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astool

🧰 Here are some scripts for processing BGC related files, such as JSON, GBK, etc.

Scripts

1. astool

1.1 ex_smiles

  • Extract SMILES of NPRs/PKs products from the antiSMASH json result file and output a table in tsv format cantaining "locus, region, smiles" information.
astool ex_smiles -i <json_dir> -o smiles.tsv -t antismash

<json_dir> could be a directory of a json file, or an txt file containing one json file directory per line.

smiles.tsv:

file_path record_id region_id smiles
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000126 1 NC([*])C(=O)O
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000020 1 CC(O)CC(=O)NC(CC(=O)N)C(=O)CC(O)NC(CC(=O)N)C(=O)NC(CCC(=O)O)C(=O)CC(O)C(=O)O
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000021 1 NC([])C(=O)NC([])C(=O)NC([*])C(=O)O
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000023 2 NC(CS)C(=O)CC(O)NC(CS)C(=O)O
  • Extract SMILES from the MIBiG json file.
astool ex_smiles -i <json_dir> -o smiles.tsv -t mibig

1.2 cds_len

  • Count the length of cds sequences in gbk files
astool cds_len -i gbk.list -o output.tsv

output.tsv:

record_id locus_tag length
NZ_CP030840.1 ACPOL_RS15070 147
NZ_CP030840.1 ACPOL_RS15075 329
NZ_CP030840.1 ACPOL_RS15080 80

1.3 cdsfromgbk2fasta

  • Save CDS sequences in gbk files in fasta format.
astool cdsfromgbk2fasta -i gbk_file -o fasta_file

2. extractHTML

2.1 ex_antismash_bgc.py

python3 ex_antismash_bgc.py antismash_results antismash_results.xlsx
# The <antismash_results> folder stores the result folders of the antismash analysis

3. extractJson

3.1 ex_polymer_from_json.py

Applicable: antiSMASH ?MIBiG

Usage:

ex_polymer_from_json.py json.list output.tsv

Output TSV:

json_file record_id region_number region_type cc_number cc_type polymer
GCA0000.json NC_0129.1 1 NRPS+T1PKS 1 NRPS (ile) + (ohmal) + (val - val)
GCA0000.json NC_0129.1 1 NRPS+T1PKS 2 NRPS+T1PKS (ile) + (ohmal) + (val - val)

If the json files fail to be processed, these files are saved in a log file.

3.2 ex_knownclusterblast_from_json.py

Applicable: antiSMASH MIBiG

Usage:

ex_knownclusterblast_from_json.py json_dir_list.txt knownclusterblast_hits_number_output.tsv knownclusterblast_hits_detail_output.tsv

knownclusterblast_hits_number_output.tsv:

file_name record_id region_number total_hits
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 1 0
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 2 0
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 3 0
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 4 15
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 5 3

knownclusterblast_hits_detail_output.tsv:

file_name record_id region_number MIBiG_accession MIBiG_description MIBiG_cluster_type blast_score MIBiG_similarity_precise_proportion MIBiG_similarity_rough_proportion
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 4 BGC0000460 vulnibactin NRP 1854 12.5 12
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 4 BGC0000451 turnerbactin NRP 1199 23.0769231 23
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 4 BGC0000294 acinetobactin NRP 1261 13.0434783 13
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 4 BGC0001502 amonabactin P 750 NRP 1245 42.8571429 42
GCF_000196475.1_ASM19647v1_genomic.json NC_012962.1 4 BGC0000368 streptobactin NRP 942 17.6470588 17

3.3 ex_smiles_from_json.py

Applicable: antiSMASH

Usage:

ex_smiles_from_json.py json.dir.list smiles.tsv

smiles.tsv:

file_path record_id region_id smiles
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000126 1 NC([*])C(=O)O
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000020 1 CC(O)CC(=O)NC(CC(=O)N)C(=O)CC(O)NC(CC(=O)N)C(=O)NC(CCC(=O)O)C(=O)CC(O)C(=O)O
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000021 1 NC([])C(=O)NC([])C(=O)NC([*])C(=O)O
antiSMASH/GCF_002968995.1_ASM296899v1_genomic NZ_PUWT01000023 2 NC(CS)C(=O)CC(O)NC(CS)C(=O)O

