Entering edit mode
9.1 years ago
R
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10
I would like to reload a pre-index file in perl which has been previously indexed as following:
./first_script.pl hg19.fa
use Bio::DB::Fasta;
my $db = Bio::DB::Fasta->new($file_fasta);
..
in an another script I would like to re-load the existing indexed file.
./script.pl hg19.fa.index input
#!/usr/bin/perl
use warnings;
use strict;
use Bio::DB::Fasta;
my $fasta_index_file = $ARGV[0];
my $input_file = $ARGV[1];
open(FH,"<$input_file");
my $db->index_file($fasta_index_file);
In the description it says
Title : index_file
Usage : $db->index_file($filename)
Function: (re)loads a sequence file and indexes sequences offsets in the file
Returns : seq offsets in the file
Args : filename,
boolean to force reloading a file
but it returns the following error:
Can't call method "index_file" on an undefined value at script.pl line
It would help if you added the line that wrote the created index into the .index file.
Does "my $db = Bio::DB::Fasta->new($file_fasta);" automatically write the index file into the current dir or I am doing sth wrong. When I ran the first script I saw the hg19.fa.index created in the curent dir!!
Something wrong with the BioPerl on my machine - I'm unable to check this out for myself :(