Add tool to detect circular sequences

tools/detect_circular_sequences/.lint_skip

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+CitationsMissing

tools/detect_circular_sequences/.shed.yml

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+name: detect_circular_sequences
+description: Detect circular sequences (e.g. circular contigs) in a FASTA file by k-mer matching
+long_description: |
+  Detect circular sequences (e.g. circular contigs) by looking for exact identical k-mer at the two
+  ends on a cadre sequence of the sequences prodvide in fasta file. In order to be able
+  to predict genes spanning the origin of circular sequences, the first 1,000 nucleotides
+  of each circular sequences are duplicated and added at the sequence's end.
+
+  Inspired by Simon Roux work for Metavir2 (2014) and Corentin Hochart work in PlasSuite
+categories:
+- Sequence Analysis
+- Assembly
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences
+homepage_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences
+type: unrestricted

tools/detect_circular_sequences/detect_circular_sequences.py

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+#!/usr/bin/env python3
+
+#########################################################################################
+# This script detect circular contigs by looking for exact identical k-mer at the two
+# ends on a cadre sequence of the sequences prodvide in fasta file. In order to be able
+# to predict genes spanning the orgin of circular contigs, the first 1,000 nucleotides
+# of each circular contigs are dulicated and added at the contig's end.
+#
+# Inspired by Simon Roux work for Metavir2 (2014) and Corentin Hochart work in PlasSuite
+#
+#########################################################################################
+
+import argparse
+import re
+import sys
+import tempfile
+import textwrap
+from pathlib import Path
+
+
+def error(message):
+    """
+    Print an error message to stderr and exit the program with a non-zero status.
+
+    Args:
+        message (str): The error message to display.
+    """
+    print(f"{sys.argv[0]} (error): {message}. Execution halted.", file=sys.stderr)
+    sys.exit(1)
+
+
+def warning(message, verbose):
+    """
+    Print a warning message to stderr if verbose mode is enabled.
+
+    Args:
+        message (str): The warning message to display.
+        verbose (bool): If True, the message will be printed.
+    """
+    if verbose:
+        print(f"{sys.argv[0]} (info): {message}", file=sys.stderr)
+
+
+def fasta_format(seq):
+    """
+    Format sequence into lines of 60 characters each.
+
+    Args:
+        seq (str): sequence to format.
+    """
+    return textwrap.wrap(seq, width=60, break_on_hyphens=False)
+
+
+def one_line_fasta(input_fp, output_fp):
+    """
+    Convert FASTA file to a format with sequences on single lines.
+
+    Args:
+        input_fp (Path): path to input FASTA file
+        output_fp (Path): path to output FASTA file
+    """
+    with input_fp.open("r") as infile, output_fp.open("w") as outfile:
+        for line in infile:
+            if line.startswith(">"):
+                outfile.write(f"\n{line}")  # Newline before header
+            else:
+                outfile.write(line.rstrip("\n"))  # Remove newline and concatenate
+        outfile.write("\n")  # Final newline (like END in awk)
+
+
+def find_kmer_occurrences(begin, end):
+    """
+    Find all starting positions of 'begin' in 'end'.
+
+    Args:
+        begin ():
+        end ():
+    """
+    pattern = re.compile(re.escape(begin))
+    return [match.start() + len(begin) for match in pattern.finditer(end)]
+
+
+def is_circular(line_chars, scale, pos):
+    """
+    Check if the sequence is circular by comparing segments.
+
+    Args:
+        line_chars (list): Sequence characters
+        scale ( ): Starting k-mer
+        pos ():
+
+    Returns:
+        bool: True if circular, False otherwise
+    """
+    for i in range(scale):
+        if line_chars[i] != line_chars[pos + i]:
+            return False
+    return True
+
+
+def process_sequence(
+    line,
+    header,
+    verbose,
+    kmer_length=10,
+    cadre_length=0,
+    duplicate_nucleotides=1000,
+):
+    """
+    Process a single sequence to detect circularity and modify if needed.
+
+    Args:
+        line ():
+        header ():
+        verbose ():
+        kmer_length ():
+        cadre_length ():
+        duplicate_nucleotides ():
+
+    Returns:
+        : True if circular, False otherwise
+    """
+    try:
+        line_chars = list(line)
+        seq_len = len(line_chars)
+
+        if seq_len < kmer_length:
+            warning(f"Short sequence ({seq_len}bp): {header}", verbose)
+            return None, None
+
+        # Determine cadre length
+        if cadre_length == 0 or cadre_length > seq_len - kmer_length:
+            cadre_length = seq_len - kmer_length
+
+        # Extract begin and end
+        begin = "".join(line_chars[:kmer_length])
+        end_part = line_chars[-cadre_length:]  # [::-1]
+        end_str = "".join(end_part)
+
