GitHub - dstern/pull_thin: Starting with tsv files from MSG, pull requested individuls and thin data

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Starting with tsv files from MSG, pull requested individuls and thin data

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Name		Name	Last commit message	Last commit date
Latest commit History 27 Commits
.DS_Store		.DS_Store
README.txt		README.txt
pt.cfg		pt.cfg
pull_thin_tsv.py		pull_thin_tsv.py
testpar1.tsv		testpar1.tsv
testpar1.tsv.sorted		testpar1.tsv.sorted
testpar1.tsv.sorted.pulled		testpar1.tsv.sorted.pulled
testpar1.tsv.sorted.pulled.converted.thinned		testpar1.tsv.sorted.pulled.converted.thinned
testpar1.tsv.sorted.pulled.converted.thinned.f2_rqtl		testpar1.tsv.sorted.pulled.converted.thinned.f2_rqtl
testpar2.tsv		testpar2.tsv
testpar2.tsv.sorted		testpar2.tsv.sorted
testpar2.tsv.sorted.pulled		testpar2.tsv.sorted.pulled
testpar2.tsv.sorted.pulled.converted.thinned		testpar2.tsv.sorted.pulled.converted.thinned
testpar2.tsv.sorted.pulled.converted.thinned.csv		testpar2.tsv.sorted.pulled.converted.thinned.csv
testpar2.tsv.sorted.pulled.converted.thinned.f2_rqtl		testpar2.tsv.sorted.pulled.converted.thinned.f2_rqtl
testpheno.tsv		testpheno.tsv
testsex.tsv		testsex.tsv
testsex.tsv.sorted		testsex.tsv.sorted
testsex.tsv.sorted.pulled		testsex.tsv.sorted.pulled

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This is a little utility for post-processing .tsv files produced by the Multiplexed Shotgun Genotyping (msg) pipeline

DEPENDENCIES

Python 2.7

USAGE

python pull_thin_tsv.0.5.1.py <config_file: default = pt.cfg> 

If no config_file provided, program looks for pt.cfg in same folder

INFORMATION
For info on msg, see 
github.com/JaneliaSciComp/msg

This utility will perform the following tasks
1 - Pull out specific individuals from across multiple tsv files
2 - Reduce each file to thinned data (defined by parameter difffac), keeping the flanking values with values < difffac
3 - Can replace the NAs in the files with priors, which is useful for some downstream applications, such as R-QTL


Known issues:
1 - Properly recognizes if *par2 files have been preprocessed, but does not recognize for *par1 files.
2 - Does not find "sex" column in phenofile for csv files, only for tab delimited files.