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BP_FASTAM9_TO_TABLE(1p) User Contributed Perl Documentation BP_FASTAM9_TO_TABLE(1p)


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


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


Command line options: -e/--evalue evalue -- filter by evalue -b/--bitscore bitscore -- filter by bitscore --header -- boolean flag to print column header -o/--out -- optional outputfile to write data, otherwise will write to STDOUT -h/--help -- show this documentation

Not technically a SearchIO script as this doesn't use any Bioperl components but is a useful and fast. The output is tabular output with the standard NCBI -m9 columns.

 hit name
 percent identity
 alignment length
 number mismatches 
 number gaps
 query start  (if on rev-strand start > end)
 query end 
 hit start (if on rev-strand start > end)
 hit end 
 bit score

Additionally 3 more columns are provided fasta score sw-score percent similar query length hit length query gaps hit gaps

AUTHOR - Jason Stajich

Jason Stajich jason_at_bioperl-dot-org
2020-10-28 perl v5.30.3