gitpan / bio-seqreader Goto Github PK

Bio::SeqReader is copyright 2012, John A. Crow and the National Center for
Genome Resources. All rights reserved.

--------------------------------------------------------------------------------

ABOUT BIO::SEQREADER

Bio::SeqReader provides developers simple-to-use classes for reading sequence
data in standard formats. This currently includes FASTA and FASTQ. This module
provides a very lightweight alternative to the fine Bioperl package.

Bio::SeqReader::Fasta
The FASTA (Pearson) sequence format is described in the documentation associated
with the FASTA suite as introduced in W. R. Pearson and D. J. Lipman. (1988)
"Improved tools for biological sequence comparison," Proceedings of the National
Academy of Sciences USA 85. See for example

  http://fasta.bioch.virginia.edu/fasta_www2/fasta_guide.pdf

or

  http://en.wikipedia.org/wiki/FASTA_format.

The original format allows for the use of a semicolon (";") to introduce the
sequence header. Bio::SeqReader::Fasta will handle this correctly.

Bio::SeqReader::Fastq
The FASTQ format is described formally in P. J. A. Cock, C. J. Fields, N. Goto,
M. L. Heuer, P. M. Rice. (2010) "The Sanger FASTQ file format for sequences with
quality scores, and the Solexa/Illumna FASTQ variants," Nucleic Acids Research
38. Note that it specifically allows for multiline sequence and quality score
information, and Bio::SeqReader::Fastq is designed to handle this correctly.

INSTALLATION

Bio::SeqReader is native Perl and, as noted below, only requires a standard Perl
installation. To install this module first create the Makefile from Makefile.PL
by running

  perl Makefile.PL

or for a nonstandard location (you'll probably need to adjust PERL5LIB later)

  perl Makefile.PL INSTALL_BASE=/path/to/my/perlmods

or

  perl Makefile.PL PREFIX=/path/to/my/perllibs

Then

  make
  make test
  make install

DEPENDENCIES

Bio::SeqReader requires only core Perl.

LICENSE

This set of modules is free software; you can redistribute it and/or modify it
under the same terms as Perl itself, either Perl version 5.10.0 or, at your option,
any later version of Perl 5 you may have available.

The modules are distributed in the hope that they will be useful, but are provided
"as is" and without any express or implied warranties.