BioPerl

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I don't think you mean to use the "less" command. Try one of these: % cat try.fa | perl ./fastaLen.pl or % perl ./fastaLen.pl < try.fa

Hi, Paul, Thanks for your quick replay and advice. Soryy for my late feedback, I can't send maill in my location yesterday. I have tried your method. But it complains that ------------------------------------ [linhy< at >bioinfo1 Script]$ ... [More] less try.fa | perl ./fastaLen.pl Name "main::DATA" used only once: possible typo at ./fastaLen.pl line 42. Use of uninitialized value in print at ./fastaLen.pl line 49. ------------------------------------ I had also tried the "-fh=>\*STDIN", and "-fh=><>",according to the documentation returned by "perldoc Bio::SeqIO" at termminal, but I still haven't got I want.Thanks again. ... ... Bio::SeqIO->new() $seqIO = Bio::SeqIO->new(-file => 'filename', -format=>$format); $seqIO = Bio::SeqIO->new(-fh => \*FILEHANDLE, -format=>$format); $seqIO = Bio::SeqIO->new(-format => $format); ... ... -fh You may provide new() with a previously-opened filehandle. For example, to read from STDIN: $seqIO = Bio::SeqIO->new(-f [Less]

Hi, Paul, Thanks for your quick replay and advice. I have tried your method. But it complains that ------------------------------------ [linhy< at >bioinfo1 Script]$ less try.fa | perl ./fastaLen.pl Name "main::DATA" used only once: possible ... [More] typo at ./fastaLen.pl line 42. Use of uninitialized value in print at ./fastaLen.pl line 49. ------------------------------------ I had also tried the "-fh=>\*STDIN", and "-fh=><>",according to the documentation returned by "perldoc Bio::SeqIO" at termminal, but I still haven't got I want.Thanks again. ... ... Bio::SeqIO->new() $seqIO = Bio::SeqIO->new(-file => 'filename', -format=>$format); $seqIO = Bio::SeqIO->new(-fh => \*FILEHANDLE, -format=>$format); $seqIO = Bio::SeqIO->new(-format => $format); ... ... -fh You may provide new() with a previously-opened filehandle. For example, to read from STDIN: $seqIO = Bio::SeqIO->new(-fh => \*STDIN); Note that you must pass filehandles as referen [Less]

Hi Haiyan, You need to use the '-fh' option in Bio::SeqIO new and have it use Perl's DATA filehandle like so: my $in = Bio::SeqIO->new(-fh => \*DATA, -format => 'fasta'); This was taken from ... [More] http://perldoc.perl.org/perldata.html#Special-Literals: "Text after __DATA__ may be read via the filehandle PACKNAME::DATA , where PACKNAME is the package that was current when the __DATA__ token was encountered." Good luck, Paul Paul Cantalupo University of Pittsburgh On Sat, Jul 12, 2014 at 8:35 AM, Haiyan Lin <linhy0120< at >gmail.com> wrote: _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

Hill, dear perlers, I‘m trying to use Bio::SeqIO to read Fasta sequence from pipe, or < at >ARGV, like "while (<>) {....}". After several trier and error, I'm failed and need to ask for herp from you. Could you please help me to check ... [More] or try following code? Thanks in advance. --------------------------------------- use Bio::SeqIO ; use Statistics::Descriptive ; my %opt = () ; my $sta = Statistics::Descriptive::Full->new(); ##### here is the key， I think. my $in = Bio::SeqIO->new(-format=>"Fasta"); while(my $s = $in->next_seq()){ $sta->add_data($s->length()) ; } print $sta->sum() if $opt{sum} ; __DATA__ AGAGAGAGA ATATATAT ----------------------------------------------- Regards Haiyan _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

NCBI recently modified the URL for eutils, and it’s possible this wasn’t changed in the module. I’ll try to have a look. chris On Jul 10, 2014, at 11:21 PM, Cacau Centurion <cacaucenturion2< at >gmail.com<mailto:cacaucenturion2< at ... [More] >gmail.com>> wrote: Hi all, I was told the following message when trying to use Bioperl. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't query website: 500 Can't connect to www.ncbi.nih.gov:80<http://www.ncbi.nih.gov/> (Bad hostname) STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368 STACK: Bio::DB::Taxonomy::entrez::get_taxonids /usr/local/share/perl5/Bio/DB/Taxonomy/entrez.pm:472<http://entrez.pm:472/> I use Bio::SearchIO and Bio::DB::Taxonomy in my script. It used to work properly but has met the problem recently. Does anyone know why? Yours, Cacau _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org<mailto:Bioperl-l< at >mailman.open-bio.org> http://mailman.open-b [Less]

I have uploaded genomic fasta sequence and GFF3 file into local mysql database using "bp_seqfeature_load.pl". Now, I want to extract sequence from position 8966215-8966961 on "+" strand of Chromosome I, and print only the mRNA segment between ... [More] 8966215-8966961. If there are many transcripts/isoforms found between these position, print each isoform sequences with name and position as fasta format. Could you please tell me what is the best approach to do it for it. My code does not work well. Thanks #!/user/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::SeqFeatureI; use Bio::DB::SeqFeature::Store; use Bio::DB::SeqFeature::Segment; my < at >features; my $db = Bio::DB::SeqFeature::Store-> new(-adaptor=> 'DBI::mysql', -dsn=> '..', -user=> '..', -pass=> '..', ); my < at >foo = $db->features(-seq_id =>'I',-start=>'8966215',-end=>'8966961', -strand =>'+1', -type => 'mRNA', ); for my $f(< at >foo){ print ">",$->name,"_",$f->start,"_",$f->end,"\n"; print $f->dna,"\n"; } exit; ______________ [Less]

I'm trying to index a large fasta file that I downloaded from NCBI's ftp site. The size of the fasta file is 700GB. I'm trying to use Bio::DB::Fasta to index this file. When the index file hits around 10GB, it seems to hang. I'm wondering if there is ... [More] a limit on the fasta file size it can index. Also, how does Bio::DB::Fasta compare to Bio::Index::Fasta? Is one better for large fasta files? Are there any other indexing schemes I can use instead of these modules? Any information would be appreciated. Thanks, KB _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

I am not sure I can help you at this time, but I would encourage you to use the mailing list for assistance. There is nothing inherent in the tool for doing anything with exons but if you want to print a feature in GFF format I would look at ... [More] Bio::Tools::GFF or Bio::FeatureIO (if that still works) Another thing in this example is to change 'fasta' to 'genbank' for the $seqout object so you can see the feature annotated in the sequence in genbank format. Jason Stajich jason< at >bioperl.org http://bioperl.org/wiki/User:Jason http://twitter.com/hyphaltip On Tue, Jul 1, 2014 at 12:18 PM, Firoz Ahmed <fa49< at >nyu.edu> wrote: _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]