Add ampcombi 2.0.1

CHANGELOG.md

@@ -7,10 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#427](https://github.com/nf-core/funcscan/pull/427) Updated AMPcombi from v0.2.2 to v2.0.1. AMP now can use multiple other databases for classifications. (by @darcy220606)
+
 ### `Fixed`
 
+- [#427](https://github.com/nf-core/funcscan/pull/427) Fixed the AMP reference database issues reported by users, due to non-ASCII characters. (by @darcy220606)
+
 ### `Dependencies`
 
+| Tool     | Previous version | New version |
+| -------- | ---------------- | ----------- |
+| AMPcombi | 0.2.2            | 2.0.1       |
+
 ### `Deprecated`
 
 ## v2.0.0 - [2024-09-05]

bin/ampcombi_download.py

@@ -1,78 +1,144 @@
 #!/usr/bin/env python3
 
 #########################################
-# Authors: [Anan Ibrahim](https://github.com/brianjohnhaas), [Louisa Perelo](https://github.com/louperelo)
+# Authors: [Anan Ibrahim](https://github.com/Darcy220606/AMPcombi), [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
 #########################################
 
-# TITLE: Download the DRAMP database if input db empty AND and make database compatible for diamond
+# TITLE: Download the reference database specified by the user.
 
 import pandas as pd
 import requests
 import os
-from datetime import datetime
+import re
 import subprocess
-from Bio import SeqIO
-import tempfile
-import shutil
+import argparse
 
+from datetime import datetime
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio import SeqIO
 
