Re: Size of sequences in fastafile

It is difficult to know quite what data structure and form you want from the description (See I know what I mean. Why don't you?). I've assumed you want an array formed with the even lines appended to the odd lines with a space between. Here's an SSCCE to demonstrate one technique for this.

use strict;
use warnings;

use Test::More tests => 1;

my @seq;
my @want = (
    '>NM_001 Homo sapiens ADA2 (CECR1) GATCCAA',
    '>NM_002 Homo sapiens IKBKG GGAGGTCTTTAGCTTTAGGGAAACCC',
);

while (<DATA>) {
    chomp;
    if (/^>/) {
        push @seq, "$_ ";
    } else {
        $seq[-1] .= $_;
    }
}

is_deeply \@seq, \@want;

__DATA__
>NM_001 Homo sapiens ADA2 (CECR1)
GATCCAA
>NM_002 Homo sapiens IKBKG
GGAGGTCTTTAGCTTTAGGGAAACCC
[download]

Comment on Re: Size of sequences in fastafile Download Code

Replies are listed 'Best First'.
Re^2: Size of sequences in fastafile by Sofie (Acolyte) on Feb 29, 2020 at 16:17 UTC
Thanks for the reply. But the code was not what I was looking for. Basically I just want to figure out the length of each sequence in a multifasta file. The files contains many sequences, each sequence has new lines inside, and I want to know how many nucleotides each sequence is and then extract only the sequences with more than x number of nt. Not sure if that makes sense? How to figure out the length of a sequence from a multifasta sequence file? Thanks!	[reply]
Re^3: Size of sequences in fastafile by hippo (Archbishop) on Feb 29, 2020 at 16:51 UTC
It's still not very clear precisely what you expect but here's my final stab at this. use strict; use warnings; use Test::More tests => 1; # Present this SSCCE as a test my @seq; # Sequences longer than $min are stored here my @want = ( 'GGAGGTCTTTAGCTTTAGGGAAACCC', ); # These are the sequeneces we expect for the given data set my $min = 15; # Minimum length of any sequence to be considered my $this = ''; while (<DATA>) { chomp; if (/^>/) { push @seq, $this if $min <= length $this; $this = ''; } else { $this .= $_; } } push @seq, $this if $min <= length $this; is_deeply \@seq, \@want; # Check that our algorithm has worked __DATA__ >NM_001 Homo sapiens ADA2 (CECR1) GATCCAA >NM_002 Homo sapiens IKBKG GGAGGTCTTTAGCTTTAGGGAAACCC [download]	[reply] [d/l]
Re^4: Size of sequences in fastafile by Sofie (Acolyte) on Mar 01, 2020 at 12:03 UTC
This is my data: >NM_030643.4 Homo sapiens apolipoprotein L4 (APOL4) GAGGTGCTGGGGAGCAGCGTGTTTGCTGTGCTTGATTGTGAGCTGCTGGGAAGTTGTGACTTTCATTTTA CCTTTCGAATTCCTGGGTATATCTTGGGGGCTGGAGGACGTGTCTGGTTATTATATAGGTGCACAGCTGG AGGTGAGATCCACACAGCTCAGACCAGCTGGATCTTGCTCAGTCTCTGTCAGAGGAAGATCCCTTGGAGG AGGCCCCGCAGCGACATGGAGGGAGCTGCTTTGCTGAAAATCTTTGTCGTCTGCATCTGGAACCAAAATC >NM_001198855.1 Homo sapiens cytochrome P450 family 2 subfamily C memb +er 8 (CYP2C8) ACATGTCAAAGAGACACACACTAAATTAGCAGGGAGTGTTATAAAAACTTTGGAGTGCAAGCTCACAGCT GTCTTAATAAGAAGAGAAGGCTTCAATGGAACCTTTTGTGGTCCTGGTGCTGTGTCTCTCTTTTATGCTT CTCTTTTCACTCTGGAGACAGAGCTGTAGGAGAAGGAAGCTCCCTCCTGGCCCCACTCCTCTTCCTATTA >NR_029834.1 Homo sapiens microRNA 200a (MIR200A), microRNA CCGGGCCCCTGTGAGCATCTTACCGGACAGTGCTGGATTTCCCAGCTTGACTCTAACACTGTCTGGTAAC GATGTTCAAAGGTGACCCGC >AC067940.1 Homo sapiens clone RP11-818E9, LOW-PASS SEQUENCE SAMPLING AAATACAACTTTAAATCAAAACGGTAAAAATTCCACTCTTTCATACTAACTTCAAAAGTATTTGCTTTAA AAAAAAAGNNNNNNNNNNAAACTGAATTTCTATTAAGCATCTATTTATAGAAGAGAGTAAACACCCCGTG AATAAAAGACAGAGAATTGTAGCAGCCCGAAGTCCCTTTTCTCTCCTCCCAAGCATTTGGCTCTGGTCCA AATTCACATATCCTGCTCCGTAAAACAAAGTGCCTTGGTTAACCTAACGTTATTCCTTGAACAGTAGTTT AGTGATCAACTAGTTTTTGTTGTTGTTGTTGTTTGAGACAGAGTCTCACTCTGTCGCCCAGGCTGGAGTG CAGTGGCGAGATCTCAGCTCACTGCAACCTCTGCTGCCCAGGTTCAAGGGATTCTCCTGCCTCAGCCTCC CAAGTAGCTGGTATTACAGGCACCTGCCACCGCGCCTGGCTAATTTTTTTTTTTTTTTTTTTTTGTATTT [download] The question is, how can I find out the sequence length of each sequence and extract those of a specific length? I have tried both to put the data in an array, which puts each line in one element, and also to put it in a scalar and tried to use the > to separate each seq, but I am stuck.	[reply] [d/l]
Re^5: Size of sequences in fastafile by zubenel0 (Sexton) on Mar 01, 2020 at 12:39 UTC
Re^4: Size of sequences in fastafile by Sofie (Acolyte) on Mar 01, 2020 at 11:03 UTC
Thank you very much for your efforts. I am obviously not able to explain very well what I am trying to do. This seems to put all the sequences in one single element of the @seq array, and the length includes the header ( not just the seq data). I just want to extract all the sequences with a minimal length. But the sequences need to still be in fasta format. How can I use the regex for > to extract the sequence in between the headers and check the length? Since each line of sequence has a newline in between. Thanks again and sorry for not being able to explain. /Sofie	[reply]