---
name: "bp_hmmer_to_table"
section: "1p"
platform: "linux"
package: "bioperl"
version: "1.7.2-3"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/bp_hmmer_to_table"
---

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

turn HMMER output into tabular format

## NAME

bp\_hmmer\_to\_table  - turn HMMER output into tabular format

## SYNOPSIS

```
 bp_hmmer_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.

```
  query sequence/domain (these are flip-flopped for hmmsearch / hmmpfam)
  query start
  query end
  domain/sequence name or PFAM accession
  hit start
  hit end
  score
  e-value
  domain/sequence name (these are flip-flopped for hmmsearch / hmmpfam)
```

## AUTHOR - Jason Stajich

Jason Stajich jason\_at\_bioperl-dot-org