[Bioperl-l] Very basic Perl/BioPerl Help

[Stefan Kirov]

Sorry Colin,
I was thinking of sort/diff but this may not work as there will be 
insertions/deletions... You can just use perl to cycle through both lists:
my $f1=shift;
my $f2=shift;
open (F1,$f1)||die;
open (F2,$f2)||die;
my @accn1=<F1>;
my @accn2=<F2>;
my @unique1;
foreach my $accn (@accn1) {
push @unique1,$accn unless (grep(/$accn/, at accn2));
}
Sorry for the confusion
Stefan

Colin Erdman wrote:

>Hello all,
>
> 
>
>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
>both.
>
>            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
>objs somehow?
>
> 
>
>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
>accession #'s. 
>
> 
>
>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.
>
> 
>
>Thanks all!
>
>Colin 
>
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>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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And all these things are swept aside"