Parsing fasta files in perl ruby python and go

append.pl

#!/usr/bin/env perl

use warnings;use strict;

my ($header,$sequence);
$header = <>;
chomp $header;
while(my $line = <>){
  chomp $line;
  if($line =~ /^>/){
    $header = substr($header,1);
    ##########
    #Process Record
    ##########
    $header = $line;
    $sequence = ''
  } else {
    $sequence .= $line;
  }
}
##########
#Process Last Record
##########

fasta-bioperl.pl

#!/usr/bin/env perl

use warnings;use strict;
use Bio::SeqIO;

my $in = Bio::SeqIO->new(-file => shift, '-format' => 'Fasta');

while(my $rec = $in->next_seq() ){
  ##########
  #Process record
  ##########
  print join(" ",$rec->display_id,$rec->length)."\n";
}

fasta-bioperl2.pl

#!/usr/bin/env perl

use warnings;use strict;
use Bio::SeqIO;

my $in = Bio::SeqIO->new(-file => shift, -format => 'Fasta' -alphabet => 'dna');

while(my $rec = $in->next_seq() ){
  ##########
  #Process record
  ##########
  print join(" ",$rec->display_id,$rec->length)."\n";
}

fasta-biopython.py

#!/usr/bin/env python

import sys
from Bio import SeqIO

for record in SeqIO.parse(sys.argv[1],'fasta'):
  ##########
  #Process record
  ##########
  print record.id, len(record)

fasta-bioruby.rb

#!/usr/bin/env ruby

require 'bio'

ff = Bio::FlatFile.new(Bio::FastaFormat,ARGF)
ff.each_entry do |record|
  ##########
  #Process record
  ##########
  puts [record.definition, record.nalen.to_s ].join(" ")
end

fasta.pl

#!/usr/bin/env perl

use warnings;use strict;

local $/ = ">";
my $first = <>;
while(my $record = <>){
  chomp $record;
  my $newline_loc = index($record,"\n");
  my $header = substr($record,0,$newline_loc);
  my $sequence = substr($record,$newline_loc+1);
  $sequence =~ tr/\n//d;
  ##########
  #Process record
  ##########
}

fasta.py

#!/usr/bin/env python

import os,sys

f = open(sys.argv[1],'rU')
header = f.readline()
header = header.rstrip(os.linesep)
sequence=''
for line in f:
  line = line.rstrip('\n')
  if(line[0] == '>'):
    header = header[1:]
    ##########
    #Process Record
    ##########
    header = line
    sequence = ''
  else:
    sequence += line

##########
#Process Last Record
##########

fasta.rb

#!/usr/bin/env ruby

$/ = ">"
ARGF.gets
while rec = ARGF.gets
  rec.chomp!
  nl = rec.index("\n")
  header = rec[0..nl-1]
  seq = rec[nl+1..-1]
  seq.gsub!(/\n/,'')
  ##########
  #Process record
  ##########
end

fasta_example.fa

>chr1|this is a fasta header|example
CCTAAACCCTGAACCCTAAACCCTAAACCCTGAACCCTAAACCCTGAACCCTGAACCCTAAACCCTGAACCCTAAACCTA
AACCCTGAACCCTGAACCCTAAACCCTGAACCCTAAACCCTAAACCCTAAACCTAAACCCTGAACCCTAAACCTAAACCC
TGAACCCTAAACCCTAAACCCTGAACCCTAAACCTAAACCCTGAACCCTAACCCCTGAACCCTAAACCCTGAACCCTAAA
CCCTGAAACCTGAACCCTGAACCCTAAACCCTAAACCCTGAACCCTAAACCCTGAACCCTGAACCCTAAACCCTGAACCC
>chr2|another record
TAAACCCTGAACCCTAAACCCTAAACCCTGAACCCTAAACCTAAACCATGAACCCTAAACCCTGAACCCTAAACCCTAAA
CCCTGAACCCTAAACCCTGAACCCTAAACCTAAACCCTAAACCCTGAACCCTAAACCTGAACCCTAAACCCCTAAACCTA
AACCCTGAAACCTAAACCCTAAACCCTGAACCCTAAACCCTAAACCCTGAACCCTGAAACCCTGAACCCTAAACCATGAA
CCCTGAACCCTAAACCCTAAACCCTAAACCCTGAACCCTGAACCCTAAACCTAAACCCTGAACCCTGAACCCTAAACCCT
GAACCCTAAACCCTAAACCCTGAACCCTAAACCCTGAACCCTAAACCCTGAACCCTGAACCCTAAACCCTGAACCCTAAA