astool

KO | EN

gitlite — search

#python #hacktoberfest #llm #linux #macos #java #awesome #kubernetes #awesome-list #vue #security #ios #mcp #openai

(★ 13)

Scripts for antiSMASH/MiBIG data extraction and manipulation

astool 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# 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.

```shell
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.

```shell
astool ex_smiles -i <json_dir> -o smiles.tsv -t mibig
```

### 1.2 cds_len

- Count the length of cds sequences in gbk files

```bash
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.

```shell
astool cdsfromgbk2fasta -i gbk_file -o fasta_file
```

## 2. extractHTML

### 2.1 ex_antismash_bgc.py

```bash
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:

```bash
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:

```bash
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:

```bash
ex_smiles_from_json.py json.dir.list smiles.tsv
```

smiles.tsv:

## 4. extractGBK

### 4.1 ex_region_info_from_gbk.py

Applicable: `antiSMASH` `?MIBiG`

Usage:

```bash
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:

```bash
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:

```bash
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:

```bash
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:

```bash
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:

```bash
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:

```bash
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:

```bash
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:

```bash
# 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:

```bash
# 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:

```bash
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.

```shell
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

```shell
download_antismash_db.py tsv_file target_path
```

`tsv_file`: downloaded form [antiSMASH database Statistic page](https://antismash-db.secondarymetabolites.org/stats.html).

`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.

```bash
# 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.

```bash
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

```bash
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:

```bash
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:

```bash
# 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 |

astool

astool 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

astool

astool 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README