Mercurial > repos > iuc > detect_circular_sequences

annotate detect_circular_sequences.py @ 0:54d2dd3f1711 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
author iuc
date Thu, 11 Dec 2025 08:53:25 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
1 #!/usr/bin/env python3
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
2
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
3 #########################################################################################
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
4 # This script detect circular contigs by looking for exact identical k-mer at the two
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
5 # ends of the sequences provided in fasta file. In order to be able to predict genes
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
6 # spanning the origin of circular contigs, the first 1,000 nucleotides of each circular
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
7 # contigs are duplicated and added at the contig's end.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
8 #
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
9 # Inspired by Simon Roux work for Metavir2 (2014) and Corentin Hochart work in PlasSuite
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
10 #
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
11 #########################################################################################
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
12
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
13 import argparse
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
14 import logging
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
15 from pathlib import Path
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
16
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
17 from Bio import SeqIO
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
18
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
19 log_levels = {
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
20 0: logging.CRITICAL,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
21 1: logging.ERROR,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
22 2: logging.WARN,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
23 3: logging.INFO,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
24 4: logging.DEBUG,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
25 }
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
26 logging.basicConfig(level=log_levels[3])
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
27 logger = logging.getLogger()
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
28
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
29
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
30 def setup_logger(verbosity: int) -> None:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
31 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
32 Configure the logger based on verbosity level.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
33
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
34 :param verbosity: verbosity level
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
35 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
36 logging.basicConfig(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
37 format="%(asctime)s - %(levelname)s - %(message)s",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
38 level=log_levels.get(verbosity, logging.INFO),
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
39 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
40
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
41
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
42 def find_occurrences(s, substring) -> list:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
43 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
44 Find all starting positions of a substring in a string
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
45
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
46 :param s: String to be searched
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
47 :param substring: Substring to search in s
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
48 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
49 return [i for i in range(len(s)) if s.startswith(substring, i)]
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
50
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
51
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
52 def is_circular(sequence, length, pos) -> bool:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
53 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
54 Determines if a sequence is circular by comparing segments starting at `start_pos`.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
55
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
56 A sequence is considered circular if the `length` elements at the beginning of the sequence match the `length`
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
57 elements starting at `start_pos` in the sequence. This is useful for detecting repeating patterns or cycles
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
58 in sequences.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
59
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
60 :param sequence: The input sequence
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
61 :param length: The number of elements to compare for circularity.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
62 :param pos: The starting index in the sequence to begin the comparison.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
63
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
64 :return bool: True if circular, False otherwise
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
65 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
66 for i in range(length):
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
67 if sequence[i] != sequence[pos + i]:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
68 return False
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
69 return True
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
70
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
71
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
72 def check_circularity(seq_record, subseq_length=10) -> int:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
73 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
74 Process a single sequence to detect circularity and return the overlap length if circular.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
75
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
76 :param seq_record: SeqRecord object
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
77 :param subseq_length: Length of 3' fragment to check on the 5' end
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
78
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
79 :return: overlap length if circular, 0 otherwise
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
80 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
81 seq_len = len(seq_record)
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
82
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
83 if seq_len < subseq_length:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
84 logging.error(f"Sequence too short ({seq_len}bp): {seq_record.id}")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
85 return 0
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
86
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
87 begin = "".join(seq_record[:subseq_length])
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
88 end = "".join(seq_record[subseq_length:])
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
89 positions = [x + subseq_length for x in find_occurrences(end, begin)]
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
90
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
91 for pos in positions:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
92 overlap_length = seq_len - pos
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
93 if is_circular(seq_record, overlap_length, pos):
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
94 return overlap_length
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
95 return 0
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
96
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
97
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
98 def extend_sequence(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
99 seq_record,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
100 overlap_length,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
101 duplication_length=1000,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
102 ):
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
103 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
104 Extends the 5' end of a sequence by duplicating a fragment from the 3' end.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
105
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
106 This function is useful for simulating circular sequences by extending the 5' end
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
107 with a fragment from the 3' end, based on the specified `overlap_length` and `duplication_length`.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
108
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
109 :param seq_record: The input sequence record to be extended.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
110 :param overlap_length: The length of the overlapping segment that was previously identified as circular.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
111 :param duplication_length: The length of the 3' end fragment to duplicate and add to the 5' end.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
112
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
113 :return: The modified sequence record with the extended 5' end.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
114 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
115 # Remove the overlapping segment from the 3' end
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
116 modified_seq = seq_record.seq[: len(seq_record.seq) - overlap_length]
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
117 # Duplicate the first `duplication_length` nucleotides from the original sequence
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
118 # and append them to the 5' end of the modified sequence
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
119 if len(modified_seq) < duplication_length:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
120 # If the modified sequence is shorter than `duplication_length`,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
