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Coverage statistics and relations #11

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Coverage statistics and relations #11

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ef4b728
Modified the id in variants to match that of ref_feat
m-emerson Jul 29, 2014
5286a5d
python is not javascript, fixed syntax
m-emerson Jul 29, 2014
39f6a15
added relations to ref_feat
m-emerson Aug 8, 2014
cd058a4
Merge remote-tracking branch 'upstream/master'
m-emerson Aug 8, 2014
ca1f8c3
Merge remote-tracking branch 'upstream/master'
m-emerson Sep 12, 2014
0c365eb
Added coverage statistics insertion
m-emerson Sep 26, 2014
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16 changes: 10 additions & 6 deletions src/BanzaiDB/banzaidb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ def init_database_with_default_tables(args):
"""
# Add additional (default) tables here...
def_tables = ['determined_variants', 'strains_under_investigation',
'references', 'reference_features']
'references', 'reference_features', 'strain_features']
with database.make_connection() as connection:
try:
r.db_create(connection.db).run(connection)
Expand Down Expand Up @@ -177,11 +177,15 @@ def populate_mapping(args):
cur_ref = r.table('references').get('current_reference').run(connection)
ref = cur_ref["reference_id"]+"_"+str(cur_ref["revision"])
for e in strains:
# open the userplot of the current reference & strain
not_called = mapping.get_N_char_positions(run_path, e['StrainID'])
ranges = misc.get_intervals(not_called)
r.table('strains_under_investigation').get(e['StrainID']).update({"reference": ref, "coverage": json.dumps(ranges)}).run(connection)

coverage = mapping.get_coverage(run_path, e['StrainID'])
r.table('strain_features').insert(coverage).run(connection)

# Add relations from ref_feat to variants
for feature in ref_meta:
r.table('variants')\
.filter({"LocusTag" : feature['LocusTag']})\
.update({"RefFeat" : feature['id']})\
.run(connection)

def populate_assembly():
"""
Expand Down
34 changes: 34 additions & 0 deletions src/BanzaiDB/mapping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,3 +45,37 @@ def get_N_char_positions(run_path, sid):
if e == 'N':
no_call.append(idx)
return no_call

def get_coverage(run_path, sid):
"""
Return any abnormal coverage information in the .consequences file
"""
filename = sid + ".consequences" #change this when we work out naming convention
strain_features = []

with open(os.path.join(os.path.join(run_path, sid), filename)) as fin:
for idx, line in enumerate(fin):
feature = {}
if idx >= 1:
cur = line.split("\t")
feature['id'] = cur[0]+'_'+sid+'_'+cur[1]
coverage = float(cur[5])

# Only store if there is interesting coverage statistics
if coverage != 1.0: #
feature['coverage'] = coverage

old_len, new_len = int(cur[2]), int(cur[3])
AA_len = old_len - new_len

# Only store if there is an indel
if AA_len != 0:
feature['aa_difference'] = AA_len

if 'coverage' in feature or 'difference' in feature:
feature['StrainID'] = sid
feature['Reference'] = cur[0]
feature['LocusTag'] = cur[1]
strain_features.append(feature)

return strain_features