Add tool to detect circular sequences #7296
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I do not understand why it fails at the "Combine chunked test results" step: https://github.com/galaxyproject/tools-iuc/actions/runs/17918115645?pr=7296 |
Co-authored-by: Saim Momin <[email protected]>
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Can you publish this python script separately (extra git repo + bioconda recipe) or re-use existing implementations? I think we should limit publishing software via IUC (except maybe for trivial cases) and restrict to Galaxy tools. IUC seems already busy with the tool wrappers and I'm afraid of the additional workload caused by scripts.
| 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 |
| Args: | ||
| seq (str): sequence to format. | ||
| """ | ||
| return textwrap.wrap(seq, width=60, break_on_hyphens=False) |
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This will probably cause problems with headers longer than 60.
use biopython for io?
| return textwrap.wrap(seq, width=60, break_on_hyphens=False) | ||
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| def one_line_fasta(input_fp, output_fp): |
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Biopython instead of this workaround?
| @@ -0,0 +1,58 @@ | |||
| <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> | |||
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I would suggest to avoid the term kmer. The word has to many implications.
The tool just checks for exact sequence identity of a single sequence.
| Returns: | ||
| : True if circular, False otherwise | ||
| """ | ||
| try: |
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This try just removes the traceback that could be useful for debugging.
| begin (): | ||
| end (): | ||
| """ | ||
| pattern = re.compile(re.escape(begin)) |
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Why use regexp if you can use simple string search?
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