121 # duplicate the entire modified sequence
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
122 extension = modified_seq
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
123 else:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
124 # Otherwise, duplicate the first `duplication_length` nucleotides
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
125 extension = seq_record.seq[:duplication_length]
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
126 # Combine the modified sequence with the duplicated fragment
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
127 extended_seq = modified_seq + extension
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
128 # Update the sequence in the SeqRecord object
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
129 seq_record.seq = extended_seq
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
130 return seq_record
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
131
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
132
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
133 def detect_circular(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
134 fasta_in,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
135 fasta_out,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
136 id_out,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
137 subseq_length=10,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
138 duplication_length=1000,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
139 ):
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
140 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
141 Detect and process circular sequences in a FASTA file.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
142
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
143 This function reads sequences from `fasta_in`, checks for circularity,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
144 extends circular sequences, and writes the results to `fasta_out` and `id_out`.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
145
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
146 :param fasta_in: Path to the input FASTA file.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
147 :param fasta_out: Path to the output FASTA file for extended circular sequences.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
148 :param id_out: Path to the output file for recording IDs of circular sequences.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
149 :param subseq_length: Length of the 3' fragment to check for circularity.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
150 :param duplication_length: Length of the 3' fragment to duplicate and add to the 5' end.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
151 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
152 records = []
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
153 ids = []
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
154 try:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
155 with fasta_in.open("r") as fasta_in_f:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
156 for seq_record in SeqIO.parse(fasta_in_f, "fasta"):
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
157 overlap_length = check_circularity(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
158 seq_record,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
159 subseq_length=subseq_length,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
160 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
161 if overlap_length > 0:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
162 records.append(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
163 extend_sequence(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
164 seq_record,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
165 overlap_length,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
166 duplication_length,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
167 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
168 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
169 ids.append(seq_record.id)
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
170 except Exception as e:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
171 logging.error(f"Error processing {fasta_in}: {e}")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
172 raise
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
173
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
174 if not records:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
175 logging.warning("Warning: No circular sequences found.")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
176
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
177 try:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
178 with fasta_out.open("w") as fasta_out_f:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
179 SeqIO.write(records, fasta_out_f, "fasta")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
180 with id_out.open("w") as id_out_f:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
181 id_out_f.write("\n".join(ids) + "\n")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
182 except IOError as e:
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
183 logging.error(f"Error writing output files: {e}")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
184 raise
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
185
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
186
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
187 def main():
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
188 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
189 Main function to detect circular contigs in a FASTA file.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
190
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
191 This function parses command-line arguments, launches function to read the input
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
192 FASTA file, process each sequence to detect circular contigs, and generate the
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
193 output files.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
194 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
195 parser = argparse.ArgumentParser(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
196 description="""
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
197 Detect circular contigs by looking for exact identical subsequences at the two
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
198 ends of the sequences provided in a FASTA file and output the circular contigs
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
199 extended on 5' end by duplication of the first nucleotides on 3' end to be able
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
200 to predict genes spanning the origin of circular contigs.
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
201 """
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
202 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
203 parser.add_argument("--fasta-in", required=True, help="Input FASTA file")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
204 parser.add_argument(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
205 "--subseq-length",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
206 type=int,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
207 default=10,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
208 help="Length of 3' fragment to check on the 5' end (default: 10)",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
209 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
210 parser.add_argument(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
211 "--duplication-length",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
212 type=int,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
213 default=1000,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
214 help="Length of the 3' end fragment to duplicate and add on the 5' end (default: 1000)",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
215 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
216 parser.add_argument(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
217 "-v",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
218 "--verbose",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
219 type=int,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
220 default=3,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
221 choices=log_levels.keys(),
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
222 help="Verbosity level (0=CRITICAL, 1=ERROR, 2=WARN, 3=INFO, 4=DEBUG)",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
223 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
224 parser.add_argument(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
225 "--fasta-out",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
226 required=True,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
227 help="Output FASTA file with extended circular contigs",
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
228 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
229 parser.add_argument(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
230 "--id-out", required=True, help="Output TXT file with circular sequence IDs"
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
231 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
232
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
233 args = parser.parse_args()
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
234 setup_logger(args.verbose)
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
235
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
236 logging.info("Starting script execution.")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
237 detect_circular(
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
238 Path(args.fasta_in),
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
239 Path(args.fasta_out),
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
240 Path(args.id_out),
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
241 subseq_length=args.subseq_length,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
242 duplication_length=args.duplication_length,
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
243 )
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
244 logging.info("Script execution completed.")
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
245
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
246
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
247 if __name__ == "__main__":
54d2dd3f1711 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences commit 7ea9f729b44c6351c52b6295c780f496d239488e
iuc
parents:
diff changeset
248 main()