1BP_FASTAM9_TO_TABLE(1)User Contributed Perl DocumentationBP_FASTAM9_TO_TABLE(1)
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NAME

6       fastm9_to_table  - turn FASTA -m 9 output into NCBI -m 9 tabular output
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SYNOPSIS

9        fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...
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DESCRIPTION

12       Comand line options:
13         -e/--evalue   evalue    -- filter by evalue
14         -b/--bitscore bitscore  -- filter by bitscore
15         --header                -- boolean flag to print column header
16         -o/--out                -- optional outputfile to write data,
17                                    otherwise will write to STDOUT
18         -h/--help               -- show this documentation
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20       Not technically a SearchIO script as this doesn't use any Bioperl
21       components but is a useful and fast.  The output is tabular output with
22       the standard NCBI -m9 columns.
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24        queryname
25        hit name
26        percent identity
27        alignment length
28        number mismatches
29        number gaps
30        query start  (if on rev-strand start > end)
31        query end
32        hit start (if on rev-strand start > end)
33        hit end
34        evalue
35        bit score
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37       Additionally 3 more columns are provided
38        fasta score
39        sw-score
40        percent similar
41        query length
42        hit length
43        query gaps
44        hit gaps
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AUTHOR - Jason Stajich

47       Jason Stajich jason_at_bioperl-dot-org
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51perl v5.12.0                      2010-04-29            BP_FASTAM9_TO_TABLE(1)