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annotate test-data/blastdb.loc @ 120:2729c2326235

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Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 31 Jul 2014 16:14:36 +0200
parents 0c2a03f9740b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #This is a sample file distributed with Galaxy that is used to define a
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2 #list of nucleotide BLAST databases, using three columns tab separated
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3 #(longer whitespace are TAB characters):
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4 #
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5 #<unique_id> <database_caption> <base_name_path>
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6 #
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7 #The captions typically contain spaces and might end with the build date.
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8 #It is important that the actual database name does not have a space in
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9 #it, and that there are only two tabs on each line.
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10 #
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11 #So, for example, if your database is nt and the path to your base name
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12 #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry
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13 #would look like this:
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14 #
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15 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
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16 #
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17 #and your /depot/data2/galaxy/blastdb/nt directory would contain all of
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18 #your "base names" (e.g.):
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19 #
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20 #-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr
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21 #-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin
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22 #-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
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23 #...etc...
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24 #
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25 #Your blastdb.loc file should include an entry per line for each "base name"
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26 #you have stored. For example:
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27 #
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28 #nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
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29 #wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk
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30 #test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test
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31 #...etc...
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32 #
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33 #You can download the NCBI provided protein databases like NT from here:
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34 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
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35 #
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36 #See also blastdb_p.loc which is for any protein BLAST database, and
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37 #blastdb_d.loc which is for any protein domains databases (like CDD).
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38
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39 EUginius_plasmid Euginius plasmid insert /opt/galaxy/blastdbs/EUginius_plasmid_insert Example Gene Bank http://example.com/example-genebank/{defline[0]}/