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chadadavis / sbglib

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Module: Domain annotation: Bio::DB:CDD #160

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 

NCBI CDD wrapper

Model after Bioperl (package?) 
Try it on GitHub

http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi?useid1=true&tdata=hits&q
ueries=

End sequence with Two new lines !

>Mm_z1COP_P61924
MEALILEPSLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTHRTDSEIA
LLEGLTVVYKSSIDLYFYVIGSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEG
LFLAVDEIVDGGVILESDPQQVVHRVALRGEDVPLTEQTVSQVLQSAKEQIKWSLLR

Then you get:

#Batch CD-search tool   NIH/NLM/NCBI
#cdsid  QM2-qcdsearch-7539BD67A8DA54A2-7539BD67A8DA54A2
#datatype   hits Concise data
#status 3   msg Job is still running

Parse out the id and fetch:

QM2-qcdsearch-7539BD67A8DA54A2-7539BD67A8DA54A2

http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi?cdsid=QM2-qcdsearch-7539
BD67A8DA54A2-7539BD67A8DA54A2

Results in TSV look like:

#Batch CD-search tool   NIH/NLM/NCBI
#cdsid  QM2-qcdsearch-7539BD67A8DA54A2-7539BD67A8DA54A2
#datatype   hits Concise data
#status 0
#Start time 2011-02-02T13:07:56 Run time    0:00:00:01
#status success msg 

Query   Hit type    PSSM-ID From    To  E-Value Bitscore    Accession   Short 
name    Incomplete  Superfamily

Documentation 
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#BatchRPSBDownloadDomain
HitsFormat

Original issue reported on code.google.com by chad.a.davis@gmail.com on 16 Feb 2011 at 10:24

GoogleCodeExporter commented 9 years ago

Original comment by chad.a.davis@gmail.com on 21 Feb 2011 at 4:10