---
name: "bp_fastam9_to_table"
section: "1p"
platform: "linux"
package: "bioperl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bp_fastam9_to_table"
---

# bp\_fastam9\_to\_table(1p)

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

## NAME

fastm9\_to\_table  - turn FASTA -m 9 output into NCBI -m 9 tabular output

## SYNOPSIS

```
 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 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.

```
 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-org