FastaReader - class for reading a fasta-like formatted file

The assumption is that the file contains a set of multi-line records separated by single-line headers starting with a specific separator (by default '>')

#!/usr/bin/perl
use FastaReader;

my $file = shift;
open(IN,$file) || die "Cannot open $ARGV[0]: $!\n";

my $parser = new FastaReader(\*IN);
while (my $seqobj = $parser->next_seq()) {
    printf ("%s\n", $seqobj->seq);
    printf ("%s\n", $seqobj->name);
    printf ("%s\n", $seqobj->length); 
}

This module iterates through a fasta-like file retrieving the records in (header, data) pairs. When creating a new parser, the user may specify both the prefix (as a string) that indicates a header (record separator) line (default is '>'), and a line separator that is used when concatenating the lines in the input forming the body of each record. This separator is useful, for example, when parsing a .qual file where the quality values are separated by spaces.

• $parser = new FastaReader($file, $head, $sep)

  Creates a new parser object reading from file $file and using a specific header separator ($header - default '>') and a line separator ($sep - default '')

• $seq = $parser->next_seq()

  Reads a record into an object of obj. If no more records remain returns undef.

• $name = $seq->name()

  Return name of current record

• $length = $seq->length()

  Return length of current record

• $posn = $seq->tell()

  Return offset of current record

• $parser->seek(posn)

  Resets the parser to a specific location (posn) in the file stream.

Wenchao Lin <linwenchao(at)yeah.net>