 ########################################
-#  FUNCTION: DOWNLOAD DRAMP DATABASE AND CLEAN IT
+#  FUNCTION: DOWNLOAD DATABASES AND CLEAN DRAMP and APD
 #########################################
-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")
+def download_ref_db(database, threads):
+    """
+    Downloads a specified AMP (antimicrobial peptide) reference database based on the
+    provided database name and saves it to the specified directory.
+    This supports downloading databases only from DRAMP, APD, and UniRef100.
+    Parameters:
+    ----------
+    db : str
+        The directory path where the downloaded database should be saved.
+    database : str
+        The name of the database to download. Must be one of 'DRAMP', 'APD', or 'UniRef100'.
+    threads : int
+        Number of threads to use when downloading the UniRef100 database with `mmseqs`.
+    """
+    # Check which database was given
+    if database == 'DRAMP':
+        # Create dir
+        db = 'amp_DRAMP_database'
+        os.makedirs(db, exist_ok=True)
+        # Download the file
+        try:
+            url = 'http://dramp.cpu-bioinfor.org/downloads/download.php?filename=download_data/DRAMP3.0_new/general_amps.txt'
+            response = requests.get(url, allow_redirects=True)
+            response.raise_for_status()  # Check for any download errors
+            date = datetime.now().strftime("%Y_%m_%d")
+            with open(db + '/' + f'general_amps_{date}.txt', 'wb') as file:
+                file.write(response.content)
+            print(f"File downloaded successfully and saved to {db}/general_amps_{date}.txt")
+            # Create fasta version and clean it
+            db_df = pd.read_csv(f'{db}/general_amps_{date}.txt', sep='\t')
+            records = []
+            valid_sequence_pattern = re.compile("^[ACDEFGHIKLMNPQRSTVWY]+$")
+            for index, row in db_df.iterrows():
+                sequence = row['Sequence']
+                if valid_sequence_pattern.match(sequence):
+                    record = SeqRecord(Seq(sequence), id=str(row['DRAMP_ID']), description="")
+                    records.append(record)
+            output_file = f'{db}/general_amps_{date}.fasta'
+            SeqIO.write(records, output_file, "fasta")
+        except requests.exceptions.RequestException as e:
+            print(f"Failed to download DRAMP AMP general database file: {e}")
+            return
+
+    if database == 'APD':
+        # Create dir
+        db = 'amp_APD_database'
+        os.makedirs(db, exist_ok=True)
+        # Download the file
+        try:
+            url = 'https://aps.unmc.edu/assets/sequences/APD_sequence_release_09142020.fasta'
+            response = requests.get(url, allow_redirects=True, verify=False)  # Disable SSL verification due to site certificate issue
+            response.raise_for_status()
+            content = response.text
+            print("APD AMP database downloaded successfully.")
+        except requests.exceptions.RequestException as e:
+            print(f"Failed to download content: {e}")
+            return
+        # Save the content line-by-line exactly as is
+        try:
+            with open(db + '/' + 'APD_orig.fasta', 'w') as file:
+                file.write(content)
+            with open(f'{db}/APD.fasta', 'w') as output_handle:
+                valid_sequence_pattern = re.compile("^[ACDEFGHIKLMNPQRSTVWY]+$")
+                for record in SeqIO.parse(f'{db}/APD_orig.fasta', "fasta"):
+                    sequence = str(record.seq)
+                    if valid_sequence_pattern.match(sequence):
+                        SeqIO.write(record, output_handle, "fasta")
+            os.remove(db + '/' + 'APD_orig.fasta')
+            print(f"APD AMP database saved successfully to {db}/APD.fasta")
+            # Fasta to table
+            headers = []
+            sequences = []
+            seq_ids = []
+            for i, record in enumerate(SeqIO.parse(f'{db}/APD.fasta', "fasta")):
+                sequence_id = record.description.split('|')[0]
+                headers.append(record.description)
+                sequences.append(str(record.seq))
+                seq_ids.append(sequence_id)
+            db_df = pd.DataFrame({
+                "APD_ID": seq_ids,
+                "APD_Description": headers,
+                "APD_Sequence": sequences})
+            db_df.to_csv(f'{db}/APD.txt', sep='\t', index=False, header=True)
+            os.remove(db + '/' + 'APD.fasta')
+            # Table to fasta
+            records = []
+            for index, row in db_df.iterrows():
+                sequence = row['APD_Sequence']
+                record = SeqRecord(Seq(sequence), id=str(row['APD_ID']), description="")
+                records.append(record)
+            output_file = f'{db}/APD.fasta'
+            SeqIO.write(records, output_file, "fasta")
+        except Exception as e:
+            print(f"Failed to save APD AMP database: {e}")
+
+    if database == 'UniRef100':
+        # Create dir
+        db = 'amp_UniRef100_database'
+        os.makedirs(db, exist_ok=True)
+        # Download the file
+        try:
+            os.makedirs(f'{db}/mmseqs2', exist_ok=True)
+            command = f"mmseqs databases UniRef100 {db}/mmseqs2/ref_DB {db}/mmseqs2/tmp --remove-tmp-files true --threads {threads} -v 0"
+            subprocess.run(command, shell=True, check=True)
+            print(f"UniRef100 protein database downloaded successfully and saved to {db}/mmseqs2/UniRef100")
+        except subprocess.CalledProcessError as e:
+            print(f"Failed to download UniRef100 protein database: {e}")
 
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Downloads a specified AMP (antimicrobial peptide) reference database based on the provided database name and saves it to the specified directory.")
+    parser.add_argument("--database_id", dest="database", type=str, required=True, choices=["DRAMP", "APD", "UniRef100"],
+                        help="Database ID - one of DRAMP, APD, or UniRef100. This parameter is required.")
+    parser.add_argument("--threads", type=int, default=4,
+                        help="Number of threads supplied to mmseqs databases. Only relevant in the case of 'UniRef100'. Default is 4.")
 
-download_DRAMP("amp_ref_database")
+    args = parser.parse_args()
+    download_ref_db(args.database, args.threads)

conf/modules.config

@@ -674,9 +674,9 @@ process {
         ]
     }
 
-    withName: DRAMP_DOWNLOAD {
+    withName: AMP_DATABASE_DOWNLOAD {
         publishDir = [
-            path: { "${params.outdir}/databases/dramp" },
+            path: { "${params.outdir}/databases/${params.amp_ampcombi_db}" },
             mode: params.publish_dir_mode,
             enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }