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fix secondary metabolite cluster plotting #820

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fix secondary metabolite cluster plotting #820

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01b23d0
Update library.py
IanDMedeiros Oct 20, 2022
4957482
Merge branch 'nextgenusfs:master' into fixAntismashNumbering
IanDMedeiros Oct 24, 2022
28706cf
Merge branch 'nextgenusfs:master' into fixAntismashNumbering
IanDMedeiros Nov 2, 2022
5c2df49
Merge branch 'nextgenusfs:master' into fixAntismashNumbering
IanDMedeiros Nov 28, 2022
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28 changes: 21 additions & 7 deletions funannotate/library.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7462,6 +7462,9 @@ def getGBKannotation(input, Database):
membrane = {}
buscos = {}
secmet = {}
hybridlist = []
pkslist = []
nrpslist = []
with open(input, 'r') as infile:
for record in SeqIO.parse(infile, 'genbank'):
for f in record.features:
Expand All @@ -7470,13 +7473,6 @@ def getGBKannotation(input, Database):
locusTag, ID, Parent = getID(f, f.type)
if not ID:
continue
product = f.qualifiers['product'][0]
if product == "Hybrid PKS-NRPS":
SMs['Hybrid'] += 1
if product == "Nonribosomal Peptide Synthase (NRPS)":
SMs['NRPS'] += 1
if 'Polyketide synthase (PKS)' in product:
SMs['PKS'] += 1
for k, v in list(f.qualifiers.items()):
if k == 'db_xref':
for i in v:
Expand Down Expand Up @@ -7540,10 +7536,28 @@ def getGBKannotation(input, Database):
membrane[hit].append(ID)
elif i.startswith('antiSMASH:'):
hit = i.replace('antiSMASH:', '')
product = f.qualifiers['product'][0]
if product == "Hybrid PKS-NRPS" or product == "putative Hybrid PKS-NRPS biosynthetic cluster":
hybridlist.append(hit)
if product == "Nonribosomal Peptide Synthase (NRPS)" or product == "NRPS" or product == "putative NRPS-like protein biosynthetic cluster":
nrpslist.append(hit)
if 'Polyketide synthase (PKS)' in product or 'polyketide synthase' in product or product == 'Type I Modular PKS' or product == 'Type I Iterative PKS':
pkslist.append(hit)
if not hit in secmet:
secmet[hit] = [ID]
else:
secmet[hit].append(ID)
for pks_hit in set(pkslist):
if not pks_hit in hybridlist:
if not pks_hit in nrpslist:
SMs['PKS'] += 1
else:
hybridlist.append(pks_hit)
for nrps_hit in set(nrpslist):
if not nrps_hit in hybridlist:
SMs['NRPS'] += 1
for hybrid_hit in set(hybridlist):
SMs['Hybrid'] += 1
return [pfams, iprs, nogs, buscos, merops, cazys, cogs, secreted, membrane, secmet, SMs]


Expand Down