Hello all,
I've a list of IDs, and I would like to extract those sequences from a fasta file, that are not included in my list. Anyone know how to do it with perl/bioperl? Anyway to modify this script in order to get the sequences NOT present in my list?
use Bio::DB::Fasta;
my $fastaFile = shift;
my $queryFile = shift;
my $db = Bio::DB::Fasta->new( $fastaFile );
open (IN, $queryFile);
while (<IN>){
chomp;
$seq = $_;
my $sequence = $db->seq($seq);
if (!defined( $sequence )) {
die "Sequence $seq not found. \n"
}
print ">$seq\n", "$sequence\n";
}
Thanks in advance
3 answers
My script might help: https://github.com/RamRS/myPerlScripts/blob/master/filterMulFa.pl
Just negate the if(exists)
Hi ram,
I am trying to use your script but I am getting this message:
perl filterMulFa.pl ids fasta -> Getopt::ArgParse: Option fasta is required.
To have this module I used cpan. Second point, how its possible to negate the sentence in perl? many thanks in advance.
pd. I am just starting with perl
•
written
by
ericpintof •
Many thanks for your answer. Actually still I cannot run the script. I created a fake sequence.fasta:
>a
CCCDDD
>b
AAAAAA
>c
list.id:
b
c
perl filterMulFa.pl -f sequence.fasta -i list.id
and the return is this:
perl filterMulFa.pl: extract subset of sequences from FASTA file
usage: 03_pick_IDs_fasta.pl --ids|-i --fasta|-f
This script reads a FASTA file with multiple \ sequences, a
text file with a list of IDs and picks from the \ FASTA file
sequences that have an ID match in the IDs file. \ These
sequences are then printed to STDOUT
required named arguments:
--ids, -i IDS file with IDs of sequences to be picked
--fasta, -f FASTA input FASTA file
I dont know what is going wrong. Thanks in advance
•
written
by
ericpintof •
You can do this with BBTools:
filterbyname.sh in=reads.fasta out=filtered.fasta names=file include=f
include toggles between including the specified reads, or excluding the specified reads. The names file can either be a list of names (one name per line) or another fasta/fastq/sam file.
•
written
by
Brian Bushnell
Many thanks, It worked perfect.
I am surprise about this java option, people says that for bioinformatic solutions perl and python are the most useful languages. Should I learn java then? I ask this because I decided to learn one of this languages
•
written
by
ericpintof •
It depends on the use-case. Perl and Python are scripting languages, better suited to interacting with the shell. Java and C are compiled languages, better suited for processing large amounts of data quickly. It's useful to know one of each.
•
written
by
Brian Bushnell
Quick and dirty.
cat dummy.fasta
>one
AAAAAAAAAAAAAAAAAAAA
>two
CCCCCCCCCCCCCCCCCCCC
>tree
GGGGGGGGGGGGGGGGGGGG
>four
TTTTTTTTTTTTTTTTTTTT
cat dummy.ID
two
grep '>' dummy.fasta | grep -v -F -f dummy.ID - | grep -A1 -w -F -f - dummy.fasta | grep -v '^--'
>one
AAAAAAAAAAAAAAAAAAAA
>tree
GGGGGGGGGGGGGGGGGGGG
>four
TTTTTTTTTTTTTTTTTTTT
Some time ago there was thread on multi-line vs single line fasta: How To Get Fasta Format Using Fastafrombed Or How To Turn Linearized Fasta To The Same Length Columns :)
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