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);
    $header = $line;
    $sequence = ''
    print "$sequence\tlength($sequence)\n";
  } else {
    $sequence .= $line;
  }
}

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 = $in->next_seq() ){
  print join(" ",$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 = $in->next_seq() ){
  print join(" ",$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'):
  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|
  puts [record.definition, record.nalen.to_s ].join(" ")
end

fasta.go

package main

import (
  "bufio"
  "io"
  "fmt"
  "os"
  "strings"
)

type fasta struct {
  header string
  sequence string
}

func NewFastxReader(f io.Reader) *FastxReader {
        return &FastxReader{
                r:         bufio.NewReader(f),
        }
}
type FastxReader struct {
  r   *bufio.Reader
}
func (r *FastxReader) next_seq() (record fasta, err error) {
  var str string
  if str, err = r.r.ReadString('>'); err == nil {
     if str, err = r.r.ReadString('>'); err == nil {
       split_result := strings.SplitN(str, "\n", 2)
       record.header = split_result[0]
       //remove newlines and trailing >
       record.sequence = chomp(strings.Replace(split_result[1], "\n", "", -1), ">")
     }
  }
  return record, err
}

//remove last char in a string if that char is the delim
func chomp(s string, delim string) string {
   if s[len(s)-1] == delim[0] {
    return s[0:len(s)-1]
  }
  return s
}

func main() {
  file, _ := os.Open(os.Args[1])
  fastx = NewFastxReader(file)
  for rec, err := fastx.next_seq(); err == nil; {
    fmt.Println(rec.header, "\t", len(rec.sequence))
    rec, err = fastx.next_seq();
  }
}

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);
  $sequence =~ tr/\n//d;
  print "$sequence\t" . length($sequence) . "\n";
}

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:]
    header = line
    print header, len(sequence)
    sequence = ''
  else:
    sequence += line

print header, len(sequence)

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/,'')
  puts [header, seq.length].join(" ")
end

fasta2.py

#!/usr/bin/env python

import os,sys

f = open(sys.argv[1],'rU')
header = f.readline()
header = header.rstrip(os.linesep)
sequences=[]
for line in f:
  line = line.rstrip('\n')
  if(line[0] == '>'):
    header = header[1:]
    header = line
    print header, len("".join(sequences))
    sequences = []
  else:
    sequences.append(line)

print header, len("".join(sequences))

fasta_example.fa

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