alphafold2: scripts/validate

annotate scripts/validate_fasta.py @ 22:3f188450ca4f draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c

author	galaxy-australia
date	Wed, 30 Oct 2024 21:46:34 +0000
parents	2f7702fd0a4c
children

rev	line source
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	1 """Validate input FASTA sequence."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	2
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	3 import argparse
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	4 import re
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	5 import sys
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	6 from typing import List
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	7
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	8 DEFAULT_MAX_SEQUENCE_COUNT = 10
18 e4a053d67e24 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ef97511263dcac81f8563ae6a98d1db2400fcf1d galaxy-australia parents: 16 diff changeset	9 STRIP_SEQUENCE_CHARS = ['\n', '\r', '\t', ' ']
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	10
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	11
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	12 class Fasta:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	13 def __init__(self, header_str: str, seq_str: str):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	14 self.header = header_str
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	15 self.aa_seq = seq_str
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	17
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	18 class FastaLoader:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	19 def __init__(self, fasta_path: str):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	20 """Initialize from FASTA file."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	21 self.fastas = []
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	22 self.load(fasta_path)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	23
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	24 def load(self, fasta_path: str):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	25 """Load bare or FASTA formatted sequence."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	26 with open(fasta_path, 'r') as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	27 self.content = f.read()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	28
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	29 if "__cn__" in self.content:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	30 # Pasted content with escaped characters
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	31 self.newline = '__cn__'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	32 self.read_caret = '__gt__'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	33 else:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	34 # Uploaded file with normal content
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	35 self.newline = '\n'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	36 self.read_caret = '>'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	37
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	38 self.lines = self.content.split(self.newline)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	39
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	40 if not self.lines[0].startswith(self.read_caret):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	41 # Fasta is headless, load as single sequence
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	42 self.update_fastas(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	43 '', ''.join(self.lines)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	44 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	45
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	46 else:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	47 header = None
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	48 sequence = None
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	49 for line in self.lines:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	50 if line.startswith(self.read_caret):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	51 if header:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	52 self.update_fastas(header, sequence)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	53 header = '>' + self.strip_header(line)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	54 sequence = ''
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	55 else:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	56 sequence += line.strip('\n ')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	57 self.update_fastas(header, sequence)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	58
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	59 def strip_header(self, line):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	60 """Strip characters escaped with underscores from pasted text."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	61 return re.sub(r'\_\_.{2}\_\_', '', line).strip('>')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	62
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	63 def update_fastas(self, header: str, sequence: str):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	64 # if we have a sequence
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	65 if sequence:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	66 # create generic header if not exists
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	67 if not header:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	68 fasta_count = len(self.fastas)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	69 header = f'>sequence_{fasta_count}'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	70
18 e4a053d67e24 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ef97511263dcac81f8563ae6a98d1db2400fcf1d galaxy-australia parents: 16 diff changeset	71 for char in STRIP_SEQUENCE_CHARS:
e4a053d67e24 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ef97511263dcac81f8563ae6a98d1db2400fcf1d galaxy-australia parents: 16 diff changeset	72 sequence = sequence.replace(char, '')
e4a053d67e24 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ef97511263dcac81f8563ae6a98d1db2400fcf1d galaxy-australia parents: 16 diff changeset	73
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	74 # Create new Fasta
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	75 self.fastas.append(Fasta(header, sequence))
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	76
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	77
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	78 class FastaValidator:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	79 def __init__(
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	80 self,
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	81 min_length=None,
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	82 max_length=None,
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	83 multiple=False,
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	84 max_sequence_count=None,
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	85 ):
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	86 self.multiple = multiple
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	87 self.min_length = min_length
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	88 self.max_length = max_length
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	89 self.iupac_characters = {
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	90 'A', 'B', 'C', 'D', 'E', 'F', 'G',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	91 'H', 'I', 'K', 'L', 'M', 'N', 'P',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	92 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	93 'Y', 'Z', '-'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	94 }
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	95 self.max_sequence_count = (
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	96 max_sequence_count
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	97 or DEFAULT_MAX_SEQUENCE_COUNT)
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	98
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	99 def validate(self, fasta_list: List[Fasta]):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	100 """Perform FASTA validation."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	101 self.fasta_list = fasta_list
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	102 self.validate_num_seqs()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	103 self.validate_length()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	104 self.validate_alphabet()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	105 # not checking for 'X' nucleotides at the moment.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	106 # alphafold can throw an error if it doesn't like it.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	107 # self.validate_x()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	108 return self.fasta_list
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	109
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	110 def validate_num_seqs(self) -> None:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	111 """Assert that only one sequence has been provided."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	112 fasta_count = len(self.fasta_list)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	113
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	114 if self.multiple:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	115 if fasta_count < 2:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	116 raise ValueError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	117 'Error encountered validating FASTA:\n'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	118 'Multimer mode requires multiple input sequence.'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	119 f' Only {fasta_count} sequences were detected in'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	120 ' the provided file.')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	121
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	122 elif fasta_count > self.max_sequence_count:
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	123 raise ValueError(
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	124 f'WARNING: detected {fasta_count} sequences but the'
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	125 f' maximum allowed is {self.max_sequence_count}'
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	126 ' sequences.')
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	127 else:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	128 if fasta_count > 1:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	129 sys.stderr.write(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	130 'WARNING: More than 1 sequence detected.'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	131 ' Using first FASTA sequence as input.\n')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	132 self.fasta_list = self.fasta_list[:1]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	133
