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VDBWRAIR / biotest

Testing framework to make python unittesting easier
GNU General Public License v2.0
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Vcf [WIP] #5

Closed averagehat closed 8 years ago

averagehat commented 8 years ago

Adds support for VCF Record dictionaries (alongside a reference sequence).

averagehat commented 8 years ago

This needs to be updated to represent Freebayes entries that look like this:

H3N2/CY074920/Managua/2010/PA_3 207 .   AC  GT,AT   8859.33 .   AB=0.432024,0.564955;ABP=16.295,15.1404;AC=1,1;AF=0.5,0.5;AN=2;AO=143,187;CIGAR=2X,1M1X;DP=331;DPB=331;DPRA=0,0;EPP=39.4698,4.41537;EPPR=0;GTI=0;LEN=2,1;MEANALT=3,3;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=716.828;PAIRED=0.503497,0.754011;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=4862,6499;QR=0;RO=0;RPL=110,89;RPP=93.0429,3.95088;RPPR=0;RPR=33,98;RUN=1,1;SAF=101,129;SAP=55.8697,61.5472;SAR=42,58;SRF=0;SRP=0;SRR=0;TYPE=mnp,snp;technology.ILLUMINA=1,1 GT:DP:RO:QR:AO:QA:GL    1/2:331:0:0:143,187:4862,6499:-922.526,-528.256,-485.208,-394.293,0,-338.001

Somewhat maddeningly, pyvcf varies the type of these fields (AO is sometimes a list, sometimes an int) which hid this possibility from me until I found it in a file.

necrolyte2 commented 8 years ago

I wonder if there is a way to make this much more general. Especially since ngs_mapper produces different result than say FreeBayes and I'm sure others make different formats for the info field

necrolyte2 commented 8 years ago

It's like the never ending python2 vs 3 issue

necrolyte2 commented 8 years ago

http://stackoverflow.com/questions/12172791/changes-in-import-statement-python3

Alright, so that basically says to do the following

from .module import whatever

which should fix this current issue of relative importing compat

necrolyte2 commented 8 years ago

Well the import error is fixed, now it is complaining about similar issue where it can't generate enough examples

averagehat commented 8 years ago

weird because the decorator test hasn't changed.

On Mon, Feb 22, 2016 at 1:32 PM, Tyghe Vallard notifications@github.com wrote:

Well the import error is fixed, now it is complaining about similar issue where it can't generate enough examples

— Reply to this email directly or view it on GitHub https://github.com/VDBWRAIR/biotest/pull/5#issuecomment-187308986.

necrolyte2 commented 8 years ago

ya, this is annoying. Maybe the servers the tests are running on are under high load right now and are a bit slower so we are getting this issue...not sure. At least the function is easier to read and doesn't use builds any more