[Bioperl-l] Parsing Genbank
Mark A. Jensen
maj at fortinbras.us
Wed Dec 2 19:48:44 UTC 2009
with fake seq data and that header, I don't get a problem:
DB<2> x $cds->location
0 Bio::Location::Simple=HASH(0x37b1df4)
'_end' => 974
'_location_type' => 'EXACT'
'_root_verbose' => 0
'_seqid' => 'subjpool12_contig3'
'_start' => 911
'_strand' => '-1'
Are you using the latest BioPerl (1.6.1 or the trunk) ?
MAJ
----- Original Message -----
From: "Brandi Cantarel" <bcantarel at som.umaryland.edu>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, December 02, 2009 2:29 PM
Subject: Re: [Bioperl-l] Parsing Genbank
Here is some of my code, the real code actually enters the data into a database.
$in = Bio::SeqIO->new(-file => $gbkfile,
'-format' => 'genbank');
W1:while (my $seq = $in->next_seq()) {
my @feats = $seq->get_all_SeqFeatures();
my $j = 0;
F1:foreach $cds (@feats) {
next F1 unless ($cds->primary_tag() eq 'CDS');
###>> debugger stops here for above output
#do something with the cds start and cds end
}
}
LOCUS subjpool12_contig3 974 bp DNA linear UNK
19-Nov-2009
ACCESSION subjpool12_contig3
KEYWORDS .
SOURCE human metagenome
ORGANISM human metagenome
unclassified sequences; organismal metagenomes,metagenomes.
FEATURES Location/Qualifiers
source 1..974
/mol_type="genomic DNA"
/isolation_source="Homo sapiens"
/organism="human metagenome"
/collection_date="19-Nov-2009"
CDS complement(911..974)
/locus_tag="subjpool12_contig3|metagene|gene_2"
/translation="IRIMTVELINPYIRHVEHST"
/score="2.52804"
/product="hypothetical protein"
/note="score=2.52804"
/note="score=2.52804"
/note="frame=1"
ORIGIN
#some sequence….
>From this example, I would like to get the coordinates 911 and 974, rather than
>1 and 64.
~~~~~~~~~~~~~~~~~~~~
Brandi Cantarel, PhD
Bioinformatics Analyst
Institute for Genome Sciences
School of Medicine
University of Maryland, Baltimore
On Dec 2, 2009, at 2:09 PM, Mark A. Jensen wrote:
> Hi Brandi-
> If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an
> ordinary Bio::Seq, that's normal.
> Can you elaborate by posting your code?
> cheers,
> MAJ
> ----- Original Message ----- From: "Brandi Cantarel"
> <bcantarel at som.umaryland.edu>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, December 02, 2009 1:36 PM
> Subject: [Bioperl-l] Parsing Genbank
>
>
>> Hi all,
>> I am not sure if this is normal, but when I use SEQIO to parse genbank files,
>> it changes the coordinates of things on the minus strand.
>>
>>
>> For example, I have a sequence that has a CDS on the minus strand at it is
>> from 911 to 974. The sequence is 974 nt.
>>
>> x $cds->start
>> 1
>> x $cds->end
>> 64
>>
>> How can I get the original coordinates? Is there a command for that or will
>> I have to just do the math?
>>
>> Feature or Bug?
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~
>> Brandi Cantarel, PhD
>> Bioinformatics Analyst
>> Institute for Genome Sciences
>> School of Medicine
>> University of Maryland, Baltimore
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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