1BP_FASTAM9_TO_TABLE(1)User Contributed Perl DocumentationBP_FASTAM9_TO_TABLE(1)
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6 fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular output
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9 fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...
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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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47 Jason Stajich jason_at_bioperl-dot-org
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51perl v5.12.0 2010-04-29 BP_FASTAM9_TO_TABLE(1)