Mercurial > repos > galaxy-australia > alphafold2

annotate validate_fasta.py @ 5:138feebde7d3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit c7fcba69096f16e6a5cfc03d363d4db28b16807f"
author galaxy-australia
date Thu, 10 Mar 2022 21:53:42 +0000
parents 6c92e000d684
children 04e95886cf24
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
1 """Validate input FASTA sequence."""
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
2
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
3 import re
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
4 import argparse
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
5 from typing import List, TextIO
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
6
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
7
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
8 class Fasta:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
9 def __init__(self, header_str: str, seq_str: str):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
10 self.header = header_str
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
11 self.aa_seq = seq_str
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
12
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
13
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
14 class FastaLoader:
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
15 def __init__(self, fasta_path: str):
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
16 """Initialize from FASTA file."""
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
17 self.fastas = []
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
18 self.load(fasta_path)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
19 print("Loaded FASTA sequences:")
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
20 for f in self.fastas:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
21 print(f.header)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
22 print(f.aa_seq)
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
23
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
24 def load(self, fasta_path: str):
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
25 """Load bare or FASTA formatted sequence."""
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
26 with open(fasta_path, 'r') as f:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
27 self.content = f.read()
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
28
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
29 if "__cn__" in self.content:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
30 # Pasted content with escaped characters
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
31 self.newline = '__cn__'
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
32 self.caret = '__gt__'
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
33 else:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
34 # Uploaded file with normal content
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
35 self.newline = '\n'
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
36 self.caret = '>'
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
37
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
38 self.lines = self.content.split(self.newline)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
39 header, sequence = self.interpret_first_line()
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
40
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
41 i = 0
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
42 while i < len(self.lines):
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
43 line = self.lines[i]
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
44 if line.startswith(self.caret):
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
45 self.update_fastas(header, sequence)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
46 header = '>' + self.strip_header(line)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
47 sequence = ''
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
48 else:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
49 sequence += line.strip('\n ')
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
50 i += 1
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
51
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
52 # after reading whole file, header & sequence buffers might be full
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
53 self.update_fastas(header, sequence)
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
54
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
55 def interpret_first_line(self):
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
56 line = self.lines[0]
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
57 if line.startswith(self.caret):
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
58 header = '>' + self.strip_header(line)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
59 return header, ''
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
60 else:
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
61 return '', line
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
62
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
63 def strip_header(self, line):
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
64 """Strip characters escaped with underscores from pasted text."""
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
65 return re.sub(r'\_\_.{2}\_\_', '', line).strip('>')
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
66
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
67 def update_fastas(self, header: str, sequence: str):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
68 # if we have a sequence
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
69 if sequence:
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
70 # create generic header if not exists
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
71 if not header:
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
72 fasta_count = len(self.fastas)
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
73 header = f'>sequence_{fasta_count}'
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
74
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
75 # Create new Fasta
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
76 self.fastas.append(Fasta(header, sequence))
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
77
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
78
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
79 class FastaValidator:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
80 def __init__(self, fasta_list: List[Fasta]):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
81 self.fasta_list = fasta_list
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
82 self.min_length = 30
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
83 self.max_length = 2000
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
84 self.iupac_characters = {
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
85 'A', 'B', 'C', 'D', 'E', 'F', 'G',
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
86 'H', 'I', 'K', 'L', 'M', 'N', 'P',
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
87 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
88 'Y', 'Z', '-'
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
89 }
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
90
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
91 def validate(self):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
92 """performs fasta validation"""
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
93 self.validate_num_seqs()
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
94 self.validate_length()
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
95 self.validate_alphabet()
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
96 # not checking for 'X' nucleotides at the moment.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
97 # alphafold can throw an error if it doesn't like it.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
98 #self.validate_x()
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
99
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
100 def validate_num_seqs(self) -> None:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
101 if len(self.fasta_list) > 1:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
102 raise Exception(f'Error encountered validating fasta: More than 1 sequence detected ({len(self.fasta_list)}). Please use single fasta sequence as input')
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
103 elif len(self.fasta_list) == 0:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
104 raise Exception(f'Error encountered validating fasta: input file has no fasta sequences')
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
105
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
106 def validate_length(self):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
107 """Confirms whether sequence length is valid. """
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
108 fasta = self.fasta_list[0]
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
109 if len(fasta.aa_seq) < self.min_length:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
110 raise Exception(f'Error encountered validating fasta: Sequence too short ({len(fasta.aa_seq)}aa). Must be > 30aa')
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
111 if len(fasta.aa_seq) > self.max_length:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
112 raise Exception(f'Error encountered validating fasta: Sequence too long ({len(fasta.aa_seq)}aa). Must be < 2000aa')
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
113
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
114 def validate_alphabet(self):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
115 """
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
116 Confirms whether the sequence conforms to IUPAC codes.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
117 If not, reports the offending character and its position.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
118 """
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
119 fasta = self.fasta_list[0]
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
120 for i, char in enumerate(fasta.aa_seq.upper()):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
121 if char not in self.iupac_characters:
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
122 raise Exception(f'Error encountered validating fasta: Invalid amino acid found at pos {i}: "{char}"')
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
123
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
124 def validate_x(self):
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
125 """checks if any bases are X. TODO check whether alphafold accepts X bases. """
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
126 fasta = self.fasta_list[0]
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
127 for i, char in enumerate(fasta.aa_seq.upper()):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
128 if char == 'X':
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
129 raise Exception(f'Error encountered validating fasta: Unsupported aa code "X" found at pos {i}')
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
130
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
131
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
132 class FastaWriter:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
133 def __init__(self) -> None:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
134 self.outfile = 'alphafold.fasta'
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
135 self.formatted_line_len = 60
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
136
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
137 def write(self, fasta: Fasta):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
138 with open(self.outfile, 'w') as fp:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
139 header = fasta.header
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
140 seq = self.format_sequence(fasta.aa_seq)
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
141 fp.write(header + '\n')
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
142 fp.write(seq + '\n')
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
143
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
144 def format_sequence(self, aa_seq: str):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
145 formatted_seq = ''
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
146 for i in range(0, len(aa_seq), self.formatted_line_len):
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
147 formatted_seq += aa_seq[i: i + self.formatted_line_len] + '\n'
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
148 return formatted_seq
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
149
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
150
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
151 def main():
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
152 # load fasta file
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
153 args = parse_args()
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
154 fas = FastaLoader(args.input_fasta)
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
155
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
156 # validate
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
157 fv = FastaValidator(fas.fastas)
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
158 fv.validate()
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
159
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
160 # write cleaned version
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
161 fw = FastaWriter()
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
162 fw.write(fas.fastas[0])
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
163
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
164
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
165 def parse_args() -> argparse.Namespace:
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
166 parser = argparse.ArgumentParser()
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
167 parser.add_argument(
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
168 "input_fasta",
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
169 help="input fasta file",
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
170 type=str
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
171 )
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
172 return parser.parse_args()
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
173
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
174
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
175
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
176 if __name__ == '__main__':
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
177 main()