Enveomics collection

HMMsearch.extractIds.rb

Extracts the sequence IDs and query model form a (multiple) HMMsearch report (for HMMer 3.0).

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

HMMsearch.extractIds.rb [opts] < in_file > out_file

§ Arguments

All evalue

 --all-evalue float  Maximum e-value of sequence to report result.

All score

 --all-score float  Minimum score of sequence to report result.

Best evalue

 --best-evalue float  Maximum e-value of best domain to report result.

Best score

 --best-score float  Minimum score of best domain to report result.

No model

 --no-model   Do not include the query model in the output list.

Quiet

 --quiet   Run quietly.

Input file*

 in_file  Input HMMsearch text file.

Output file*

 out_file  Output list of IDs.

* Mandatory.