config.yaml

# Created by Michal Bukowski (michal.bukowski@tuta.io) under GPL-3.0 license

# Locations of Pfam database (Pfam-A.hmm file) and directory with genomic sequences.
pfam_db: input/Pfam-A.hmm
gen_dir: genomes

# Dictionary describing domain architectures to search for as pairs of
# architecture custom label : regex describing the architecure with a prefix
# (GRP| or ACC|) that indicates whether domain group labels or Pfam accession
# version number are used. Domains are assigned to groups in input/domain.tsv file.
# In regex strings do not use characters that may confuse Bash (e.g. &;`'"),
# only letters, numbers, dash and underscore symbols are advised.
# Example architectures:
# GRP|CAT-CWT                 : find sequences with two domain only, one from
#                               the group CAT and one from the group GRP,
#                               former directly preceeds the latter
# GRP|.*CWT.*CAT.*            : similar to the previous one, but around the domains
#                               any other may exist (.*), and the order of CAT
#                               and CWT domains is reversed
# NAM|Peptidase_M14-SH3_5     : like the first example, but instead of domains
#                               from certain groups, find exactly two domains
#                               referenced by Pfam names Peptidase_M14 and SH3_5
# ACC|PF01551\.25-PF08460\.13 : instead of domains from certain groups, find
#                               exactly two domains referenced by Pfam accession
#                               version numbers PF01551.25 and PF08460.13
archs:
    CAT-CWT   : GRP|CAT-CWT
    xCWTxCATx : GRP|.*CWT.*CAT.*
    M23-SH3   : NAM|Peptidase_M23-SH3_5
    M23-SLH   : NAM|Peptidase_M23-SLH