Mercurial > repos > galaxy-australia > alphafold2
changeset 6:04e95886cf24 draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 724a7a389c878dded1c0332f3b6e507e0c4cd52a-dirty"
| author | galaxy-australia |
|---|---|
| date | Mon, 04 Apr 2022 01:46:22 +0000 |
| parents | 138feebde7d3 |
| children | eb085b3dbaf8 |
| files | alphafold.xml validate_fasta.py |
| diffstat | 2 files changed, 92 insertions(+), 58 deletions(-) [+] |
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--- a/alphafold.xml Thu Mar 10 21:53:42 2022 +0000 +++ b/alphafold.xml Mon Apr 04 01:46:22 2022 +0000 @@ -29,7 +29,10 @@ echo '$fasta_or_text.fasta_text' > input.fasta && #end if -python3 '$__tool_directory__/validate_fasta.py' input.fasta && +python3 '$__tool_directory__/validate_fasta.py' input.fasta +--min_length \${ALPHAFOLD_AA_LENGTH_MIN:-30} +--max_length \${ALPHAFOLD_AA_LENGTH_MAX:-2000} +> alphafold.fasta && ## env vars ------------------------------- export TF_FORCE_UNIFIED_MEMORY=1 && @@ -49,7 +52,7 @@ --max_template_date=\$DATE --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 -## use_gpu_relax introduced in AlphaFold v2.1.2 +## Param introduced in AlphaFold v2.1.2: --use_gpu_relax=True &&
--- a/validate_fasta.py Thu Mar 10 21:53:42 2022 +0000 +++ b/validate_fasta.py Mon Apr 04 01:46:22 2022 +0000 @@ -1,6 +1,7 @@ """Validate input FASTA sequence.""" import re +import sys import argparse from typing import List, TextIO @@ -16,10 +17,6 @@ """Initialize from FASTA file.""" self.fastas = [] self.load(fasta_path) - print("Loaded FASTA sequences:") - for f in self.fastas: - print(f.header) - print(f.aa_seq) def load(self, fasta_path: str): """Load bare or FASTA formatted sequence.""" @@ -29,36 +26,32 @@ if "__cn__" in self.content: # Pasted content with escaped characters self.newline = '__cn__' - self.caret = '__gt__' + self.read_caret = '__gt__' else: # Uploaded file with normal content self.newline = '\n' - self.caret = '>' + self.read_caret = '>' self.lines = self.content.split(self.newline) - header, sequence = self.interpret_first_line() + + if not self.lines[0].startswith(self.read_caret): + # Fasta is headless, load as single sequence + self.update_fastas( + '', ''.join(self.lines) + ) - i = 0 - while i < len(self.lines): - line = self.lines[i] - if line.startswith(self.caret): - self.update_fastas(header, sequence) - header = '>' + self.strip_header(line) - sequence = '' - else: - sequence += line.strip('\n ') - i += 1 - - # after reading whole file, header & sequence buffers might be full - self.update_fastas(header, sequence) - - def interpret_first_line(self): - line = self.lines[0] - if line.startswith(self.caret): - header = '>' + self.strip_header(line) - return header, '' else: - return '', line + header = None + sequence = None + for line in self.lines: + if line.startswith(self.read_caret): + if header: + self.update_fastas(header, sequence) + header = '>' + self.strip_header(line) + sequence = '' + else: + sequence += line.strip('\n ') + self.update_fastas(header, sequence) def strip_header(self, line): """Strip characters escaped with underscores from pasted text.""" @@ -77,10 +70,14 @@ class FastaValidator: - def __init__(self, fasta_list: List[Fasta]): + def __init__( + self, + fasta_list: List[Fasta], + min_length=None, + max_length=None): + self.min_length = min_length + self.max_length = max_length self.fasta_list = fasta_list - self.min_length = 30 - self.max_length = 2000 self.iupac_characters = { 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', @@ -93,68 +90,89 @@ self.validate_num_seqs() self.validate_length() self.validate_alphabet() + # not checking for 'X' nucleotides at the moment. # alphafold can throw an error if it doesn't like it. - #self.validate_x() + # self.validate_x() def validate_num_seqs(self) -> None: + """Assert that only one sequence has been provided.""" if len(self.fasta_list) > 1: - raise Exception(f'Error encountered validating fasta: More than 1 sequence detected ({len(self.fasta_list)}). Please use single fasta sequence as input') + raise Exception( + 'Error encountered validating fasta:' + f' More than 1 sequence detected ({len(self.fasta_list)}).' + ' Please use single fasta sequence as input.') elif len(self.fasta_list) == 0: - raise Exception(f'Error encountered validating fasta: input file has no fasta sequences') + raise Exception( + 'Error encountered validating fasta:' + ' input file has no fasta sequences') def validate_length(self): - """Confirms whether sequence length is valid. """ + """Confirm whether sequence length is valid.""" fasta = self.fasta_list[0] - if len(fasta.aa_seq) < self.min_length: - raise Exception(f'Error encountered validating fasta: Sequence too short ({len(fasta.aa_seq)}aa). Must be > 30aa') - if len(fasta.aa_seq) > self.max_length: - raise Exception(f'Error encountered validating fasta: Sequence too long ({len(fasta.aa_seq)}aa). Must be < 2000aa') + if self.min_length: + if len(fasta.aa_seq) < self.min_length: + raise Exception( + 'Error encountered validating fasta: Sequence too short' + f' ({len(fasta.aa_seq)}AA).' + f' Minimum length is {self.min_length}AA.') + if self.max_length: + if len(fasta.aa_seq) > self.max_length: + raise Exception( + 'Error encountered validating fasta:' + f' Sequence too long ({len(fasta.aa_seq)}AA).' + f' Maximum length is {self.max_length}AA.') def validate_alphabet(self): """ - Confirms whether the sequence conforms to IUPAC codes. - If not, reports the offending character and its position. + Confirm whether the sequence conforms to IUPAC codes. + If not, report the offending character and its position. """ fasta = self.fasta_list[0] for i, char in enumerate(fasta.aa_seq.upper()): if char not in self.iupac_characters: - raise Exception(f'Error encountered validating fasta: Invalid amino acid found at pos {i}: "{char}"') + raise Exception( + 'Error encountered validating fasta: Invalid amino acid' + f' found at pos {i}: "{char}"') def validate_x(self): - """checks if any bases are X. TODO check whether alphafold accepts X bases. """ + """Check for X bases.""" fasta = self.fasta_list[0] for i, char in enumerate(fasta.aa_seq.upper()): if char == 'X': - raise Exception(f'Error encountered validating fasta: Unsupported aa code "X" found at pos {i}') + raise Exception( + 'Error encountered validating fasta: Unsupported AA code' + f' "X" found at pos {i}') class FastaWriter: def __init__(self) -> None: - self.outfile = 'alphafold.fasta' - self.formatted_line_len = 60 + self.line_wrap = 60 def write(self, fasta: Fasta): - with open(self.outfile, 'w') as fp: - header = fasta.header - seq = self.format_sequence(fasta.aa_seq) - fp.write(header + '\n') - fp.write(seq + '\n') + header = fasta.header + seq = self.format_sequence(fasta.aa_seq) + sys.stdout.write(header + '\n') + sys.stdout.write(seq) def format_sequence(self, aa_seq: str): formatted_seq = '' - for i in range(0, len(aa_seq), self.formatted_line_len): - formatted_seq += aa_seq[i: i + self.formatted_line_len] + '\n' + for i in range(0, len(aa_seq), self.line_wrap): + formatted_seq += aa_seq[i: i + self.line_wrap] + '\n' return formatted_seq def main(): # load fasta file args = parse_args() - fas = FastaLoader(args.input_fasta) + fas = FastaLoader(args.input) # validate - fv = FastaValidator(fas.fastas) + fv = FastaValidator( + fas.fastas, + min_length=args.min_length, + max_length=args.max_length, + ) fv.validate() # write cleaned version @@ -165,13 +183,26 @@ def parse_args() -> argparse.Namespace: parser = argparse.ArgumentParser() parser.add_argument( - "input_fasta", + "input", help="input fasta file", type=str ) + parser.add_argument( + "--min_length", + dest='min_length', + help="Minimum length of input protein sequence (AA)", + default=None, + type=int, + ) + parser.add_argument( + "--max_length", + dest='max_length', + help="Maximum length of input protein sequence (AA)", + default=None, + type=int, + ) return parser.parse_args() - if __name__ == '__main__': main()