4. extractGBK

4.1 ex_region_info_from_gbk.py

Applicable: antiSMASH ?MIBiG

Usage:

ex_region_info_from_gbk.py gbk.list output.tsv

output.tsv:

file_dir file_name bgc_type bgc_length
antiSMASH/GCA_000003645.1_ASM364v1_genomic/CM000714.1.region001.gbk CM000714.1.region001.gbk LAP+RiPP-like 23507
antiSMASH/GCA_000003645.1_ASM364v1_genomic/CM000714.1.region002.gbk CM000714.1.region002.gbk NRPS 47158

4.2 ex_ripp_from_gbk.py

Applicable: antiSMASH ?MIBiG

Usage:

ex_ripp_from_gbk.py gbk.list output.tsv

output.tsv:

gbk_file gbk_name leader_seq core_seq
antiSMASH/GCA_000147815.3_ASM14781v3_genomic/CP002994.1.region002.gbk CP002994.1.region002.gbk MSMNPEAATTQVDVDFTLDVRVIEAGLPVR DLLRDTSDNCGSSCSGTACTSFVGDPA
antiSMASH/GCA_000147815.3_ASM14781v3_genomic/CP002994.1.region037.gbk CP002994.1.region037.gbk MSTEAKNWKEAESTTSPAG AGFGELSLAELREDQSAHAPLSSGWVCTLTTECGC
antiSMASH/GCA_000147815.3_ASM14781v3_genomic/CP002994.1.region037.gbk CP002994.1.region037.gbk VRELPRGCRADCGHVLQPTVRGG DQGCYRAATC

4.3 ex_completeness_from_gbk.py

Applicable: antiSMASH MIBiG

Usage:

ex_completeness_from_gbk.py gbk.list output.tsv

output.tsv:

gbk_name region_completeness
NC_012962.1.region004.gbk FALSE
NC_012962.1.region008.gbk FALSE

4.4 stats_domain_in_nrps_pks.py

Applicable: antiSMASH MIBiG

Usage:

stats_domain_in_nrps_pks.py gbk.list output.tsv

output.tsv:

gbk_name ACP ACPS AMP-binding Aminotran_1_2 Aminotran_3 Aminotran_4 Aminotran_5
AE009951.2.region001.gbk 1 1
CP002994.1.region001.gbk 1
CP002994.1.region003.gbk 1
CP002994.1.region004.gbk 1

The number of columns in the TSV file depends on the number of Domain types.

4.5 ex_a_domain_from_gbk.py

Applicable: antiSMASH

Usage:

ex_a_domain_from_gbk.py gbk.list output.faa

output.faa:

>nrpspksdomains_ctg1_871_AMP-binding.1 consensus: thrfromfile: NC_012962.1.region004
KSAIICGERQIAYSELGEYVQKIVNNLHRCGMHKGSVVAICLPRSPEHVMVTIACALLGI
IWVPIDVNSPSERLEYLLTNCHPDLIVNTGELNSDKAITLETLLTSVSENALFSLETLSS
LSHSIDPAYYLYTSGTTGKPKCVVLNNKATSNVIEQTMNKWEVKQDDVFISVTPLHHDMS
VFDLFASLTIGATLVIPEPHEEKDAIHWNRLVSKHKVSIWCSVPAILEMLIACQKGSSLS
SLRLIAQGGDYIKPMVIKEIRTTYPDIRLFSLGGPTETTIWSIWHEITSEDVSLIPYGKP
LPATQYFICNDSHEHCPAFVTGRIYTTGVNLALGYLEGGIVVQKDFVTITTPKGEQLRAF
RTGDQGYYRKDGTIIFASRVNGYVKIR
>nrpspksdomains_ctg1_881_AMP-binding.1 consensus: dhbfromfile: NC_012962.1.region004
DNGKIALICGERQFSYAELNLLVDSLAAALQQRGVKRGQTALVQLGNEAEFYIVFFALLR
LGVVPINAVFSHQRSELCAYADQINPALLIADRNHSLFSDDDFIDELRIRIPSLCHVVLR
GDNDSILDVETLLAQGAGDFVANPTPADEVAFFQLSGGSTGTPKLIPRTHNDYYYSIRAS
AEICQFNAETRYLCALPAAHNFPMSSPGALGAFYCGGQVILAHNPGADCCFPLIQQHRVN
AVALVPPAVSVWLEAIALGGNCDALKSLRLLQVGGARLSESLARRIPKEMGCQLQQVFGM
AEGLVNYTRLDDDEQHIFMTQGRPISPDDEVWVADNDGNPVPHGIAGRLMTQGPYTFRGY
YRSPQHNQQCFDSNGFYCSGDLVIMTPDGYLQVVGREKDQINR

4.6 ex_asdomain_number_from_gbk.py

Applicable: antiSMASH MIBiG

Usage:

ex_asdomain_number_from_gbk.py gbk.list output.tsv

output.tsv:

filename bgc_type bgc_length number_domain smiles
CP029716.1.region002.gbk bacteriocin 11139 0
CP029716.1.region003.gbk thiopeptide 26303 1
CP029716.1.region001.gbk siderophore 14429 0
CP029716.1.region004.gbk NRPS 52094 9 NC(CO)C(=O)O
CP029716.1.region005.gbk bacteriocin 10624 0
CP029716.1.region006.gbk arylpolyene 43591 8
AE009951.2.region001.gbk NRPS-like 42499 3 NC([*])C(=O)O

4.7 ex_nrps_monomers_from_gbk.py

Applicable: antiSMASH ?MIBiG

Usage:

ex_nrps_monomers_from_gbk.py gbk.list output.tsv

output.tsv:

file_name locus_tag monomers count
NZ_CP030840.1.region004 ACPOL_RS11395 X 1
CP002994.1.region032 ctg1_5994 pk 1
CP002994.1.region032 ctg1_5995 mal 1
CP002994.1.region032 ctg1_6003 X 1

4.8 ex_gene_info_from_an_antismash_output_folder.py

Applicable: antiSMASH

Usage:

ex_gene_info_from_an_antismash_output_folder.py GCA_000007325.1_ASM732v1_genomic GCA_000007325.1_ASM732v1_genomic.tsv

output.tsv:

genome_id contig_id gene_id location gene_function AA_seq gene_id pfam_hits
GCA_000007325.1 AE009951.2 ctg1_1385 753:2553(+) MNLDGLNKQREKYQIEGNILKEIEILKEILVETEKEYGSESDEYIKALNELGGTLKYVGYYDEAENNLKKSLEFIKKKYGDNNLAYATSLLNLTEVYRFAQKFNLLEENYKKIVKIYQDNSADNSFSYAGLCNNFGLYYQNIGDMKSAYDLHLKSLDILKHYDSEEYLLEYAVTLSNLFNPSYQLGMKEKAVEYLNKAIDIFEKNVGIEHPLYSASLNNMAIYYYNERELNKAIEFFERAAEISKKTMGVDSDNYKNILSNIDFIKKEVVKSGDNIKVQDTKKDNIINSSDLKNIKGLELSKRYFYDIVLPEFEKSLENILPLCAFGLVGEGSECYGYDDELSQDHDFGPSVCIWLRKDDYLKYKDRINKVLKNLPKTYLGFRELKESEWGYNRRGLLNIEDFYFKFIGSANPPQTINDWQKIPETALATVTNGEIFLDNLGEFTKIREQLLNYYPEVIRQNKIATRLMNISQHGQYNYVRCLRRNDLVSANQCLYLFVDEVIHLVFLLNKRYKIFYKWANRALLNLKILGNEIHKLLQDMVFTQNKIPYVKKICKVLADELRNQKLTDCESEFLGDLGVDIQKNIDDEFFKNYSPWLD
GCA_000007325.1 AE009951.2 ctg1_1386 2569:3184(+) MEKEKLIEEILEKEWSYFSKLNNIGGRADCQDNREDFIIMRKSQWETFNEETLISYLDDLNSKNNPLFQKYGQMMKYNSPQEYEKIKDILENPNKNKITLVEKIMSIYIEWEEEFFKKYPIFSSMGRPLYSTEDDNIETSIETYLRGELLSYSEKTLELYLKYIIEMKEKNINLAIKNMDNLASMQGFKNSDEVEEYYKNLQKN
GCA_000007325.1 AE009951.2 ctg1_1387 3279:4413(+) biosynthetic-additional (smcogs) SMCOG1109:8-amino-7-oxononanoate synthase (Score: 358.6; E-value: 6.6e-109) MQKEKIIQELQELKNDNRFRTVKTNDKSLYNFSSNDYLSLAHDKDLLQKFYQNYNFDNYKLSSSSSRLIDGSYLTVMRLEKKVEEIYGKPCLVFNSGFDANSSVIETFFDKKSLIITDRLNHASIYEGCINSRAKILRYKHLDVSALEKLLKKYSENYNDILVVTETVYSMDGDCAEIKQICDLKEKYNFNLMVDEAHSYGAYGYGIAYNEKLVNKIDFLVIPLGKAGASVGAYVICDEIYKNYLINKSKKFIYSTALPPVNNLWNLFVLENLVNFQDRIEKFQELVTFSLNTLKKLNLKTKSTSHIISIIIGDNLNAVNLSNNLKELGYLAYAIKEPTVPKDTARLRISLTADMKKEDIETFFKTLKAEMKKIGVI
GCA_000007325.1 AE009951.2 ctg1_1388 4413:5004(+) MSKIYFFNGWGMDKNLLIPIKNSTDYDIEVINFPYDIDKDFIDKDDSFIGYSFGVYYLNKFLSENKDLKYKKAIGINGLPQTIGKFGINEKMFNITLDTLNEENLEKFLINMDIDDSFCKSNKSFDEIKNELQFFKNNYRIIDNHIDFYYIGKNDRIIPANRLEKYCQNHSLAYKLLECGHYPFSYFKDFKDILDI

