAF file, if not using cached version
18 -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
19 -i, --interval_file=i: Input interval file
20 -o, --output_file=o: Output MAF file
21 -p, --species=p: Species to include in output
22 -P, --split_blocks_by_species=P: Split blocks by species
23 -r, --remove_all_gap_columns=r: Remove all Gap columns
24 -l, --indexLocation=l: Override default maf_index.loc file
25 -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc )
26 """
27 # Dan Blankenberg
28 from __future__ import print_function
29
30 import bx.align.maf
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 __main__():
38 index = index_filename = None
39
40 # Parse Command Line
41 options, args = doc_optparse.parse(__doc__)
42
43 if options.dbkey:
44 dbkey = options.dbkey
45 else:
46 dbkey = None
47 if dbkey in [None, "?"]:
48 maf_utilities.tool_fail("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.")
49
50 species = maf_utilities.parse_species_option(options.species)
51
52 if options.chromCol:
53 chromCol = int(options.chromCol) - 1
54 else:
55 maf_utilities.tool_fail("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.")
56
57 if options.startCol:
58 startCol = int(options.startCol) - 1
59 else:
60 maf_utilities.tool_fail("Start column not set, click the pencil icon in the history item to set the metadata attributes.")
61
62 if options.endCol:
63 endCol = int(options.endCol) - 1
64 else:
65 maf_utilities.tool_fail("End column not set, click the pencil icon in the history item to set the metadata attributes.")
66
67 if options.strandCol:
68 strandCol = int(options.strandCol) - 1
69 else:
70 strandCol = -1
71
72 if options.interval_file:
73 interval_file = options.interval_file
74 else:
75 maf_utilities.tool_fail("Input interval file has not been specified.")
76
77 if options.output_file:
78 output_file = options.output_file
79 else:
80 maf_utilities.tool_fail("Output file has not been specified.")
81
82 split_blocks_by_species = remove_all_gap_columns = False
83 if options.split_blocks_by_species and options.split_blocks_by_species == 'split_blocks_by_species':
84 split_blocks_by_species = True
85 if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns':
86 remove_all_gap_columns = True
87 else:
88 remove_all_gap_columns = True
89 # Finish parsing command line
90
91 # Open indexed access to MAFs
92 if options.mafType:
93 if options.indexLocation:
94 index = maf_utilities.maf_index_by_uid(options.mafType, options.indexLocation)
95 else:
96 index = maf_utilities.maf_index_by_uid(options.mafType, options.mafIndexFile)
97 if index is None:
98 maf_utilities.tool_fail("The MAF source specified (%s) appears to be invalid." % (options.mafType))
99 elif options.mafFile:
100 index, index_filename = maf_utilities.open_or_build_maf_index(options.mafFile, options.mafIndex, species=[dbkey])
101 if index is None:
102 maf_utilities.tool_fail("Your MAF file appears to be malformed.")
103 else:
104 maf_utilities.tool_fail("Desired source MAF type has not been specified.")
105
106 # Create MAF writter
107 out = bx.align.maf.Writer(open(output_file, "w"))
108
109 # Iterate over input regions
110 num_blocks = 0
111 num_regions = None
112 for num_regions, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(interval_file, 'r'), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)):
113 src = maf_utilities.src_merge(dbkey, region.chrom)
114 for block in index.get_as_iterator(src, region.start, region.end):
115 if split_blocks_by_species:
116 blocks = [new_block for new_block in maf_utilities.iter_blocks_split_by_species(block) if maf_utilities.component_overlaps_region(new_block.get_component_by_src_start(dbkey), region)]
117 else:
118 blocks = [block]
119 for block in blocks:
120 block = maf_utilities.chop_block_by_region(block, src, region)
121 if block is not None:
122 if species is not None:
123 block = block.limit_to_species(species)
124 block = maf_utilities.orient_block_by_region(block, src, region)
125 if remove_all_gap_columns:
126 block.remove_all_gap_columns()
127 out.write(block)
128 num_blocks += 1
129
130 # Close output MAF
131 out.close()
132
133 # remove index file if created during run
134 maf_utilities.remove_temp_index_file(index_filename)
135
136 if num_blocks:
137 print("%i MAF blocks extracted for %i regions." % (num_blocks, (num_regions + 1)))
138 elif num_regions is not None:
139 print("No MAF blocks could be extracted for %i regions." % (num_regions + 1))
140 else:
141 print("No valid regions have been provided.")
142
143
144 if __name__ == "__main__":
145 __main__()