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.