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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
27 lines
1.8 KiB
Markdown
27 lines
1.8 KiB
Markdown
# OBIFORMATS Package: Semantic Description
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The `obiformats` package provides robust, format-agnostic sequence reading capabilities for biological data in the OBITools4 ecosystem.
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It supports automatic detection and parsing of common bioinformatics file formats via MIME-type inference:
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- **FASTA** (`text/fasta`): identified by lines starting with `>`.
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- **FASTQ** (`text/fastq`): detected via leading `@` characters.
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- **ecoPCR2**: recognized by the header line `#@ecopcr-v2`.
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- **EMBL** (`text/embl`): detected by lines starting with `ID `.
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- **GenBank** (`text/genbank`): identified by either `LOCUS ` or legacy `"Genetic Sequence Data Bank"` headers.
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- **CSV** (`text/csv`): generic tabular support.
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Core functionality is exposed through:
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- `OBIMimeTypeGuesser()`: inspects the first ~1 MiB of an input stream to infer MIME type using `github.com/gabriel-vasile/mimetype`, while preserving unread data for downstream processing.
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- `ReadSequencesFromFile()`: reads sequences from a file path, infers format via MIME detection, and dispatches to dedicated parsers (e.g., `ReadFasta`, `ReadFastq`).
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- `ReadSequencesFromStdin()`: convenience wrapper to read from stdin, treating `"-"` as filename and auto-closing the stream.
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Internally leverages:
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- `obiutils.Ropen()` for unified file opening (including stdin handling).
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- Path extension stripping and source tagging via `OptionsSource()`.
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- Logging (`logrus`) for format diagnostics.
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- Iterator interface (`obiiter.IBioSequence`) to abstract sequential access over sequences.
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The package ensures extensibility: new formats can be added by extending the `switch` dispatch in `ReadSequencesFromFile()` and registering corresponding MIME types.
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Error handling covers empty files, invalid streams, and unsupported formats via explicit logging or fatal exits.
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