[Bioperl-l] Blast returns result, but does not return hits

Chris Fields cjfields at uiuc.edu
Wed Feb 22 16:55:34 EST 2006


You know, I assumed you were using ActivePerl b/c of the older version of
Bioperl (and since it’s the most commonly used Perl for Windows build).  My
goof.  It looks like you're using Apache/mod_perl/perl, right?  The only
Perl/Apache/mod_perl combos for Windows I know of are listed here:

http://perl.apache.org/docs/2.0/os/win32/install.html

The only Perl for Windows we have actively supported is ActivePerl AFAIK,
but maybe we can walk through this.  Anything learned here can be added to
the installation instructions in case this comes up again.

To start, what mod_perl/Perl version are you using, and from what
distributor (IndigoStar, Apache, etc)?  Each distribution should have some
documentation for installing CPAN modules or prebuilt/pretested packages,
like ActiveState's PPM or IndigoStar's GPM.  I think Apache's Perl build is
from ActiveState's source code so should come with PPM.

Next: you obviously have installed Bioperl before (v1.2.3); did you use
'make' or 'nmake', or was it from a repository (like IndigoPerl's GPM)?
AFAIK, you would install it like you would any other perl module; there
should be no problem with 'make/nmake', though 'make/nmake test' will not
pass completely (it should pass most tests, though, otherwise something is
seriously wrong).

The other option, though not as nice, is setting the PERL5LIB variable to
include the bioperl-live directory; it works for me while I'm developing.  I
don’t know how this may affect other mod_perl-related functions, though.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: Raghunath Verabelli [mailto:iamvela at yahoo.com]
> Sent: Wednesday, February 22, 2006 3:07 PM
> To: Chris Fields; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Blast returns result, but does not return hits
> 
> Thanks Chris. I am getting below mentioned errors with
> nmake.
> 
> As suggested, I downloaded the nmake utility from
> Microsoft website and the bioperl-live tarball.
> 
> After untaring, I replaced the blast.pm file (under
> bioperl-live\Bio\SearchIO) with the blast.pm (86 KB
> size) attached to the bug report 1934.
> 
> I then did the following to install packages using
> nmake:
> 
> 1) perl Makefile.pl was successful without any errors.
> 
> 
> 2) 'c:\nmake' results in following errors
> 
>         pl2bat.bat blib\script\bp_unflatten_seq.pl
>         C:\mod_perl\Perl\bin\perl.exe
> -MExtUtils::Command -e cp ./scripts_temp/b
> p_taxid4species.pl blib\script\bp_taxid4species.pl
>         pl2bat.bat blib\script\bp_taxid4species.pl
>         C:\mod_perl\Perl\bin\perl.exe
> -MExtUtils::Command -e cp ./scripts_temp/b
> p_seqret.pl blib\script\bp_seqret.pl
>         pl2bat.bat blib\script\bp_seqret.pl
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> bioscripts.pod
> Can't open bioscripts.pod: No such file or directory.
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> biodatabases.pod
> Can't open biodatabases.pod: No such file or
> directory.
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> biodesign.pod
> Can't open biodesign.pod: No such file or directory.
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> bioperl.pod
> Can't open bioperl.pod: No such file or directory.
