[Bioperl-l] Very basic Perl/BioPerl Help
skirov at utk.edu
Thu Apr 14 11:29:42 EDT 2005
case B is pretty straightforward by using unix diff.
Colin Erdman wrote:
>I certainly pounded away at this one last night, I thought this part would
>be easy, but after spending so much time getting my Entrez gene data parsed
>etc my brain was a bit rubbery.
>What I am trying to do is take either A) Two fasta files with refseq/genbank
>data OR B) Two text files with 1 accession# per line and compare them,
>outputting only those fasta seqs or accession #'s that are not present in
> So is it easier to just use perl somehow to compare the two raw
>acc# text files?
> Or should I keep them as FASTA seqs and compare using Bio::Seq
>The idea is to update a list of Chromosome 21 genes last revised in 2003 by
>comparing those accession numbers in our list with all of those accession
>#'s that I pulled from an entrezgene 21[CHR] AND Homo sapiens[ORGN] NOT
>pseudogene query and then saved the output as an ASN.1 file. I have all the
>I just will need to match up those accession #'s NOT currently in our list
>with the appropriate Entrez Genes using gene2accession, but I am not sure
>how to do that either. I am assuming using a hash, but they have been steep
>for me in terms of learning curve, but I'd like to learn them now, I will
>just need some intuitive support.
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
e-mail: skirov at utk.edu
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