@fishka/seqio 0.8.0 → 0.8.2

package/dist/index.d.mts

@@ -1,23 +1,5 @@
 export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, AbifChromatogramBundle, AbifDataChannelRole, AbifDecodedValue, AbifDirEntry, AbifDirectory, AbifEntry, AbifEntryRaw, AbifFile, AbifMetadata, ChannelSignals, Chromatogram, CropAbifOptions, CropAbifRange, ENTRY_SIZE, HEADER_SIZE, ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, insertEntrySorted, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif } from './abif/index.mjs';
 
-/**
- * Content-based file-format detection.
- *
- * Sniffs the bytes, never the file extension: binary magic first (ABIF at offset 0, or at
- * 128 behind a MacBinary preamble; SCF's ".scf" magic), then the first non-blank line for
- * the text formats. Text signatures are matched on the leading line's content (a keyword
- * like `LOCUS`, or the first character `>` / `;` / `@`), so a mislabeled or extension-less
- * file still resolves.
- */
-/** A format {@link detectFormat} can recognize. Some are detected before their reader ships. */
-type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'pir' | 'gff' | 'sam' | 'bam' | 'gfa' | 'unknown';
-/**
- * Detect the sequencing file format from its content. Returns 'unknown' when no signature
- * matches (empty input, or a leading line that is neither a known magic nor a recognized
- * text marker).
- */
-declare function detectFormat(bytes: Uint8Array): SeqFileFormat;
-
 /**
  * The common "a sequence with a name" record produced by every reader that extracts
  * sequences for downstream picking/export (GenBank, EMBL, Swiss-Prot, the alignment
@@ -38,6 +20,47 @@ interface SeqRecord {
 /** Build a {@link SeqRecord}, dropping an empty description so records compare cleanly. */
 declare function makeSeqRecord(id: string, description: string, sequence: string): SeqRecord;
 
+/**
+ * ACE (`.ace`) reader — assembly sequence extraction (Phrap/consed).
+ *
+ * An ACE file describes one or more contigs. Each contig is a `CO <name> <nBases> <nReads> …` line
+ * followed by the consensus sequence (wrapped over several lines), then per-read records
+ * `RD <readName> <nPaddedBases> …` each followed by that read's padded sequence. Other records
+ * (`AS`, `BQ`, `QA`, `AF`, `BS`, `DS`, `WA`, `CT`, `RT`, …) carry qualities/metadata and are skipped.
+ *
+ * This reader returns every sequence it finds, in file order:
+ *   - each contig consensus  → id `Contig<name>`, description `consensus`
+ *   - each read              → id `<readName>`,   description `read`
+ * The pad character `*` (an alignment gap in ACE) is kept verbatim — de-gapping is the caller's
+ * choice.
+ *
+ * A `CO`/`RD` header declares the block's exact base count, so the sequence is accumulated until that
+ * many residues are read (or a blank line ends it). This length-driven boundary — rather than
+ * "stop at the next two-letter tag" — avoids swallowing a following record and avoids truncating at a
+ * short residue line that merely looks like a tag (e.g. a line that is literally `BQ`/`CT`, both
+ * valid residues). Deliberately lenient (see AGENTS.md): never throws; a truncated final block is kept.
+ */
+
+declare function parseAce(input: string | Uint8Array): SeqRecord[];
+
+/**
+ * Content-based file-format detection.
+ *
+ * Sniffs the bytes, never the file extension: binary magic first (ABIF at offset 0, or at
+ * 128 behind a MacBinary preamble; SCF's ".scf" magic), then the first non-blank line for
+ * the text formats. Text signatures are matched on the leading line's content (a keyword
+ * like `LOCUS`, or the first character `>` / `;` / `@`), so a mislabeled or extension-less
+ * file still resolves.
+ */
+/** A format {@link detectFormat} can recognize. Some are detected before their reader ships. */
+type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'mega' | 'pir' | 'gff' | 'sam' | 'bam' | 'gfa' | 'pdb' | 'ace' | 'unknown';
+/**
+ * Detect the sequencing file format from its content. Returns 'unknown' when no signature
+ * matches (empty input, or a leading line that is neither a known magic nor a recognized
+ * text marker).
+ */
+declare function detectFormat(bytes: Uint8Array): SeqFileFormat;
+
 /**
  * EMBL / Swiss-Prot (UniProtKB) flat-file reader — sequence extraction only.
  *
@@ -213,7 +236,7 @@ declare function parseGff(input: string | Uint8Array): SeqRecord[];
  * Multiple-sequence-alignment readers — one aligned row = one record.
  *
  * Covers the common alignment formats: Clustal (`.aln`), Stockholm (`.sto`/`.stk`),
- * PHYLIP (`.phy`), NEXUS (`.nex`) and GCG/MSF (`.msf`). Each returns the alignment's rows
+ * PHYLIP (`.phy`), NEXUS (`.nex`), GCG/MSF (`.msf`) and MEGA (`.meg`). Each returns the alignment's rows
  * as {@link SeqRecord}s: `id` = the taxon/sequence name, `sequence` = that row **with its
  * gap characters preserved** (an aligned row is data; de-gapping is a caller's choice).
  * Only line spacing and wrap are removed. No description field — these formats don't carry
@@ -250,6 +273,37 @@ declare function parsePhylip(input: string | Uint8Array): SeqRecord[];
 declare function parseNexus(input: string | Uint8Array): SeqRecord[];
 /** Read a GCG/MSF (`.msf`) alignment (the sequence blocks after the header's `//`). */
 declare function parseMsf(input: string | Uint8Array): SeqRecord[];
+/**
+ * Read a MEGA (`.meg`) alignment / sequence set.
+ *
+ * MEGA files open with `#mega` (or `#MEGA`), carry `!Command …;` directives (Title/Format/…), then
+ * the sequences as `#Name residues` rows — interleaved (each name repeats per block) or with the
+ * residues wrapped onto following lines. Rows are accumulated by name. Gap `-` and the identity
+ * match-char `.` are kept verbatim (de-gapping is the caller's choice; note `.` means "same as the
+ * first sequence" in MEGA, like NEXUS). Deliberately lenient: never throws.
+ */
+declare function parseMega(input: string | Uint8Array): SeqRecord[];
+
+/**
+ * PDB (`.pdb`) reader — sequence extraction from `SEQRES` records.
+ *
+ * A PDB file lists each macromolecular chain's primary sequence in `SEQRES` records:
+ *   `SEQRES  <serNum> <chainID> <numRes>  <res1> <res2> … <res13>`
+ * with the residues as three-letter codes (13 per line, continued across records). This reader
+ * collects the SEQRES residues per chain, in file order, and maps the three-letter codes to the
+ * one-letter sequence: the 20 standard amino acids (+ SEC→U, PYL→O, the ambiguity codes B/Z/X),
+ * and nucleotides (DA/DC/DG/DT/DU and A/C/G/U/T/I/N). Anything unrecognized becomes `X`.
+ *   - id: the chain identifier (e.g. `A`).
+ *   - sequence: the chain's residues, one letter each (no gaps — SEQRES is the primary sequence).
+ *
+ * SEQRES is the declared sequence and is preferred. For a chain with no SEQRES record (common in
+ * coordinate-only files — predicted models, fragments), the sequence is reconstructed from the
+ * first model's `ATOM` records instead (one residue per chain + residue number), plus any `HETATM`
+ * whose residue is a recognized polymer/modified code (e.g. MSE selenomethionine) — solvent, ions
+ * and ligands are left out. Deliberately lenient (see AGENTS.md): never throws.
+ */
+
+declare function parsePdb(input: string | Uint8Array): SeqRecord[];
 