> 
> 
> 3) 'c:\nmake test' fails with following errors:
> 
> NMAKE : fatal error U1095: expanded command line
> 'C:\mod_perl\Perl\bin\perl.exe
> "-MExtUtils::Command::MM" "-e" "test_harness(0,
> 'blib\lib', 'blib\arch')" t\AACh
> ange.t t\AAReverseMutate.t t\abi.t t\ace.t t\AlignIO.t
> t\AlignStats.t t\AlignUti
> l.t t\alignUtilities.t t\Allele.t t\Alphabet.t
> t\Annotation.t t\AnnotationAdapto
> r.t t\asciitree.t t\Assembly.t t\Biblio.t
> t\Biblio_biofetch.t t\Biblio_eutils.t
> t\BiblioReferences.t t\BioDBGFF.t t\BioFetch_DB.t
> t\BioGraphics.t t\BlastIndex.t
>  t\BPbl2seq.t t\BPlite.t t\BPpsilite.t t\bsml_sax.t
> t\Chain.t t\chaosxml.t t\cig
> arstring.t t\ClusterIO.t t\Coalescent.t t\CodonTable.t
> t\Compatible.t t\consed.t
>  t\CoordinateGraph.t t\CoordinateMapper.t
> t\Correlate.t t\ctf.t t\CytoMap.t t\DB
> .t t\DBCUTG.t t\DBFasta.t t\DNAMutation.t t\Domcut.t
> t\ECnumber.t t\ELM.t t\embl
> .t t\EMBL_DB.t t\EMBOSS_Tools.t t\EncodedSeq.t
> t\entrezgene.t t\ePCR.t t\ESEfind
> er.t t\est2genome.t t\Exception.t t\Exonerate.t
> t\exp.t t\fasta.t t\FeatureIO.t
> t\flat.t t\FootPrinter.t t\game.t t\GbrowseGFF.t
> t\gcg.t t\GDB.t t\Gel.t t\genba
> nk.t t\GeneCoordinateMapper.t t\Geneid.t t\Genewise.t
> t\Genomewise.t t\Genpred.t
>  t\GFF.t t\GOR4.t t\GOterm.t t\GraphAdaptor.t
> t\GuessSeqFormat.t t\hmmer.t t\HNN
> .t t\HtSNP.t t\Index.t t\InstanceSite.t t\interpro.t
> t\InterProParser.t t\IUPAC.
> t t\kegg.t t\largefasta.t t\LargeLocatableSeq.t
> t\largepseq.t t\LinkageMap.t t\L
> iveSeq.t t\LocatableSeq.t t\Location.t
> t\LocationFactory.t t\LocusLink.t t\lucy.
> t t\Map.t t\MapIO.t t\masta.t t\Matrix.t t\Measure.t
> t\MeSH.t t\metafasta.t t\Me
> taSeq.t t\MicrosatelliteMarker.t t\MiniMIMentry.t
> t\MitoProt.t t\Molphy.t t\Mult
> iFile.t t\multiple_fasta.t t\Mutation.t t\Mutator.t
> t\NetPhos.t t\Node.t t\OddCo
> des.t t\OMIMentry.t t\OMIMentryAllelicVariant.t
> t\OMIMparser.t t\Ontology.t t\On
> tologyEngine.t t\OntologyStore.t t\PAML.t t\Perl.t
> t\phd.t t\Phenotype.t t\Phyli
> pDist.t t\PhysicalMap.t t\pICalculator.t t\Pictogram.t
> t\pir.t t\pln.t t\PopGen.
> t t\PopGenSims.t t\primaryqual.t t\PrimarySeq.t
> t\primedseq.t t\Primer.t t\prime
> r3.t t\Promoterwise.t t\ProtDist.t t\protgraph.t
> t\ProtMatrix.t t\ProtPsm.t t\Ps
> eudowise.t t\psm.t t\QRNA.t t\qual.t
> t\RandDistFunctions.t t\RandomTreeFactory.t
>  t\Range.t t\RangeI.t t\raw.t t\RefSeq.t t\Registry.t
> t\Relationship.t t\Relatio
> nshipType.t t\RemoteBlast.t t\RepeatMasker.t
> t\RestrictionAnalysis.t t\Restricti
> onEnzyme.t t\RestrictionIO.t t\RNAChange.t
> t\Root-Utilities.t t\RootI.t t\RootIO
> .t t\RootStorable.t t\Scansite.t t\scf.t
> t\SearchDist.t t\SearchIO.t t\Seq.t t\s
> eq_quality.t t\SeqAnalysisParser.t t\SeqBuilder.t
> t\SeqDiff.t t\SeqFeatCollectio
> n.t t\SeqFeature.t t\seqfeaturePrimer.t
> t\SeqHound_DB.t t\SeqIO.t t\SeqPattern.t
>  t\seqread_fail.t t\SeqStats.t t\SequenceFamily.t
> t\sequencetrace.t t\SeqUtils.t
>  t\SeqVersion.t t\seqwithquality.t t\SeqWords.t
> t\Sigcleave.t t\Sim4.t t\Similar
> ityPair.t t\SimpleAlign.t t\simpleGOparser.t
> t\singlet.t t\sirna.t t\SiteMatrix.
