BLAST TEST DATA FILES
=====================

This directory contains various data files for testing the
BLAST-related code in Biopython. All files are grouped by BLAST
release version, from the most recent first.

BLAST+ 2.2.30
-------------
text_2230_blastp_001         single query, match with full line of dashes

BLAST 2.2.28+
-------------
tab_2228_tblastn_001         single query, custom columns: evalue sallseqid qseqid, commented

tab_2228_tblastx_001         single query with all columns (including new ones added in this version), commented


BLAST 2.2.26+
-------------
tab_2226_tblastn_001         multiple queries
tab_2226_tblastn_002         single query, no hits
tab_2226_tblastn_003         single query, hits @ single hsp
tab_2226_tblastn_004         single query, multiple hsps per hit present
tab_2226_tblastn_005         multiple queries, commented
tab_2226_tblastn_006         single query, no hits, commented
tab_2226_tblastn_007         single query, hits @ single hsp, commented
tab_2226_tblastn_008         single query, multiple hsps per hit present, commented
tab_2226_tblastn_009         multiple queries with custom columns
tab_2226_tblastn_010         multiple queries with custom columns, commented
tab_2226_tblastn_011         multiple queries with all columns, commented
tab_2226_tblastn_012         multiple quries, remote search, standard columns, commented
tab_2226_tblastn_013         single query, custom columns: qsseq std sseq

text_2226_blastn_001         single query, no hits
text_2226_blastn_002         single query, hits @ single hsp
text_2226_blastn_003         single query, multiple hsps per hit present
text_2226_blastn_004         multiple queries
text_2226_blastp_001         single query, no hits
text_2226_blastp_002         single query, hits @ single hsp
text_2226_blastp_003         single query, multiple hsps per hit present
text_2226_blastp_004         multiple queries
text_2226_blastx_001         single query, no hits
text_2226_blastx_002         single query, hits @ single hsp
text_2226_blastx_003         single query, multiple hsps per hit present
text_2226_blastx_004         multiple queries
text_2226_tblastn_001        single query, no hits
text_2226_tblastn_002        single query, hits @ single hsp
text_2226_tblastn_003        single query, multiple hsps per hit present
text_2226_tblastn_004        multiple queries
text_2226_tblastx_001        single query, no hits
text_2226_tblastx_002        single query, hits @ single hsp
text_2226_tblastx_003        single query, multiple hsps per hit present
text_2226_tblastx_004        multiple queries

xml_2226_blastn_001.xml      multiple queries
xml_2226_blastn_002.xml      single query, no hits
xml_2226_blastn_003.xml      single query, hits @ single hsp
xml_2226_blastn_004.xml      single query, multiple hsps per hit present
xml_2226_blastn_005.xml      multiple queries, remote search on NCBI's database
xml_2226_blastn_006.xml      single query, against a database with duplicate entries
xml_2226_blastp_001.xml      multiple queries
xml_2226_blastp_002.xml      single query, no hits
xml_2226_blastp_003.xml      single query, hits @ single hsp
xml_2226_blastp_004.xml      single query, multiple hsps per hit present
xml_2226_blastp_005.xml      multiple queries, remote search on NCBI's database
xml_2226_blastx_001.xml      multiple queries
xml_2226_blastx_002.xml      single query, no hits
xml_2226_blastx_003.xml      single query, multiple hsps per hit present
xml_2226_blastx_004.xml      multiple queries, remote search on NCBI's database
xml_2226_tblastn_001.xml     multiple queries
xml_2226_tblastn_002.xml     single query, no hits
xml_2226_tblastn_003.xml     single query, hits @ single hsp
xml_2226_tblastn_004.xml     single query, multiple hsps per hit present
xml_2226_tblastn_005.xml     multiple queries, remote search on NCBI's database
xml_2226_tblastx_001.xml     multiple queries
xml_2226_tblastx_002.xml     single query, no hits
xml_2226_tblastx_003.xml     single query, multiple hsps per hit present
xml_2226_tblastx_004.xml     multiple queries, remote search on NCBI's database


BLAST 2.2.22+
-------------
text_2222_blastx_001.txt     multiple queries

xml_2222_blastp_001.xml      n/a
xml_2222_blastx_001.xml      compare with text_2222_blastx_001.txt


BLAST 2.2.22 (Legacy)
---------------------
text_2222L_blastx_001.txt    multiple queries


BLAST 2.2.21 (Legacy)
---------------------
text_2221L_blastp_001.txt    multiple queries


BLAST 2.2.20 (Legacy)
---------------------
text_2220L_blastx_001.txt    multiple hits @ single hsp
text_2220L_blastx_002.txt    multiple queries, most with no hits


