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Filter by sample#66

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jamescasbon merged 25 commits intojamescasbon:masterfrom
lennax:lenna
Feb 23, 2014
Merged

Filter by sample#66
jamescasbon merged 25 commits intojamescasbon:masterfrom
lennax:lenna

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@lennax
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@lennax lennax commented Jul 9, 2012

  • New class vcf.SampleFilter modifies Reader to filter each row's samples as they are being read
  • Class destructor removes monkey patch but modified Reader does work normally
  • Class can be used as a module or via the command line interface vcf_sample_filter.py
  • Samples to filter can be specified by name or index
  • Specified samples are filtered by default but can be kept by specifying "invert"
  • Filter can write to any writable object (stdout, specified outfile, etc)
  • Errors and status are given with warnings and logging to allow customization

Lenna Peterson added 23 commits July 2, 2012 11:48
Initial per-sample line filtering.
75cf8f8
Improved samp filter performance, allow invert.
18deb2a
Args can be provided all at once or in sequence.
8477e6f 
The latter style (filt3) allows semi-interactive at Python prompt.
Reduced amount of sample filter code in parser.
73376c8
Actually write out sample-filtered file.
362bbab
Switched Writer \r\n to os.linesep.
d71b2cd
Fixed sample name list update/printing.
bce2c47
Moved all sample filtering to filter script.
67744c0
Implemented argparse.
a048ec0
Tweak args, pep8, move empty outfile warning.
19ce645
Fixed argparse arg names.
95fc70b
Changed default out to sys.stdout
67afb27
Added unit test for sample filtering script.
33d2b5c
Added authorship statement.
792d685
Added sample filter to list of scripts in setup.
d78a945
Moved sample filter object to src dir.
75c4775
Using logging for easy quiet mode.
0047032
Unit test for sample filter module.
6b1fa89
Docs/test for undo_monkey_patch
817f5e9
Changed tests to use subprocess returncode.
0b0d809
Destructor undoes patch; warn if 0 samples kept
746ece9
Recommend explicit use of del.
30321c5
Added empty filter list; del is now less critical.
49f8897
@benjeffery
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benjeffery commented Sep 5, 2012

Hi,
I only came across this pull after I needed a sample filter and wrote a quick one myself (albeit without CLI integration). Am I right in thinking that this code still parses all the samples even if they are to be filtered? I have a VCF with 1600 samples so parsing them all is very costly and the main point of the filter was to prevent this. I only pass the wanted samples to the "_parse_samples" call. You can see my diff at https://github.com/benjeffery/PyVCF/compare/optimise
Thanks!

@lennax
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lennax commented Sep 5, 2012

My goal was to not modify the source code of the Reader class at all. My monkey patch/decorator intercepts the sample parameter to _parse_samples and removes the undesired samples, so it doesn't fully parse each sample. It might be worth doing some profiling to see if there's a significant difference in performance.

@janedanes
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janedanes commented Feb 14, 2013

Hi

I'm a beginner to Python and I'm trying to understand your code and how to use it to remove certain samples. If I wanted to remove a sample from the example file ['NA00001'] from the vcf file what is the code I would use?

@jamescasbon
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jamescasbon commented Feb 6, 2014

People want this. We should definitely rebase it!

@lennax
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lennax commented Feb 10, 2014

I'm a little overwhelmed at the moment but I will set aside time to rebase this within the next two weeks.

@jamescasbon
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jamescasbon commented Feb 10, 2014

Thanks, Lenna!

On 10 February 2014 18:33, Lenna Peterson notifications@github.com wrote:

I'm a little overwhelmed at the moment but I will set aside time to rebase
this within the next two weeks.

Reply to this email directly or view it on GitHubhttps://github.com//pull/66#issuecomment-34664948
.

James
http://casbon.me/

Merge branch 'master' of https://github.com/jamescasbon/PyVCF into lenna
ba00d83 
Conflicts:
	vcf/parser.py
	vcf/test/test_vcf.py
@lennax
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lennax commented Feb 22, 2014

I've merged master back into this and it passes the tests.

@jamescasbon
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jamescasbon commented Feb 23, 2014

Wow, thank you so much Lenna - lots of people have requested this. Sorry for letting it sit here so long.

jamescasbon added a commit that referenced this pull request Feb 23, 2014
@jamescasbon
Merge pull request #66 from lennax/lenna
45513dd 
Filter by sample
@jamescasbon jamescasbon merged commit 45513dd into jamescasbon:master Feb 23, 2014
@lennax lennax deleted the lenna branch February 23, 2014 21:05
gotgenes pushed a commit to gotgenes/PyVCF that referenced this pull request May 13, 2014
@jamescasbon
Merge pull request jamescasbon#66 from lennax/lenna
21fd89a 
Filter by sample
@gotgenes gotgenes mentioned this pull request May 13, 2014
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4 participants

@lennax @benjeffery @janedanes @jamescasbon