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kmkocot 04-22-2010 06:44 PM
Trying to number every other line and append those numbers to end of line
 
Hi all,

I have a file formatted like this:
Code:
>Contig
ATGCATGCAATGCATGCAATGCACGGATGCAATGCATGCA
>Contig
CAATGCACGGATGCATGCCAATGATGCAATGCAT
>Contig
ATGCCGCAGTCTGACTTGCAACTGCCGTCACAGCTGCA
>Contig
CAATAACGCACGGATGCATGCTACCAATGTATGCAATGCAT
Every odd-numbered line is ">Contig" while the even numbered lines vary but are a DNA sequence of variable length and composition.

I am trying to give each Contig a number such that my output would be:
Code:
>Contig1
ATGCATGCAATGCATGCAATGCACGGATGCAATGCATGCA
>Contig2
CAATGCACGGATGCATGCCAATGATGCAATGCAT
>Contig3
ATGCCGCAGTCTGACTTGCAACTGCCGTCACAGCTGCA
>Contig4
ATGCCGCAGTCTGACTTGCAACTGCCGTCACAGCTGCA
I know this has to be really simple but I can't figure it out. Any suggestions would be greatly appreciated.

Thanks!
Kevin

kbp 04-22-2010 11:18 PM
Code:
#!/usr/bin/perl

use strict;
use warnings;

my @data;
my $match = 1;

open( FH, "<test.txt") or die "Cannot open source";
@data=<FH>;
close(FH);

open( FH, ">test.txt") or die "Cannot open dest";
foreach ( @data ) {
        if ( s/(>Contig)/$1$match/ ) { $match++; }
        print FH;
}

close(FH);

dina3e 04-22-2010 11:35 PM
try this..
Code:
#!/bin/sh
counter=0
for line in `cat file_name.txt`
do
if [ $line = '>Contig' ];then
let counter=$counter+1
echo $line$counter
else
echo $line
fi
done

David the H. 04-22-2010 11:55 PM
I did it this way using awk.
Code:
awk -F "i=1" '{if (/>Contig/){print $0i++} else print}' file

grail 04-23-2010 12:33 AM
Same idea:
Code:
awk '/>/{print $0(++i)}!/>/' file

David the H. 04-23-2010 04:02 AM
Quote:
Originally Posted by grail (Post 3944834)
Same idea:
Code:
awk '/>/{print $0(++i)}!/>/' file
Thank you. I knew it could be shorter, but I couldn't quite work out the syntax. (Parentheses around the pre-increment variable...I should've guessed.)

grail 04-23-2010 07:20 AM
Quote:
Parentheses around the pre-increment variable
Took me a couple of tries ;)

kmkocot 04-23-2010 11:17 AM
Thanks!


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