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

Raghunath Verabelli iamvela at yahoo.com
Wed Feb 22 16:06:54 EST 2006


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 ===


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


More information about the Bioperl-l mailing list