BLAST 2.2.18+
-------------
xml_2218_blastp_001.xml      n/a
xml_2218_blastp_002.xml      n/a


BLAST 2.2.18 (Legacy)
---------------------
xml_2218L_blastp_001.xml     n/a
xml_2218L_rpsblast_001.xml   n/a


BLAST 2.2.16 (Legacy)
---------------------
text_2216L_tblastn_001.txt   multiple hits, multiple hsps per hit present


BLAST 2.2.15 (Legacy)
---------------------
text_2215L_blastx_001.txt    no hits, single query


BLAST 2.2.12 (Legacy)
---------------------
xml_2212L_blastn_001.xml     n/a
xml_2212L_blastp_001.xml     n/a
xml_2212L_blastx_001.xml     n/a
xml_2212L_tblastn_001.xml    n/a
xml_2212L_tblastx_001.xml    n/a


BLAST 2.2.8 (Legacy)
--------------------
text_2208L_psiblast_001.txt  no 'Searching...' lines


BLAST 2.2.2 (Legacy)
--------------------
text_2202L_blastn_001.txt    no hits, with errors
text_2202L_blastn_002.txt    no hits
text_2202L_blastp_001.txt    n/a


BLAST 2.2.1 (Legacy)
--------------------
text_2201L_blastx_001.txt    No 'length of query'


BLAST 2.1.2 (Legacy)
--------------------
text_2102L_blastn_001.txt    no hits


BLAST 2.0.14 (Legacy)
---------------------
text_2014L_blastn_001.txt    multiple hits @ single hsp
text_2014L_psiblast_001.txt  no model sequences found (from Mike Poidinger)


BLAST 2.0.12 (Legacy)
---------------------
text_2012L_psiblast_001.txt  multiple db (from Mike Poidinger)


BLAST 2.0.11 (Legacy)
---------------------
text_2011L_blastp_001.txt    multiple hits @ single hsp
text_2011L_blastp_002.txt    no hits
text_2011L_blastp_003.txt    multiple hits, multiple hsps per hit present
text_2011L_blastp_004.txt    no descriptions
text_2011L_blastp_005.txt    hit table only
text_2011L_blastp_006.txt    master-slave
text_2011L_blastp_007.txt    master-slave, no descriptions
text_2011L_phiblast_001.txt  converged in 2 rounds
text_2011L_phiblast_002.txt  no new sequences before 'CONVERGED!' message
text_2011L_phiblast_003.txt  master-slave
text_2011L_blastn_001.txt    multiple hits @ single hsp
text_2011L_blastn_002.txt    hit table only
text_2011L_blastn_003.txt    no descriptions
text_2011L_blastn_004.txt    master-slave
text_2011L_blastx_001.txt    multiple hits @ single hsp
text_2011L_blastx_002.txt    no hits
text_2011L_tblastn_001.txt   multiple hits @ single hsp
text_2011L_tblastn_002.txt   no hits
text_2011L_tblastx_001.txt   multiple hits @ multiple hsps


BLAST 2.0.10 (Legacy)
---------------------
text_2010L_blastp_001.txt    multiple hits @ single hsp
text_2010L_blastp_002.txt    no hits
text_2010L_blastp_003.txt    multiple hits, multiple hsps per hit present
text_2010L_blastp_004.txt    no descriptions
text_2010L_blastp_005.txt    hit table only
text_2010L_blastp_006.txt    master-slave
text_2010L_blastp_007.txt    master-slave, no descriptions
text_2010L_phiblast_001.txt  converged in 1 round
text_2010L_phiblast_002.txt  converged in 3 rounds
text_2010L_phiblast_003.txt  no new sequences before 'CONVERGED!' message
text_2010L_blastn_001.txt    multiple hits @ single hsp
text_2010L_blastn_002.txt    no hits
text_2010L_blastn_003.txt    multiple hits @ single hsp, no hit table
text_2010L_blastn_004.txt    master-slave
text_2010L_blastx_001.txt    multiple hits @ single hsp
text_2010L_blastx_002.txt    no hits
text_2010L_tblastn_001.txt   multiple hits @ single hsp
text_2010L_tblastn_002.txt   no hits
text_2010L_tblastx_001.txt   multiple hits @ multiple hsps


Mock files for mocked qblast searches
-------------------------------------
This are minimal xml/html files mimicking NCBI qblast responses
for our mocked online tests in test_NCBI_qlast_mock.py:

mock_actin.xml
mock_disco.xml
mock_orchid.xml
mock_pcr.xml
mock_short_empty.xml
mock_short_result.xml
mock_wait.html