> t t\SNP.t t\Sopma.t t\Species.t t\Spidey.t
> t\splicedseq.t t\StandAloneBlast.t t\
> StructIO.t t\Structure.t t\swiss.t t\Symbol.t t\tab.t
> t\TagHaplotype.t t\Taxonom
> y.t t\TaxonTree.t t\Tempfile.t t\Term.t t\tigrxml.t
> t\tinyseq.t t\Tools.t t\Tree
> .t t\TreeBuild.t t\TreeIO.t t\trim.t t\tRNAscanSE.t
> t\tutorial.t t\UCSCParsers.t
>  t\Unflattener.t t\Unflattener2.t t\UniGene.t
> t\Variation_IO.t t\WABA.t t\XEMBL_
> DB.t t\ztr.t' too long
> Stop.
> 
> C:\bioperl-live\bioperl-live>
> 
> 
> 
> 4) 'c:\nmake install' results in following errors:
> 
>         C:\mod_perl\Perl\bin\perl.exe
> -MExtUtils::Command -e cp ./scripts_temp/b
> p_taxid4species.pl blib\script\bp_taxid4species.pl
>         pl2bat.bat blib\script\bp_taxid4species.pl
>         C:\mod_perl\Perl\bin\perl.exe
> -MExtUtils::Command -e cp ./scripts_temp/b
> p_seqret.pl blib\script\bp_seqret.pl
>         pl2bat.bat blib\script\bp_seqret.pl
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> bioscripts.pod
> Can't open bioscripts.pod: No such file or directory.
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> biodatabases.pod
> Can't open biodatabases.pod: No such file or
> directory.
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> biodesign.pod
> Can't open biodesign.pod: No such file or directory.
>         C:\mod_perl\Perl\bin\perl.exe "-Iblib\arch"
> "-Iblib\lib" doc/makedoc.PL
> bioperl.pod
> Can't open bioperl.pod: No such file or directory.
> Appending installation info to
> C:\mod_perl\Perl\lib/perllocal.pod
> NMAKE : fatal error U1095: expanded command line '@
> C:\mod_perl\Perl\bin\perl.ex
> e "-MExtUtils::Command::MM" -e perllocal_install
> "Module" "Bio"  "installed int
> o" "C:\mod_perl\Perl\site\lib"  LINKTYPE "dynamic"
> VERSION "1.5"  EXE_FILES "./
> scripts_temp/bp_biblio.pl
> ./scripts_temp/bp_genbank2gff.pl ./scripts_temp/bp_bul
> k_load_gff.pl ./scripts_temp/bp_fast_load_gff.pl
> ./scripts_temp/bp_genbank2gff3.
> pl ./scripts_temp/bp_generate_histogram.pl
> ./scripts_temp/bp_load_gff.pl ./scrip
> ts_temp/bp_meta_gff.pl
> ./scripts_temp/bp_process_gadfly.pl
> ./scripts_temp/bp_pro
> cess_sgd.pl ./scripts_temp/bp_process_wormbase.pl
> ./scripts_temp/bp_embl2picture
> .pl ./scripts_temp/bp_glyphs1-demo.pl
> ./scripts_temp/bp_glyphs2-demo.pl ./script
> s_temp/bp_biofetch_genbank_proxy.pl
> ./scripts_temp/bp_bioflat_index.pl ./scripts
> _temp/bp_biogetseq.pl ./scripts_temp/bp_flanks.pl
> ./scripts_temp/bp_contig_draw.
