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Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: remoteblast
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 14th May 2014 16:24:22 UTC (over 2 years ago)
It seems to be working for me using the regression tests on the 1.6.x
branch (taking a while):

[[email protected] bioperl-live (v1.6.x)]$ export BIOPERLDEBUG=1
[[email protected] bioperl-live (v1.6.x)]$ prove -lrv
t/Tools/Run/RemoteBlast.t
t/Tools/Run/RemoteBlast.t ..
1..21
ok 1 - use Bio::Tools::Run::RemoteBlast;
ok 2
ok 3 - Text BLAST
ok 4 - BLAST text output submitted
ok 5 - Estimated retrieval time
ok 6 - should only be one RID
# Time remaining: 8
# Retrieving R75G4ADZ01R...
# Retrieval attempt: 1

# Retrieval attempt: 2
# Retrieval attempt: 3
# Retrieval attempt: 4
# Retrieval attempt: 5
# Retrieval attempt: 6
# Retrieval attempt: 7
# Retrieval attempt: 8
# Retrieval attempt: 9
# Retrieval attempt: 10
# Retrieval attempt: 11
# Retrieval attempt: 12
# Retrieval attempt: 13
# Retrieval attempt: 14
# Retrieval attempt: 15
retrieve request is POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
Content-Length: 95
Content-Type: application/x-www-form-urlencoded

DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&ALIGNMENTS=50&CMD=Get&RID=R75G4ADZ01R
ok 7 - retrieve_blast succeeded
ok 8 - An object of class 'Bio::SearchIO::blast' isa 'Bio::SearchIO'
sbjct name is sp|P00561.2|AK1H_ECOLI
score is 1567
sbjct name is sp|P00562.3|AK2H_ECOLI
score is 331
sbjct name is sp|P08660.2|AK3_ECOLI
score is 184
ok 9 - HSPs returned
going to remove files
/var/folders/2b/8p0tbdb524sdzxdbsbrs5n4w0000gn/T/ezFTzsGnfp
going to remove files
/var/folders/2b/8p0tbdb524sdzxdbsbrs5n4w0000gn/T/ezFTzsGnfp
Use of uninitialized value $Bio::Tools::Run::RemoteBlast::MODVERSION in
concatenation (.) or string at Bio/Tools/Run/RemoteBlast.pm line 459.
ok 10 - Tabular BLAST submitted
ok 11 - Estimated retrieval time
ok 12 - should only be one RID
# Time remaining: 19
# waiting [R75YBF2B014]...
# Retrieval attempt: 1
retrieve request is POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
Content-Length: 94
Content-Type: application/x-www-form-urlencoded

CMD=Get&RID=R75YBF2B014&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Tabular&ALIGNMENTS=50
ok 13 - retrieve_blast succeeded
ok 14 - An object of class 'Bio::SearchIO::blasttable' isa 'Bio::SearchIO'
sbjct name is gi|34395933|sp|P00561.2|AK1H_ECOLI
score is 1567
sbjct name is gi|416596|sp|P00562.3|AK2H_ECOLI
score is 331
sbjct name is gi|416597|sp|P08660.2|AK3_ECOLI
score is 184
ok 15 - HSPs returned
going to remove files
/var/folders/2b/8p0tbdb524sdzxdbsbrs5n4w0000gn/T/jeSXOFZDxr
going to remove files
/var/folders/2b/8p0tbdb524sdzxdbsbrs5n4w0000gn/T/jeSXOFZDxr
Use of uninitialized value $Bio::Tools::Run::RemoteBlast::MODVERSION in
concatenation (.) or string at Bio/Tools/Run/RemoteBlast.pm line 459.
ok 16 - XML BLAST submitted
ok 17 - Estimated retrieval time
ok 18 - should only be one RID
# Time remaining: 9
# waiting [R75ZA7NV01R]...
# Retrieval attempt: 1
# Retrieval attempt: 2
# Retrieval attempt: 3
# Retrieval attempt: 4
…


chris

On May 14, 2014, at 9:48 AM, Jason Stajich <[email protected]> wrote:

