v1.0.6

added number_hits_noingroup parameter

avp

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-#v1.0.5
+#v1.0.6
 
 from depot.interface import main
 

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['<module>'] == 'prepare':
         import depot.prepare as prepare
         prepare.main()

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()
 

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