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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 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.
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