[Bioperl-l] Parsing Genbank
Chris Fields
cjfields at illinois.edu
Wed Dec 2 19:39:40 UTC 2009
That one's odd; the coordinates should relate back to the original sequence. Any chance you could pass on the sequence file so we can confirm it? you can do this off-list if the information is sensitive, or you can create a faux sequence that has the same problem).
chris
On Dec 2, 2009, at 1:29 PM, Brandi Cantarel wrote:
> 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');
> #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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