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Introducing randomness for template selection #27

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Introducing randomness for template selection #27

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14 changes: 10 additions & 4 deletions antibody/antibody.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@

from optparse import OptionParser, IndentedHelpFormatter
from time import time
import random

_script_path_ = os.path.dirname( os.path.realpath(__file__) )

Expand Down Expand Up @@ -987,13 +988,18 @@ def try_to_float(v):
else:
selected_template = table[0]['subject-id']
else: # if there is no template... table is a list, which has a blast result
pdb_entries_of_same_length=[]
for v in cdr_info.items():
check_length = '%s_length' % k
if len_cdr == int(v[1][check_length]):
pdb_random = v[0]
break
print '\nWARNING: No template avaliable for %s after filtering! Using a random template of the same length as the query\n' % k
selected_template = pdb_random
pdb_entries_of_same_length.append(v[0])
print '\n\nWARNING: No template avaliable for %s after filtering! Seeking templates of the same length %d as the query.\n' % (k,len_cdr)
if 0 == len(pdb_entries_of_same_length):
print 'ERROR: Could not find any template with that same length.\n'
sys.exit(1)
else:
print 'INFO: Making a random choice from %d entries found featuring %s with length %d.\n' % (len(pdb_entries_of_same_length),k,len_cdr)
selected_template = random.choice(pdb_entries_of_same_length)
#sys.exit(1)
print "%s template: %s" % (k, selected_template)
else:
Expand Down