bp_hmmer_to_table - turn HMMER output into tabular format
bp_hmmer_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.
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)
Jason Stajich jason_at_bioperl-dot-org
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.