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	134 elif len(self.fasta_list) == 0:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	135 raise ValueError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	136 'Error encountered validating FASTA:\n'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	137 ' no FASTA sequences detected in input file.')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	138
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	139 def validate_length(self):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	140 """Confirm whether sequence length is valid."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	141 fasta = self.fasta_list[0]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	142 if self.min_length:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	143 if len(fasta.aa_seq) < self.min_length:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	144 raise ValueError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	145 'Error encountered validating FASTA:\n Sequence too short'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	146 f' ({len(fasta.aa_seq)}AA).'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	147 f' Minimum length is {self.min_length}AA.')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	148 if self.max_length:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	149 if len(fasta.aa_seq) > self.max_length:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	150 raise ValueError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	151 'Error encountered validating FASTA:\n'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	152 f' Sequence too long ({len(fasta.aa_seq)}AA).'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	153 f' Maximum length is {self.max_length}AA.')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	154
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	155 def validate_alphabet(self):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	156 """Confirm whether the sequence conforms to IUPAC codes.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	157
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	158 If not, report the offending character and its position.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	159 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	160 fasta = self.fasta_list[0]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	161 for i, char in enumerate(fasta.aa_seq.upper()):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	162 if char not in self.iupac_characters:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	163 raise ValueError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	164 'Error encountered validating FASTA:\n Invalid amino acid'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	165 f' found at pos {i}: "{char}"')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	166
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	167 def validate_x(self):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	168 """Check for X bases."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	169 fasta = self.fasta_list[0]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	170 for i, char in enumerate(fasta.aa_seq.upper()):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	171 if char == 'X':
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	172 raise ValueError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	173 'Error encountered validating FASTA:\n Unsupported AA code'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	174 f' "X" found at pos {i}')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	175
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	176
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	177 class FastaWriter:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	178 def __init__(self) -> None:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	179 self.line_wrap = 60
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	180
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	181 def write(self, fasta: Fasta):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	182 header = fasta.header
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	183 seq = self.format_sequence(fasta.aa_seq)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	184 sys.stdout.write(header + '\n')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	185 sys.stdout.write(seq)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	186
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	187 def format_sequence(self, aa_seq: str):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	188 formatted_seq = ''
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	189 for i in range(0, len(aa_seq), self.line_wrap):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	190 formatted_seq += aa_seq[i: i + self.line_wrap] + '\n'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	191 return formatted_seq.upper()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	192
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	193
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	194 def main():
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	195 # load fasta file
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	196 try:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	197 args = parse_args()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	198 fas = FastaLoader(args.input)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	199
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	200 # validate
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	201 fv = FastaValidator(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	202 min_length=args.min_length,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	203 max_length=args.max_length,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	204 multiple=args.multimer,
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	205 max_sequence_count=args.max_sequence_count,
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	206 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	207 clean_fastas = fv.validate(fas.fastas)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	208
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	209 # write clean data
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	210 fw = FastaWriter()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	211 for fas in clean_fastas:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	212 fw.write(fas)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	213
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	214 sys.stderr.write("Validated FASTA sequence(s):\n\n")
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	215 for fas in clean_fastas:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	216 sys.stderr.write(fas.header + '\n')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	217 sys.stderr.write(fas.aa_seq + '\n\n')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	218
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	219 except ValueError as exc:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	220 sys.stderr.write(f"{exc}\n\n")
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	221 raise exc
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	222
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	223 except Exception as exc:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	224 sys.stderr.write(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	225 "Input error: FASTA input is invalid. Please check your input.\n\n"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	226 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	227 raise exc
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	228
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	229
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	230 def parse_args() -> argparse.Namespace:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	231 parser = argparse.ArgumentParser()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	232 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	233 "input",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	234 help="input fasta file",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	235 type=str
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	236 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	237 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	238 "--min_length",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	239 dest='min_length',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	240 help="Minimum length of input protein sequence (AA)",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	241 default=None,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	242 type=int,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	243 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	244 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	245 "--max_length",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	246 dest='max_length',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	247 help="Maximum length of input protein sequence (AA)",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	248 default=None,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	249 type=int,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	250 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	251 parser.add_argument(
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	252 "--max-sequences",
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	253 dest='max_sequence_count',
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	254 help="Maximum number of input sequences",
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	255 default=None,
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	256 type=int,
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	257 )
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	258 parser.add_argument(
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	259 "--multimer",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	260 action='store_true',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	261 help="Require multiple input sequences",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	262 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	263 return parser.parse_args()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	264
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	265
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	266 if __name__ == '__main__':
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	267 main()

Mercurial > repos > galaxy-australia > alphafold2

annotate scripts/validate_fasta.py @ 22:3f188450ca4f draft default tip