[Bioperl-l] remoteblast

Wed May 14 16:24:22 UTC 2014

It seems to be working for me using the regression tests on the 1.6.x branch (taking a while):

[cjfields at cjfields bioperl-live (v1.6.x)]$ export BIOPERLDEBUG=1
[cjfields at cjfields 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 <jason.stajich at gmail.com> 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
> jason.stajich at gmail.com
> 
> 
> On Thu, May 8, 2014 at 8:34 AM, Jolyon Holdstock
> <Jolyon.Holdstock at ogt.com>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
>> 
>> <html>
>> <head><title>An Error Occurred</title></head>
>> <body>
>> <h1>An Error Occurred</h1>
>> <p>301 Moved Permanently</p>
>> </body>
>> </html>
>> 
>> ---------------------------------------------------
>> 
>> 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: jolyon.holdstock at ogt.com<mailto:jolyon.holdstock at ogt.com>
>> W: www.ogt.com
>> 
>> [cid:image001.png at 01CB24EA.6FBDAD80]
>> 
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>> 
>> 
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