> pl ./scripts_temp/bp_feature_draw.pl
> ./scripts_temp/bp_frend.pl ./scripts_temp/b
> p_search_overview.pl ./scripts_temp/bp_fetch.pl
> ./scripts_temp/bp_index.pl ./scr
> ipts_temp/bp_seqret.pl
> ./scripts_temp/bp_composite_LD.pl
> ./scripts_temp/bp_heter
> ogeneity_test.pl ./scripts_temp/bp_fastam9_to_table.pl
> ./scripts_temp/bp_filter_
> search.pl ./scripts_temp/bp_hmmer_to_table.pl
> ./scripts_temp/bp_search2table.pl
> ./scripts_temp/bp_extract_feature_seq.pl
> ./scripts_temp/bp_make_mrna_protein.pl
> ./scripts_temp/bp_seqconvert.pl
> ./scripts_temp/bp_split_seq.pl ./scripts_temp/bp
> _translate_seq.pl ./scripts_temp/bp_unflatten_seq.pl
> ./scripts_temp/bp_aacomp.pl
>  ./scripts_temp/bp_chaos_plot.pl
> ./scripts_temp/bp_gccalc.pl ./scripts_temp/bp_o
> ligo_count.pl
> ./scripts_temp/bp_classify_hits_kingdom.pl
> ./scripts_temp/bp_local
> _taxonomydb_query.pl
> ./scripts_temp/bp_query_entrez_taxa.pl
> ./scripts_temp/bp_ta
> xid4species.pl ./scripts_temp/bp_blast2tree.pl
> ./scripts_temp/bp_nexus2nh.pl ./s
> cripts_temp/bp_tree2pag.pl
> ./scripts_temp/bp_mrtrans.pl ./scripts_temp/bp_nrdb.p
> l ./scripts_temp/bp_sreformat.pl
> ./scripts_temp/bp_dbsplit.pl ./scripts_temp/bp_
> mask_by_search.pl ./scripts_temp/bp_mutate.pl
> ./scripts_temp/bp_pairwise_kaks.pl
>  ./scripts_temp/bp_remote_blast.pl
> ./scripts_temp/bp_search2alnblocks.pl ./scrip
> ts_temp/bp_search2BSML.pl
> ./scripts_temp/bp_search2gff.pl ./scripts_temp/bp_sear
> ch2tribe.pl ./scripts_temp/bp_seq_length.pl"  >>
> C:\mod_perl\Perl\lib\perllocal.
> pod' too long
> Stop.
> 
> C:\bioperl-live\bioperl-live>
> 
> --- Chris Fields <cjfields at uiuc.edu> wrote:
> 
> > Upgrade bioperl from CVS using nmake.
> >
> > Installation instructions for using nmake:
> >
> >
> http://www.bioperl.org/wiki/INSTALL.WIN#Beyond_the_Core
> >
> > You can download a tarball using anonymous CVS (link
> > at bottom):
> >
> >
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
> >
> > or use CVS directly:
> >
> > http://www.bioperl.org/wiki/Using_CVS
> >
> > Then make sure to grab the last SearchIO::last
> > bugfix, which is not in CVS
> > yet:
> >
> > http://bugzilla.bioperl.org/show_bug.cgi?id=1934
> >
> > Replace the blast.pm in \site\lib\Bio\SearchIO in
> > your Perl directory.
> >
> > Does that fix it?
> >
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-
> > > bounces at lists.open-bio.org] On Behalf Of Raghunath
> > Verabelli
> > > Sent: Wednesday, February 22, 2006 11:22 AM
> > > To: bioperl-l at lists.open-bio.org
> > > Subject: [Bioperl-l] Blast returns result, but
> > does not return hits
> > >
> > > Hi All:
> > >
> > > I am new to Perl/BioPerl world.
> > >
> > > I am debugging a program that used to work fine
> > > before.
> > > Blast works fine and returns results, but I am
> > unale
> > > to get any hits from the results.
> > >
> > > Here is the relevant code:
> > >
> > > $blastObj = new Bio::SearchIO
> > (-file=>$resultsFile,
> > > -format=>'blast');
> > >   while (my $result = $blastObj->next_result()) {
> > >      while (my $bioPerlHit = $result->next_hit())
> > {
> > >          .......
> > >
> > >
> > > The first while condition returns true, but the
> > second
> > > while condition returns false. So looks like there
> > is
> > > some result, but it is unable to identify the hits
> > in
> > > the result. I printed the $result (pasted below).
> > >
> > > Any ideas/comments to resolve this? Thanks in
> > advance.
> > >
> > > I am using Perl 5.8.7, BioPerl 1.2.3, Apache
> > 1.3.34 on
> > > Windows XP platform.
> > >
> > > Like I said before, this application was running
> > fine
> > > on a different windows machine with similar
> > > environment,so looks like there is some change in
> > the
> > > products/versions that is causing the problem.
> > >
> > > thanks again,
> > > Raghu
> > >
> > >
> > >
> > >
> > > Blast result (i can send complete result if you
> > need
> > > it):
> > >
> > > <p><!--
> > > QBlastInfoBegin
> > > 	Status=READY
> > > QBlastInfoEnd
> > > --><p><PRE>
> > > BLASTP 2.2.13 [Nov-27-2005]
> > > Reference: Altschul, Stephen F., Thomas L. Madden,
> > > Alejandro A. Schäffer,
> > > Jinghui Zhang, Zheng Zhang, Webb Miller, and David
> > J.
