Skip to content

Filter by sample #66

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jamescasbon merged 25 commits into from
Feb 23, 2014
Merged

Filter by sample #66

Changes from 1 commit
Commits
Show all changes
25 commits
Select commit Hold shift + click to select a range
75cf8f8
Initial per-sample line filtering.
Jul 2, 2012
18deb2a
Improved samp filter performance, allow invert.
Jul 2, 2012
8477e6f
Args can be provided all at once or in sequence.
Jul 2, 2012
73376c8
Reduced amount of sample filter code in parser.
Jul 2, 2012
362bbab
Actually write out sample-filtered file.
Jul 3, 2012
d71b2cd
Switched Writer \r\n to os.linesep.
Jul 3, 2012
bce2c47
Fixed sample name list update/printing.
Jul 3, 2012
67744c0
Moved all sample filtering to filter script.
Jul 6, 2012
a048ec0
Implemented argparse.
Jul 7, 2012
19ce645
Tweak args, pep8, move empty outfile warning.
Jul 7, 2012
95fc70b
Fixed argparse arg names.
Jul 7, 2012
67afb27
Changed default out to sys.stdout
Jul 7, 2012
33d2b5c
Added unit test for sample filtering script.
Jul 7, 2012
792d685
Added authorship statement.
Jul 7, 2012
d78a945
Added sample filter to list of scripts in setup.
Jul 7, 2012
75c4775
Moved sample filter object to src dir.
Jul 9, 2012
0047032
Using logging for easy quiet mode.
Jul 9, 2012
6b1fa89
Unit test for sample filter module.
Jul 9, 2012
817f5e9
Docs/test for undo_monkey_patch
Jul 9, 2012
0b0d809
Changed tests to use subprocess returncode.
Jul 9, 2012
746ece9
Destructor undoes patch; warn if 0 samples kept
Jul 9, 2012
30321c5
Recommend explicit use of del.
Jul 9, 2012
49f8897
Added empty filter list; del is now less critical.
Jul 9, 2012
ba00d83
Merge branch 'master' of https://github.com/jamescasbon/PyVCF into lenna
Feb 22, 2014
cbe8d90
Restore subprocess import to test
Feb 22, 2014
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Fixed argparse arg names.
  • Loading branch information
Lenna Peterson committed Jul 7, 2012
commit 95fc70b0bac79aca2ace82221ef78c0e66bd592f
3 changes: 2 additions & 1 deletion scripts/vcf_sample_filter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,4 +107,5 @@ def write(self, outfile=None):

args = parser.parse_args()

SampleFilter(args.file, args.outfile, args.filter, args.invert)
SampleFilter(infile=args.file, outfile=args.o,
filters=args.f, invert=args.invert)