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2.5 years ago
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Hello everyone,
I used this program called antismash to predict the secondary metabolite clusters in my genome of interest. The output I got is gene bank like format whish is shown below:
LOCUS scaffold_10 47160 bp DNA linear UNK 01-JAN-1980
DEFINITION scaffold_10.
ACCESSION scaffold_10
VERSION scaffold_10
KEYWORDS .
SOURCE
ORGANISM
.
COMMENT ##antiSMASH-Data-START##
Version :: 6.0.1-25e43a7(changed)
Run date :: 2021-11-05 17:39:45
NOTE: This is a single cluster extracted from a larger record!
Orig. start :: 2049841
Orig. end :: 2097001
##antiSMASH-Data-END##
FEATURES Location/Qualifiers
protocluster 1..47160
/aStool="rule-based-clusters"
/contig_edge="False"
/core_location="join{[2069841:2070128](+),
[2070175:2070449](+), [2070507:2071973](+),
[2072023:2074178](+), [2074232:2074784](+),
[2074838:2077001](+)}"
/cutoff="20000"
/detection_rule="cds(PKS_AT and (PKS_KS or ene_KS or mod_KS
or hyb_KS or itr_KS or tra_KS))"
/neighbourhood="20000"
/product="T1PKS"
/protocluster_number="1"
/tool="antismash"
proto_core join(20001..20287,20335..20608,20667..22132,22183..24337,
24392..24943,24998..27160)
/aStool="rule-based-clusters"
/tool="antismash"
/cutoff="20000"
/detection_rule="cds(PKS_AT and (PKS_KS or ene_KS or mod_KS
or hyb_KS or itr_KS or tra_KS))"
/neighbourhood="20000"
/product="T1PKS"
/protocluster_number="1"
cand_cluster 1..47160
/SMILES="CC(=O)C(=O)O"
/candidate_cluster_number="1"
/contig_edge="False"
/detection_rules="cds(PKS_AT and (PKS_KS or ene_KS or
mod_KS or hyb_KS or itr_KS or tra_KS))"
/kind="single"
/product="T1PKS"
/protoclusters="1"
/tool="antismash"
region 1..47160
/candidate_cluster_numbers="1"
/contig_edge="False"
/product="T1PKS"
/region_number="1"
/rules="cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or
hyb_KS or itr_KS or tra_KS))"
/tool="antismash"
CDS 1899..2720
/ID="CDS_13110"
/NRPS_PKS="Domain: PKS_KR (26-149). E-value: 7.6e-08.
Score: 24.2. Matches aSDomain:
nrpspksdomains_jgi.p_FusspF11_1_766668_PKS_KR.1"
/NRPS_PKS="type: other"
/gene="jgi.p_FusspF11_1_766668"
/gene_functions="biosynthetic-additional (smcogs)
SMCOG1001:short-chain dehydrogenase/reductase SDR (Score:
161.6; E-value: 3.9e-49)"
/gene_kind="biosynthetic-additional"
/phase="0"
/source="prediction"
/transl_table=1
/translation="MTPPPKSALESDPAVGAQRRFSVTGNAVVTGGAGVLGLHACDALL
EHGLEGLMILDVNPAQSQGQITSLQNKFPRAKIMALKVDVTDENVVNAAMEETARVLGS
IDTLICFVGVVGCVETLDMPVPQWRKILDINTTGSFICAQAAARQMVKRGRGGSIVFVA
SISAHRVNYPQPQAAYNVSKSALLMLKSCLAAEWARYGIRTNSISPGYMDTILNEGDGI
AEHRKIWAEHNPSGRMGAPSELTGTVVLLASSAGSYINGADIVVDGGGIVL"
aSDomain 1977..2345
/aSDomain="PKS_KR"
/aSTool="nrps_pks_domains"
/database="nrpspksdomains.hmm"
/detection="hmmscan"
/domain_id="nrpspksdomains_jgi.p_FusspF11_1_766668_PKS_KR.1
