FASTA TEST DATA FILES
=====================

This directory contains various data files for testing the
Fasta-related code in Biopython.

The following are the common sequence file format, originally
introduced as the input file format for Bill Pearson's FASTA
tools.  These are for tested in Bio.SeqIO and Bio.AlignIO
(where the format is called "fasta") as well as other older
parts of Biopython such as the Bio.Fasta module.

ID     Description
f001   1 protein sequence
f002   3 DNA sequences
f003   2 proteins, with comments
fa01   fasta alignment

The following are example "machine readable" pairwise alignment
output files from the FASTA tools when using the -m 10 command
line option.  These are for testing the Bio.AlignIO and Bio.SearchIO
code where the format is called "fasta-m10".

output001.m10 - fasta35 protein-protein, 3 query sequences,
                no histogram, with expectation threshold
output002.m10 - fasta34 protein-protein, 3 query sequences,
                with offsets and word size, max 2 hits per query
output003.m10 - fasta34 protein-protein, 5 query sequences,
                very strict threshold so not all have hits.
output004.m10 - fasta35 nucleotide-nucleotide, 3 queries where
                only the middle one has a single hit.
output005.m10 - ssearch35 protein-protein, 3 queries where
                only the middle one has a single hit.
output006.m10 - fasta35 nucleotide-nucleotide, 1 query, in the
                alignment the query has been reversed.
output007.m10 - recreation of output001.m10 using fasta-36.3.4 (note that
                histogram is now off by default, -H now turns it on, and the
                -Q quiet flag no longer exists). Get more hits due to revised
                e-value calculations, also ">>><<<" marks end of a query, not
                just end of the file!
output008.m10 - tfastx36 protein-nucleotide, 4 queries, some with no hits,
                some matches with multiple HSPs (new feature in FASTA v36)
output009.m10 - fasta36, multiple dna queries
output010.m10 - fasta36, single dna query, no hit
output011.m10 - fasta36, single dna query, each hit contains a single hsp
output012.m10 - fasta36, single dna query, some hits contain multiple hsps
output013.m10 - fasta36, multiple protein queries
output014.m10 - fasta36, single protein query, no hit
output015.m10 - fasta36, single protein query, each hit contains a single hsp
output016.m10 - fasta36, single protein query, some hits contain multiple hsps