diff --git a/avp b/avp index f7c2ae7..ea4f0d8 100755 --- a/avp +++ b/avp @@ -1,5 +1,5 @@ #!/usr/bin/env python3 -#v1.0.5 +#v1.0.6 from depot.interface import main diff --git a/depot/interface.py b/depot/interface.py index 4d7aa9f..37fd250 100644 --- a/depot/interface.py +++ b/depot/interface.py @@ -23,7 +23,7 @@ from docopt import docopt def main(): - args = docopt(__doc__,version='1.0.5', options_first=True) + args = docopt(__doc__,version='1.0.6', options_first=True) if args[''] == 'prepare': import depot.prepare as prepare prepare.main() diff --git a/depot/prepare.py b/depot/prepare.py index 2d3c10f..417ebdc 100755 --- a/depot/prepare.py +++ b/depot/prepare.py @@ -102,6 +102,7 @@ def main(): selection = config_opts["selection"] percent_identity = config_opts["percent_identity"] cutoffextend = config_opts["cutoffextend"] + number_hits_noingroup = config_opts["number_hits_noingroup"] min_num_hits = config_opts["min_num_hits"] percentage_similar_hits = config_opts["percentage_similar_hits"] mode = config_opts["mode"] @@ -167,8 +168,8 @@ def main(): ingroup_pos = 0 else: ingroup_pos = int(L_ingroup[1]) - #Select at least 50 hits - last_pos = min(max(max(ingroup_pos,donor_pos) + cutoffextend, 50), int(row[i_nbhits])) + #Select at least number_hits_noingroup hits + last_pos = min(max(max(ingroup_pos,donor_pos) + cutoffextend, number_hits_noingroup), int(row[i_nbhits])) queries_info[row[i_query]] = {'pos':last_pos} query_dict_set[row[i_query]] = set() diff --git a/depot/sample.config.yaml b/depot/sample.config.yaml index 8b7b7fd..6335119 100644 --- a/depot/sample.config.yaml +++ b/depot/sample.config.yaml @@ -15,6 +15,7 @@ outg_pct_cutoff: 80 selection: "ai or ahs" # select sequences based on which metrics, another example "(ai or ahs) and outg_pct" percent_identity: 100 # select hits equal or below this number cutoffextend: 20 # when ingroup hit is found, we take this hit + n hits +number_hits_noingroup: 50 # when no ingroup hit is found, we take this number of hits trimal: false min_num_hits: 4 # select queries with at least that many blast hits percentage_similar_hits: 0.7 # group queries based on this