Mercurial > repos > devteam > join
comparison gops_join.py @ 3:ffbd1de29c28 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:48:58 -0500 |
parents | e56b47dce68a |
children | a10f49d9218a |
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2:de21bdbb8d28 | 3:ffbd1de29c28 |
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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 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file | 7 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file |
8 -m, --mincols=N: Require this much overlap (default 1bp) | 8 -m, --mincols=N: Require this much overlap (default 1bp) |
9 -f, --fill=N: none, right, left, both | 9 -f, --fill=N: none, right, left, both |
10 """ | 10 """ |
11 import sys, traceback, fileinput | 11 import fileinput |
12 from warnings import warn | 12 import sys |
13 from bx.intervals import * | 13 from bx.intervals.io import NiceReaderWrapper |
14 from bx.intervals.io import * | 14 from bx.intervals.operations.join import join |
15 from bx.intervals.operations.join import * | |
16 from bx.cookbook import doc_optparse | 15 from bx.cookbook import doc_optparse |
17 from galaxy.tools.util.galaxyops import * | 16 from bx.tabular.io import ParseError |
17 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped | |
18 | 18 |
19 assert sys.version_info[:2] >= ( 2, 4 ) | 19 assert sys.version_info[:2] >= ( 2, 4 ) |
20 | 20 |
21 | |
21 def main(): | 22 def main(): |
22 mincols = 1 | 23 mincols = 1 |
23 upstream_pad = 0 | |
24 downstream_pad = 0 | |
25 leftfill = False | 24 leftfill = False |
26 rightfill = False | 25 rightfill = False |
27 | 26 |
28 options, args = doc_optparse.parse( __doc__ ) | 27 options, args = doc_optparse.parse( __doc__ ) |
29 try: | 28 try: |
30 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | 29 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) |
31 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) | 30 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) |
32 if options.mincols: mincols = int( options.mincols ) | 31 if options.mincols: |
32 mincols = int( options.mincols ) | |
33 if options.fill: | 33 if options.fill: |
34 if options.fill == "both": | 34 if options.fill == "both": |
35 rightfill = leftfill = True | 35 rightfill = leftfill = True |
36 else: | 36 else: |
37 rightfill = options.fill == "right" | 37 rightfill = options.fill == "right" |