> So the BLAST services changed - not sure if we will still even support
perl
> based - it will require a developer tracking and testing to the new NCBI
> resources since the have discontinued the older submission CGI resource.
> 
> You can run remote blast with commandline tool from NCBI as an
alternative.
> 
> I think we will need to have a developer volunteer who wants to keep
> working on tracking the webservices for NCBI to keep this module working.
> 
> Jason
> 
> Jason Stajich
> [email protected]
> 
> 
> On Thu, May 8, 2014 at 8:34 AM, Jolyon Holdstock
> <[email protected]>wrote:
> 
>> Hi,
>> 
>> I have a script that runs blast jobs against the databases at the NCBI.
>> 
>> I use the  Bio::Tools::Run::RemoteBlast module for the blasting.
>> 
>> It was working but is not now.
>> 
>> The following is an example of the response I now get:
>> 
>> --------------------- WARNING ---------------------
>> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
>> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.006901
>> Content-Length: 788
>> Content-Type: application/x-www-form-urlencoded
>> 
>> 
>>
DATABASE=nr&QUERY=%3EHCV-54_contig_15+%0D%0ATCATAACAACCTTTTATGGTAAATACTAACAGCATGCCCATTTTACATGTGAGGAAACTGAGGCTTAGATCAGGTAAGTAGCTTATTCAGTGTTGCTCAAGTAAATACGTTTTAAGAACCCTCAGCCTCGCTCTCCTCTTCCTCAGGGCACACTTTTTTTTTTTTCCTTCCTACTGTGTGAGCTGTGGTGGGAATGTTAATCGGGATGCCTGTCTTTCCCTAGTCTTGGGGTCAGGCAAGTGCTCAAAGTCAGGATAAGCAAACTCTCCTTCCTGGGACTCTGAGGAAAGGCTCATTGATGGGGGAAATGGAGGGAGTGGATTCACTCCAGCTCAGCTCCGGGACAAGATGGCCATGGAGCTCCTGCTACATAAATGTCAGGGACTATCCTGGCTCCATCCTGCCTGCTTCCCTAGCTGCTGCCCAGCACTCACCTTATAAACATCCTTCGAGCTGGAGTTAGCCCGAATTGGTTTCTGTCCCTTGTGACCACTGAGCCCTGGCTGACACAATCACAGGCTGGCGAGCAGAGGTACCAGAC&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=plain&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&HITLIST_SIZE=5&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastn
>> 
>> 
>> An Error Occurred
>> 
>> 

An Error Occurred

>>

301 Moved Permanently

>> >> >> >> --------------------------------------------------- >> >> Can anyone suggest a fix? >> >> Thanks, >> >> Jolyon >> >> >> Dr. Jolyon Holdstock, >> Oxford Gene Technology >> Begbroke Science Park >> Begbroke Hill, Woodstock Road >> Begbroke, Oxfordshire >> OX5 1PF, UK >> >> T: +44 (0)1865 856852 >> F: +44 (0)1865 848684 >> E: [email protected] >> W: www.ogt.com >> >> [cid:[email protected]] >> >> Oxford Gene Technology - The Molecular Genetics Company(tm) >> >> >> * CytoSure(tm) arrays<http://www.ogt.com/clinical_genetics> - >> Class-leading products and services offering the complete array solution >> for clinical genetics research >> * Cytocell(r) FISH probes<http://www.cytocell.com> - High-quality >> products for the detection of gene rearrangements related to inherited >> genetic disease and cancer >> * Genefficiency(tm) genomic services< >> http://www.ogt.com/genomic_services> - A tailored microarray and >> sequencing service enabling high-throughput, high-quality genomic studies >> for a variety of applications >> >> Oxford Gene Technology (Operations) Ltd. Registered in England No: >> 03845432 Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, >> Oxfordshire, OX5 1PF, UK >> Confidentiality Notice: The contents of this email from the Oxford Gene >> Technology Group of Companies are confidential and intended solely for the >> person to whom it is addressed. It may contain privileged and confidential >> information. If you are not the intended recipient you must not read, >> copy, distribute, discuss or take any action in reliance on it. If you have >> received this email in error please advise the sender so that we can >> arrange for proper delivery. Then please delete the message from your >> inbox. Thank you. >> CytoSure(tm) and Genefficiency(tm) NGS browser: For Research Use Only; Not >> for Use in Diagnostic Procedures< >> http://www.ogt.co.uk/terms_conditions/trademarks_and_disclaimers> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/bioperl-l
 
CD: 3ms