"
/evalue="7.60E-08"
/label="jgi.p_FusspF11_1_766668_PKS_KR.1"
/locus_tag="jgi.p_FusspF11_1_766668"
/protein_end="149"
/protein_start="26"
/score="24.2"
/specificity="KR activity: inactive"
/specificity="KR stereochemistry: C1"
/tool="antismash"
/translation="AVVTGGAGVLGLHACDALLEHGLEGLMILDVNPAQSQGQITSLQN
KFPRAKIMALKVDVTDENVVNAAMEETARVLGSIDTLICFVGVVGCVETLDMPVPQWRK
ILDINTTGSFICAQAAARQ"
aSModule 1977..2345
/domains="nrpspksdomains_jgi.p_FusspF11_1_766668_PKS_KR.1"
/incomplete
/locus_tags="jgi.p_FusspF11_1_766668"
/tool="antismash"
/type="pks"
CDS_motif 1980..2042
/aSTool="nrps_pks_domains"
/database="abmotifs"
/detection="hmmscan"
/domain_id="nrpspksmotif_jgi.p_FusspF11_1_766668_0001"
/evalue="1.90E-05"
/label="PKSI-KR_m1"
/locus_tag="jgi.p_FusspF11_1_766668"
/protein_end="48"
/protein_start="27"
/score="17.3"
/tool="antismash"
/translation="VVTGGAGVLGLHACDALLEHG"
CDS join(3252..3263,3321..3443,3493..4428)
/ID="CDS_13111"
/NRPS_PKS="Domain: PKS_ER (28-277). E-value: 6.4e-13.
Score: 40.2. Matches aSDomain:
nrpspksdomains_jgi.p_FusspF11_1_794272_PKS_ER.1"
/NRPS_PKS="type: other"
/gene="jgi.p_FusspF11_1_794272"
/gene_functions="biosynthetic-additional (smcogs)
SMCOG1040:alcohol dehydrogenase (Score: 275.7; E-value:
7.6e-84)"
/gene_kind="biosynthetic-additional"
/phase="0"
/source="prediction"
/transl_table=1
/translation="MSQTNLSCVLYGPGKARFENRPVPSLKDAHDVIIRISYVGVCGSD
VHFWTDGGFARKVSEDQPLVMGHEASGIVRSIGPDVTLLKPGDRVAIEPGFSCRRCKQC
KDGRYNLCPKMKFAADPPLTQGTLSRFFSIPEDFAYKIPDSLSLEEAVLVEPLAVAVHG
IRLAGLEVGQRVLVQGSGTIGLLTAAVAKAYGAKQVYITDVNLDKIKFAKKYLECSAFI
PDLGSTPEENAARFKTETGLDDGVDAVIECTGVEASTQTGLLALSAGGVLVQVGLGKPV
QAIPIHAMSEKEIVLKTSFRYGPGDYEIALELLESGKVSVRPLISSITPFEKATEAWEK
TRKGKGIKNLIRGVQD"
and so on......
Now from this file I want to extract protein sequence of the CDS having PKS domain ( could be PKS_ER, PKS_KS or PKS_anything). In the output file I want to include LOCUS Id and CDS ID and location. I have never used python but I found a similar issue in Biostar using python and have made few lines of codes based on that. Please help me
from Bio import SeqIO
from Bio.SeqFeature import SeqFeature
gbk = "myfile_predicted_SMclusters.gbk"
fa = "myfile_PKS_protein.fa"
input_handle = open(gbk, "r")
output_handle = open(fa, "w")
for record in SeqIO.parse(input_handle, "genbank"):
features = [feature for feature in record.features if feature.type == "CDS"]
for feature in features:
if feature.qualifiers["NRPS_PKS"][1] == "PKS":
assert len(seq_feature.qualifiers['translation'])==1
output_handle.write(">%s %s\n%s\n" % (
record.description,
feature.location,
SeqFeature(feature.location).extract(record.seq)))
output_handle.close()
input_handle.close()
The error is as follows:
if feature.qualifiers["NRPS_PKS"][1] == "PKS":
KeyError: 'NRPS_PKS'
Please help!!!
Thanks
