[Bioperl-l] Output a subset of FASTA data from a single large file
oldham at ucla.edu
Thu Jun 8 22:07:34 EDT 2006
I am a total Bioperl newbie struggling to accomplish a conceptually simple
task. I have a single large fasta file containing about 200,000 probe
sequences (from an Affymetrix microarray), each of which looks like this:
>probe:HG_U95Av2:1138_at:395:301; Interrogation_Position=2631; Antisense;
What I would like to do is extract from this file a subset of ~130,800
probes (both the header and the sequence) and output this subset into a new
fasta file. These 130,800 probes correspond to 8,175 probe set IDs
("1138_at" is the probe set ID in the header listed above); I have these
8,175 IDs listed in a separate file. I *think* that I managed to create an
index of all 200,000 probes in the original fasta file using the following
# script 1: create the index
my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(
-filename => $Index_File_Name,
-write_flag => 1);
I'm not sure if this is the most sensible approach, and even if it is, I'm
not sure what to do next. Any help would be greatly appreciated!
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