+        # Find all positions where 'begin' appears in the reversed end part
+        end_positions = find_kmer_occurrences(begin, end_str)
+
+        if not end_positions:
+            return None, None
+
+        # Check for circularity at each position
+        status = False
+        for pos in end_positions:
+            scale = len(line_chars) - pos
+            if is_circular(line_chars, scale, pos):
+                status = True
+
+        if not status:
+            return None, None
+
+        # Modify the sequence
+        modified_seq = line_chars[: len(line_chars) - scale]
+
+        if len(modified_seq) < duplicate_nucleotides:
+            modified_seq += modified_seq
+        else:
+            modified_seq += line_chars[:duplicate_nucleotides]
+
+        return header, "".join(modified_seq)
+    except Exception as e:
+        error(f"Error processing sequence {header}: {e}")
+
+
+def detect_circular(
+    fasta_in,
+    fasta_out,
+    id_out,
+    kmer_length=10,
+    cadre_length=0,
+    duplicate_nucleotides=1000,
+    verbose=False,
+):
+    """
+    Detect and process circular sequences.
+
+    Args:
+        fasta_in (Path): Input FASTA file
+        fasta_out (Path): Output FASTA file with modifications
+        id_out (Path): File to record identifiers of circular sequences
+        kmer_length (int): Length of k-mer to search for
+        cadre_length (int): Length of sequence end to inspect
+        duplicate_nucleotides (int): Number of nucleotides to duplicate at the end
+        verbose (bool): Enable verbose output
+    """
+    tmp_file = tempfile.NamedTemporaryFile(mode="w", delete=False)
+    one_line_fasta(fasta_in, Path(tmp_file.name))
+
+    with Path(tmp_file.name).open("r") as infile, fasta_out.open(
+        "w"
+    ) as fasta_output, id_out.open("w") as id_output:
+
+        sequence = ""
+        header = ""
+        for line in infile.readlines():
+            # print(line)
+            # Read header
+            if line.startswith(">"):
+                header = line[1:].strip()
+                sequence = ""
+                continue
+            else:
+                sequence = line.strip()
+
+            # Process the sequence
+            header, modified_seq = process_sequence(
+                sequence,
+                header,
+                verbose=verbose,
+                kmer_length=kmer_length,
+                cadre_length=cadre_length,
+                duplicate_nucleotides=duplicate_nucleotides,
+            )
+
+            if modified_seq:
+                # Write to output files
+                id_output.write(f"{header}\n")
+
+                fasta_output.write(f">{header}\n")
+                formatted = fasta_format(modified_seq)
+                for line in formatted:
+                    fasta_output.write(f"{line}\n")
+
+    # Clean up temporary file
+    Path(tmp_file.name).unlink()
+
+
+def main():
+    """
+    Main function to detect circular contigs in a FASTA file.
+
+    This function parses command-line arguments, reads the input FASTA file,
+    processes each sequence to detect circular contigs, and prints the results.
+    It handles both verbose and non-verbose modes, and can optionally print only circular sequences.
+
+    Command-line arguments:
+        --fasta-in: Path to the input FASTA file (required).
+        --kmer-length: Length of the k-mer used to identify circular sequences (default: 10).
+        --cadre: Length of the fragment at the sequence 5' end to inspect for k-mer identity.
+                 If 0, the entire sequence is screened (default: 0).
+        --only_circular: If set, only circular sequences are printed.
+        --verbose: If set, warning messages are printed during execution.
+        --output: Path to output file
+
+    The function processes each sequence in the FASTA file, checks for circularity,
+    and prints the results in FASTA format, with circular sequences marked in the header.
+    """
+    parser = argparse.ArgumentParser(
+        description="Detect circular contigs by k-mer matching."
+    )
+    parser.add_argument("--fasta-in", required=True, help="Input FASTA file")
+    parser.add_argument(
+        "--kmer-length", type=int, default=10, help="Length of k-mer (default: 10)"
+    )
+    parser.add_argument(
+        "--cadre-length",
+        type=int,
+        default=0,
+        help="Inspect fragment length (default: 0)",
+    )
+    parser.add_argument("--verbose", action="store_true", help="Enable verbose output")
+    parser.add_argument("--fasta-out", required=True, help="Output FASTA file")
+    parser.add_argument(
+        "--id-out", required=True, help="File to write circular sequence IDs"
+    )
+
+    args = parser.parse_args()
+
+    warning("Starting script execution.", args.verbose)
+    detect_circular(
+        Path(args.fasta_in),
+        Path(args.fasta_out),
+        Path(args.id_out),
+        kmer_length=args.kmer_length,
+        cadre_length=args.cadre_length,
+        verbose=args.verbose,
+    )
+    warning("Script execution completed.", args.verbose)
+
+
+if __name__ == "__main__":
+    main()

