cath-sc-merge-alignmentΒΆ

usage: cath-sc-merge-alignment [-h] --cv CATH_VERSION --in SC_FILE --out
                              OUT_STO [--ff_dir FF_DIR] [--ff_tmpl FF_TMPL]
                              [--verbose]

Merge FunFams using a structure-based alignment

optional arguments:
  -h, --help         show this help message and exit
  --cv CATH_VERSION  cath version
  --in SC_FILE       input reference structure-based alignment (FASTA)
  --out OUT_STO      output merged alignment file (STOCKHOLM)
  --ff_dir FF_DIR    directory in which funfam alignments can be found
                    (default: <sc_dir>)
  --ff_tmpl FF_TMPL  template used to help locate funfam file (default:
                    __SFAM__-ff-__FF_NUM__.reduced.sto)
  --verbose, -v      more verbose logging