> > > Lipman
> > > (1997), "Gapped BLAST and PSI-BLAST: a new
> > generation
> > > of
> > > protein database search programs", Nucleic Acids
> > Res.
> > > 25:3389-3402.
> > >
> > > RID: 1140573059-19990-140117828872.BLASTQ1
> > >
> > >
> > > Database: All non-redundant GenBank CDS
> > > translations+PDB+SwissProt+PIR+PRF excluding
> > > environmental samples
> > >            3,297,000 sequences; 1,129,354,045
> > total
> > > letters
> > > Query=
> > > Length=360
> > >
> > >
> > >
> > >             Score     E
> > > Sequences producing significant alignments:
> > >             (Bits)  Value
> > >
> > > ref|XP_534770.2|  PREDICTED: similar to
> > > Mitogen-activated prot...   739    0.0
> > > gb|AAX36107.1|  mitogen-activated protein kinase 1
> > > [synthetic con   739    0.0
> > > pdb|1WZY|A  Chain A, Crystal Structure Of Human
> > Erk2
> > > Complexed...   739    0.0
> > > pdb|1TVO|A  Chain A, The Structure Of Erk2 In
> > Complex
> > > With A S...   739    0.0
> > > ref|NP_786987.1|  mitogen-activated protein kinase
> > 1
> > > [Bos taur...   739    0.0
> > > emb|CAA77752.1|  41kD protein kinase [Homo
> > sapiens]
> > > >prf||1813...   738    0.0
> > > gb|AAQ02541.1|  mitogen-activated protein kinase 1
> > > [synthetic con   736    0.0
> > > gb|AAH99905.1|  Mitogen-activated protein kinase 1
> > > [Homo sapiens]   735    0.0
> > > emb|CAI29602.1|  hypothetical protein [Pongo
> > pygmaeus]
> > >              734    0.0
> > > gb|AAH58258.1|  Mitogen activated protein kinase 1
> > > [Mus muscul...   731    0.0
> > > pdb|4ERK|   The Complex Structure Of The Map
> > Kinase
> > > Erk2OLOMOU...   731    0.0
> > > pdb|1GOL|   Coordinates Of Rat Map Kinase Erk2
> > With An
> > > Arginin...   730    0.0
> > > ref|XP_860750.1|  PREDICTED: similar to
> > > Mitogen-activated prot...   729    0.0
> > > gb|AAK56503.1|  extracellular signal-regulated
> > kinase
> > > 2 [Gallu...   726    0.0
> > > ref|XP_860716.1|  PREDICTED: similar to
> > > Mitogen-activated prot...   726    0.0
> > > pdb|2ERK|   Phosphorylated Map Kinase Erk2
> > >              726    0.0
> > > pdb|1PME|   Structure Of Penta Mutant Human Erk2
> > Map
> > > Kinase Co...   725    0.0
> > > ref|XP_860682.1|  PREDICTED: similar to
> > > Mitogen-activated prot...   720    0.0
> > > ref|XP_860651.1|  PREDICTED: similar to
> > > Mitogen-activated prot...   720    0.0
> > > emb|CAA77753.1|  40kDa protein kinase [Homo
> > sapiens]
> > > >prf||181...   717    0.0
> > > ref|NP_001017127.1|  mitogen-activated protein
> > kinase
> > > 1 [Xenopus    715    0.0
> > > dbj|BAE28679.1|  unnamed protein product [Mus
> > > musculus]             713    0.0
> > > emb|CAA42482.1|  MAP kinase [Xenopus laevis]
> > > >gb|AAH60748.1| M...   711    0.0
> > > sp|P26696|MK01_XENLA  Mitogen-activated protein
> > kinase
> > > 1 (Myel...   711    0.0
> > > gb|AAH76730.1|  Xp42 protein [Xenopus laevis]
> > >              706    0.0
> > > gb|AAH65868.1|  Mitogen-activated protein kinase 1
> > > [Danio rerio]    696    0.0
> > > dbj|BAD23843.1|  extracellular signal regulated
> > > protein kinase...   694    0.0
> > > ref|NP_878308.2|  mitogen-activated protein kinase
> > 1
> > > [Danio re...   694    0.0
> > > emb|CAG07778.1|  unnamed protein product
> > [Tetraodon
> >
> === message truncated ===
> 
> 
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