/ 
Bio-Lite-0.001
River stage zero No dependents
/ Bio::Lite

NAME

Bio::Lite - Bio::Lite is a perl module that aims to answer the same questions as Bio-perl, FASTER and using a SIMPLIFIED API.

VERSION

version 0.001

SYNOPSIS

Keep it simple, keep it fast.

Bio::Lite is a set of subroutines that aim to answer similar question as Bio-perl distribution without the complexity.

Bio::Lite is fast, simple and does not make use of complexe data struture and object that lead to slow execution.

All methods can be imported with a single "use Bio::Lite"

Bio::Lite is also a lightweigth, single, module with no dependencies.

UTILS

reverseComplemente

Reverse complemente the (nucleotid) sequence in arguement.

PARSING

This are some tools that aim to read (bio) files like - Sequence files : FASTA, FASTQ - Annotation files : GFF3, GTF2, BED6, BED12, ... - Alignement files : SAM, BAM -

seqFileIterator

Open Fasta, or Fastq files (can be gziped). seqFileIterator has an automatic file extension detection but you can force it using a second parameter with the format : 'fasta' or 'fastq'

my $it = seqFileIterator('file.fastq','fastq');
while(my $entry = $it->()) {
  print "Sequence name   : $entry->{name}
         Sequence        : $entry->{seq}
         Sequence quality: $entry->{qual}","\n";
}

pairedEndSeqFileIterator

Open Paired-End Sequence file unsing seqFileIterator()

my $it = pairedEndSeqFileIterator($file);
while (my $entry = $it->()) {
  print "Read_1 : $entry->{read1}->{seq}
         Read_2 : $entry->{read2}->{seq}";
}

gffFileIterator

manage GFF3 and GTF2 file format

Return a hashref with the annotation parsed :

{ chr => ...,
  source => ...,
  feature => ...,
  start => ...,
  end => ...,
  strand ...,
  frame ...,
  attributes => { id => val, ...}
}

FILES IO

getReadingFileHandle

Return a file handle for the file in argument. Display errors if file cannot be oppenned and manage gzipped files (based on .gz file extension)

TODO

- add a seqFileIterator that manage paired-end files

AUTHOR

Jérôme Audoux <jerome.audoux@gmail.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2014 by Jérôme Audoux.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007