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Merge pull request #268 from nf-core/dev
Release - v1.1.0 - British Beans on Toast
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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/env python3 | ||
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| ######################################### | ||
| # Authors: [Anan Ibrahim](https://github.com/brianjohnhaas), [Louisa Perelo](https://github.com/louperelo) | ||
| # File: amp_database.py | ||
| # Source: https://github.com/Darcy220606/AMPcombi/blob/main/ampcombi/amp_database.py | ||
| # Source+commit: https://github.com/Darcy220606/AMPcombi/commit/a75bc00c32ecf873a133b18cf01f172ad9cf0d2d/ampcombi/amp_database.py | ||
| # Download Date: 2023-03-08, commit: a75bc00c | ||
| # This source code is licensed under the MIT license | ||
| ######################################### | ||
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| # TITLE: Download the DRAMP database if input db empty AND and make database compatible for diamond | ||
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| import pandas as pd | ||
| import requests | ||
| import os | ||
| from datetime import datetime | ||
| import subprocess | ||
| from Bio import SeqIO | ||
| import tempfile | ||
| import shutil | ||
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| ######################################## | ||
| # FUNCTION: DOWNLOAD DRAMP DATABASE AND CLEAN IT | ||
| ######################################### | ||
| def download_DRAMP(db): | ||
| ##Download the (table) file and store it in a results directory | ||
| url = "http://dramp.cpu-bioinfor.org/downloads/download.php?filename=download_data/DRAMP3.0_new/general_amps.xlsx" | ||
| r = requests.get(url, allow_redirects=True) | ||
| with open(db + "/" + "general_amps.xlsx", "wb") as f: | ||
| f.write(r.content) | ||
| ##Convert excel to tab sep file and write it to a file in the DRAMP_db directly with the date its downloaded | ||
| date = datetime.now().strftime("%Y_%m_%d") | ||
| ref_amps = pd.read_excel(db + "/" + r"general_amps.xlsx") | ||
| ref_amps.to_csv(db + "/" + f"general_amps_{date}.tsv", index=None, header=True, sep="\t") | ||
| ##Download the (fasta) file and store it in a results directory | ||
| urlfasta = ( | ||
| "http://dramp.cpu-bioinfor.org/downloads/download.php?filename=download_data/DRAMP3.0_new/general_amps.fasta" | ||
| ) | ||
| z = requests.get(urlfasta) | ||
| fasta_path = os.path.join(db + "/" + f"general_amps_{date}.fasta") | ||
| with open(fasta_path, "wb") as f: | ||
| f.write(z.content) | ||
| ##Cleaning step to remove ambigous aminoacids from sequences in the database (e.g. zeros and brackets) | ||
| new_fasta = db + "/" + f"general_amps_{date}_clean.fasta" | ||
| seq_record = SeqIO.parse(open(fasta_path), "fasta") | ||
| with open(new_fasta, "w") as f: | ||
| for record in seq_record: | ||
| id, sequence = record.id, str(record.seq) | ||
| letters = [ | ||
| "A", | ||
| "C", | ||
| "D", | ||
| "E", | ||
| "F", | ||
| "G", | ||
| "H", | ||
| "I", | ||
| "K", | ||
| "L", | ||
| "M", | ||
| "N", | ||
| "P", | ||
| "Q", | ||
| "R", | ||
| "S", | ||
| "T", | ||
| "V", | ||
| "W", | ||
| "Y", | ||
| ] | ||
| new = "".join(i for i in sequence if i in letters) | ||
| f.write(">" + id + "\n" + new + "\n") | ||
| return os.remove(fasta_path), os.remove(db + "/" + r"general_amps.xlsx") | ||
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| download_DRAMP("amp_ref_database") |
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