tools/detect_circular_sequences/detect_circular_sequences.xml

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+<tool id="detect_circular_sequences" name="Detect circular sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>(e.g. circular contigs) in a FASTA file by k-mer matching</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">24.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="3.13">python</requirement>
+    </requirements>
+    <command><![CDATA[
+python '${__tool_directory__}/detect_circular_sequences.py'
+    --fasta-in '$fasta_in'
+    --kmer-length $kmer_length
+    --cadre-length $cadre_length
+    $verbose
+    --fasta-out '$fasta_out'
+    --id-out '$id_out'
+    ]]></command>
+    <inputs>
+        <param argument="--fasta-in" type="data" format="fasta" label="Input FASTA file"/>
+        <param argument="--kmer-length" type="integer" min="0" value="10" label="Length of k-mer"/>
+        <param argument="--cadre-length" type="integer" min="0" value="0" label="Inspect fragment length"/>
+        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" default_value="" label="Inspect fragment length"/>
+    </inputs>
+    <outputs>
+        <data name="fasta_out" format="fasta" label="${tool.name} on ${on_string}: Circular sequences"/>
+        <data name="id_out" format="txt" label="${tool.name} on ${on_string}: Circular sequence IDs"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="fasta_in" value="input.fasta"/>
+            <param name="kmer_length" value="10"/>
+            <param name="cadre_length" value="0"/>
+            <param name="verbose" value="false"/>
+            <output name="fasta_out">
+                <assert_contents>
+                    <has_text text=">SRR17300492_25544"/>
+                    <has_text text="GCGATCCAACTGAACCGGATCTAGAGCCGTGGGGTCAACCGC"/>
+                </assert_contents>
+            </output>
+            <output name="id_out">
+                <assert_contents>
+                    <has_text text="SRR17300492_25544"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This script detect circular sequences (e.g. circular contigs) by looking for exact identical k-mer at the two
+ends on a cadre sequence of the sequences prodvide in fasta file. In order to be able
+to predict genes spanning the orgin of circular sequences, the first 1,000 nucleotides
+of each circular sequence are duplicated and added at the sequence's end.
+
+Inspired by Simon Roux work for Metavir2 (2014) and Corentin Hochart work in PlasSuite
+    ]]></help>
+</tool>