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Thread Tools |
11-11-2013, 01:59 PM
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#1 |
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Member
Location: Canada, Quebec Join Date: Apr 2012
Posts: 53
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Generate consensus from MultiFasta
Hi,
I have a multifasta like: >sequence1 ATCGATCATCG >sequence2 ATCGATNNTCG >sequence3 ATCGATCATCG All sequences are the same, except there are some N. I want to make a consensus with the N if there are. Do you know I can do this? Thanks! |
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11-13-2013, 05:30 PM
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#2 |
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Member
Location: Canada, Quebec Join Date: Apr 2012
Posts: 53
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A little up!
Please 
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11-13-2013, 07:43 PM
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#3 |
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David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 838
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here's my rough 5-minute attempt:
Code:
#!/usr/bin/perl
use warnings;
use strict;
my @sequence = ();
while(<>){
if(!/^>/){
chomp;
my @bases = split(//,$_);
for(my $i = 0; $i < @bases; $i++){
if($bases[$i] eq "N"){
$sequence[$i] = "N";
} elsif($sequence[$i] ne "N") {
$sequence[$i] = $bases[$i];
}
}
}
}
print(">consensus\n".join("",@sequence)."\n");
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