4.9 ex_CDS_from_region_gbk.py

Extract CDS feature in region GBK file. There are 3 output files for one region GBK file, cds.faa, cds.fna, cds.tsv. If the antiSMASH results are extracted in batch, three subfolders will be generated first, fna, faa, tsv, and then the results of each region GBK file extraction will be saved in the corresponding subfolders.

Usage:

# 查看帮助
python3 ex_CDS_from_region_gbk.py -h

# example1：提取单个 region GBK 文件
python ex_CDS_from_region_gbk.py -i GG657748.1.region001.gbk -o CDS

# example1：批量提取 antiSMASH 结果中的 region GBK 文件
python ex_CDS_from_region_gbk.py -i antismash_result_folder.list -o CDS

4.10 ex_candidate_cluster_from_region_gbk.py

Usage:

# 查看帮助
python3 ex_candidate_cluster_from_region_gbk.py -h

# example1: 
python ex_candidate_cluster_from_region_gbk.py -i Genome000001.region001.gbk -n 1 -o cc.fna

4.11 ex_CDS_number_from_region_gbk.py

Usage:

python3 ex_CDS_number_from_region_gbk.py -l gbk.list -o cds_number.tsv

5. Others

5.1 collect_gbk_file.py

Collect target gbk files from antiSMASH result folders.

collect_gbk_file.py smiles.tsv target_folder

smiles.tsv: output from astool ex_smiles -i <json_dir> -o smiles.tsv -t antismash.

target_folder: find the target gbk files and copy to the target folder.

5.2 download_antismash_db.py

download antiSMASH database

download_antismash_db.py tsv_file target_path

tsv_file: downloaded form antiSMASH database Statistic page.

target_path: the path where the downloaded file is saved.

5.3 table2fasta.py

Convert sequences stored in tsv or excel files to fasta format.

# help
table2fasta.py -h

# tsv2fasta
table2fasta.py -i input.tsv -n seq_id -s seq -t tsv -o output.fasta

# excel2fasta
table2fasta.py -i input.xlsx -n seq_id -s seq -t excel -o output.fasta

5.4 concat_tsv.py

Combine all tsv files in a folder into one file.

concat_tsv.py tsv tsv/antismash.cds.len.tsv

5.5 as2bs.py

Convert antiSMASH-BGC-Types to BiGSPACE-BGC-Types

Support file format: xlsx, tsv

as2bs.py -i antiSMASH-BGC-Type.xlsx -o bigscape-BGC-Type.xlsx
# Here, antiSMASH-BGC-Type.xlsx is the output from ex_antismash_bgc.py

Convert for one column:

as2bs.py -i antiSMASH-BGC-Type.tsv -c antiSMASH-BGC -o bigscape-BGC-Type.tsv

6. shell

6.1 hoge

Copy and rename files based on map.

Usage:

# help
hoge -h

# usage
hoge map.tsv

map.tsv:

wlabkit/astool/test_data/antiSMASH/GCA_003204095.1_ASM320409v1_genomic/CP029716.1.region002.gbk seq1.gbk
wlabkit/astool/test_data/antiSMASH/GCA_003204095.1_ASM320409v1_genomic/CP029716.1.region003.gbk seq2.gbk
wlabkit/astool/test_data/antiSMASH/GCA_003204095.1_ASM320409v1_genomic/CP029716.1.region001.gbk seq3.gbk

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Scripts for antiSMASH/MiBIG data extraction and manipulation

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