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comparison gops_basecoverage.py @ 6:9c5ff4695c97 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
author devteam
date Mon, 13 Jun 2022 16:27:23 +0000
parents 2cedec3759e4
children
comparison
equal deleted inserted replaced
5:21898544368b 6:9c5ff4695c97
6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file 6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
7 """ 7 """
8 from __future__ import print_function 8 from __future__ import print_function
9 9
10 import fileinput 10 import fileinput
11 import sys
12 11
13 from bx.cookbook import doc_optparse 12 from bx.cookbook import doc_optparse
14 from bx.intervals.io import NiceReaderWrapper 13 from bx.intervals.io import NiceReaderWrapper
15 from bx.intervals.operations.base_coverage import base_coverage 14 from bx.intervals.operations.base_coverage import base_coverage
16 from bx.tabular.io import ParseError 15 from bx.tabular.io import ParseError
17 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped 16 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
18 17
19 assert sys.version_info[:2] >= ( 2, 4 )
20
21 18
22 def main(): 19 def main():
23 options, args = doc_optparse.parse( __doc__ ) 20 options, args = doc_optparse.parse(__doc__)
24 try: 21 try:
25 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) 22 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(options.cols1)
26 in_fname, out_fname = args 23 in_fname, out_fname = args
27 except: 24 except Exception:
28 doc_optparse.exception() 25 doc_optparse.exception()
29 26
30 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), 27 g1 = NiceReaderWrapper(
31 chrom_col=chr_col_1, 28 fileinput.FileInput(in_fname),
32 start_col=start_col_1, 29 chrom_col=chr_col_1,
33 end_col=end_col_1, 30 start_col=start_col_1,
34 strand_col=strand_col_1, 31 end_col=end_col_1,
35 fix_strand=True ) 32 strand_col=strand_col_1,
33 fix_strand=True
34 )
36 35
37 try: 36 try:
38 bases = base_coverage(g1) 37 bases = base_coverage(g1)
39 except ParseError as exc: 38 except ParseError as exc:
40 fail( "Invalid file format: %s" % str( exc ) ) 39 fail("Invalid file format: %s" % str(exc))
41 out_file = open( out_fname, "w" ) 40 out_file = open(out_fname, "w")
42 out_file.write( "%s\n" % str( bases ) ) 41 out_file.write("%s\n" % str(bases))
43 out_file.close() 42 out_file.close()
44 if g1.skipped > 0: 43 if g1.skipped > 0:
45 print(skipped( g1, filedesc="" )) 44 print(skipped(g1, filedesc=""))
46 45
47 46
48 if __name__ == "__main__": 47 if __name__ == "__main__":
49 main() 48 main()