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BP_FASTAM9_TO_TABLE(1p) | User Contributed Perl Documentation | BP_FASTAM9_TO_TABLE(1p) |
NAME¶
fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular outputSYNOPSIS¶
fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...
DESCRIPTION¶
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 documentationNot 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.
queryname 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 evalue 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-org2018-10-27 | perl v5.26.2 |