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