[Bioperl-l] need help ??parse AcNum from fasta?

[Smithies, Russell]

I know this is the Bioperl list but how about just doing it with grep?

	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of outaleb Issame
> Sent: Wednesday, 3 October 2007 3:51 a.m.
> To: outaleb Issame
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> 
> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
> 
> 
> 
> outaleb Issame wrote:
> 
> >thx for the help, but i got a empty output file,
> >i think its problem with matching the acc number, my fasta file look
like:
> >
> >*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU...
> > >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU..
> > >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >MMMMM..*
> >
> >and my i Accnum File look like:
> >*IPI00177321
> >IPI00453473
> >
> >*i hopt it helps to understand.*
> >*.
> >
> >
> >Nathan S. Haigh wrote:
> >
> >
> >
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>
> >>>hi,
> >>>with this file i mean, i picked out this Accession Number from
> >>>IPI-Human Dbase,they come from a fasta file,
> >>>so they re under eachother like a i a table in separate file now.
> >>>what i want is how how can i check it in the fasta File (so in the
> >>>IPI-Human FAsta File), i they re really there;
> >>>if yes please copy the entire entry of this Number (>....the
sequence
> >>>also)in new fasta file.so that i get at the end a new
> >>>FASTA file with jus this IPI Accession Number.
> >>>thx and hope was clearly.
> >>>
> >>>
> >>>
> >>>
> >>Ok, first of all, I'd read the contents of your Accession numbers
into a
> >>hash, something like the following (this could be written in a
shorter
> >>form, but since you're a newbie I'll leave it in a longer form so
you
> >>can follow easier).
> >>
> >>-- start script --
> >>use strict;
> >>use Bio::SeqIO;
> >>
> >># change the following three lines to point to the relevant paths
> >># of your list of accessions file, your fasta file and your output
> >># fasta file
> >>my $acc_file = "/path/to/your/file";
> >>my $fasta_file_in = "/path/to/your/fasta/file";
> >>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>
> >># Use a hash to keep a record of accessions we want to find
> >>my %hash_of_req_acc;
> >>
> >># read all the required accessions from the file into the hash as
keys
> >>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>while (<ACC_FILE>) {
> >> my $line = $_;
> >> chomp $line;
> >> $hash_of_req_acc{$_} = 1;
> >>}
> >>close ACC_FILE;
> >>
> >>my $seqio_object_in = Bio::SeqIO->new(
> >> -file => $fasta_file_in,
> >> -format => 'fasta'
> >>);
> >>my $seqio_object_out = Bio::SeqIO->new(
> >> -file => $fasta_file_out,
> >> -format => 'fasta'
> >>);
> >>
> >># loop through all the sequences in the fasta file
> >>while (my $seq_object = $seqio_object_in->next_seq) {
> >> # get the sequence accession for easy matching
> >> my $seq_acc = $seq_object->accession_number;
> >>
> >> # write the sequence object to the output fasta file if we have a
> >>matching accession
> >> $seqio_object_out->write_seq($seq_object) if exists
> >>$hash_of_req_acc{$seq_acc};
> >>}
> >>-- end script --
> >>
> >>I haven't tested this, but it should at least get you started. Also,
the
> >>fasta description line in the output file may not be exactly as it
was
> >>in the input fasta file - if this really matters, you may need to
get
> >>back to us. Also, if the input fasta file is huge (many thousands of
> >>sequences) it may be wise to create an index of the fasta file in
order
> >>to speed up retrieval.
> >>
> >>You may find this page helpful:
> >>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>
> >>Anyway, hope this helps to get you started.
> >>Nath
> >>
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >>
> >
> >_______________________________________________
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> >
> >
> >
> 
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