I have a fasta format file. It looks like. test.fa
>WP1_11_x10
CCATGCGCGGGTTCAATTCCTGTCGTTCGACCC
>WP1_16_x1
ACAAGCGAAGGCTCCTCAACGACGCCTCATCGGATG
>WP1_17_x1
AGAACAAGATTGTTGAAAACTTGAGGA
>WP1_21_x11
CCTGGGATGCGCAAGGAAGCTGAC
I want the below format.The number(10,1,1,11) is in the fasta header .
CCATGCGCGGGTTCAATTCCTGTCGTTCGACCC 10
ACAAGCGAAGGCTCCTCAACGACGCCTCATCGGATG 1
AGAACAAGATTGTTGAAAACTTGAGGA 1
CCTGGGATGCGCAAGGAAGCTGAC 11
Who can help me?Thank you very much!!!
•
written
by
2011101101 •
hai 21.., Please refer to code below written in perl
#! /usr/bin/perl -w
open(F1, '<', "$ARGV[0]") or die;
while (<F1>){
if ($.%2 != 0) {
@val = split(/\_/);
$cnt = $val[1];
}
else{ chomp($_); print "$_ $cnt \n"; }
}
This code was not written in a defensive way, this should work normally with out any problems.
Thank you ,but I 'm sorry i give you the wrong number ,I have edit it.I have got the answer,thank you
#! /usr/bin/perl -w
open(F1, '<', "$ARGV[0]") or die;
while (<F1>){
if ($.%2 != 0) {
@val = split(/\_x/);
$cnt = $val[1];
}
else{ chomp($_); print "$_ $cnt \n"; }
}
Consider upvoting the answer, if it was useful for you.
Or at the command line:
more test.fa | perl -ane 'if(/>/){($dum,$x)=split(/x/,$F[0]);}else{print "$F[0]\t$x\n";}'
Here's another option:
use strict;
use warnings;
my $num;
while (<>) {
if (/>/) {
($num) = /(\d+)$/;
}
elsif ( $num and /\S/ ) {
chomp;
print "$_\t$num\n";
}
}
Usage: perl script.pl fastaFile [>resultsFile]
The last, optional parameter will redirect output to a file.
Results on your dataset:
CCATGCGCGGGTTCAATTCCTGTCGTTCGACCC 10
ACAAGCGAAGGCTCCTCAACGACGCCTCATCGGATG 1
AGAACAAGATTGTTGAAAACTTGAGGA 1
CCTGGGATGCGCAAGGAAGCTGAC 11
Here is how to do it with Biopieces www.biopieces.org):
read_fasta -i test.fa | split_vals -k SEQ_NAME -d 'x' | write_tab -k SEQ,SEQ_NAME_1 -x
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