 /**
  * PIR / NBRF (`.pir`) reader — sequence extraction.
@@ -309,4 +363,34 @@ declare function parseBam(bytes: Uint8Array): SeqRecord[];
 
 declare function parseSam(input: string | Uint8Array): SeqRecord[];
 
-export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseBam, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGfa, parseGff, parseMsf, parseNexus, parsePhylip, parsePir, parseSam, parseStockholm, parseSwissprot };
+/**
+ * SCF (`.scf`) reader — the called base sequence from a Staden chromatogram trace.
+ *
+ * SCF (Standard Chromatogram Format) is a binary trace file. Only the **called bases** are
+ * extracted here (the trace samples/qualities are ignored — this library reads sequences):
+ *
+ *   Header (128 bytes, big-endian). The fields this reader uses:
+ *     off  field
+ *       0  magic ".scf"
+ *      12  bases          (uint32 — number of called bases)
+ *      24  bases_offset   (uint32 — start of the bases section)
+ *      36  version[4]     (ASCII, e.g. "2.00" / "3.00")
+ *      28  comments_size  (uint32)
+ *      32  comments_offset(uint32)
+ *
+ *   Bases section — two layouts by version:
+ *     • v3.x (column/SoA): peak indices (bases×uint32), then prob_A/C/G/T (bases bytes each),
+ *       then the **base characters** (bases bytes), then spare (bases×3). So the characters begin
+ *       at `bases_offset + bases*8`.
+ *     • v2.x (interleaved/AoS): `bases` records of 12 bytes each — peak_index(uint32),
+ *       prob_A/C/G/T(4), **base char(1)**, spare(3). The character of record i is at
+ *       `bases_offset + i*12 + 8`.
+ *
+ * The record id comes from a `NAME=` field in the comments section when present, else `"scf"`.
+ * Deliberately lenient (see AGENTS.md): never throws; returns `[]` for a truncated/unreadable
+ * file, and best-effort (whatever bases fit) for one truncated mid-section.
+ */
+
+declare function parseScf(input: string | Uint8Array): SeqRecord[];
+
+export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseAce, parseBam, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGfa, parseGff, parseMega, parseMsf, parseNexus, parsePdb, parsePhylip, parsePir, parseSam, parseScf, parseStockholm, parseSwissprot };

package/dist/index.d.ts

@@ -1,23 +1,5 @@
 export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, AbifChromatogramBundle, AbifDataChannelRole, AbifDecodedValue, AbifDirEntry, AbifDirectory, AbifEntry, AbifEntryRaw, AbifFile, AbifMetadata, ChannelSignals, Chromatogram, CropAbifOptions, CropAbifRange, ENTRY_SIZE, HEADER_SIZE, ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, insertEntrySorted, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif } from './abif/index.js';
 
-/**
- * Content-based file-format detection.
- *
- * Sniffs the bytes, never the file extension: binary magic first (ABIF at offset 0, or at
- * 128 behind a MacBinary preamble; SCF's ".scf" magic), then the first non-blank line for
- * the text formats. Text signatures are matched on the leading line's content (a keyword
- * like `LOCUS`, or the first character `>` / `;` / `@`), so a mislabeled or extension-less
- * file still resolves.
- */
-/** A format {@link detectFormat} can recognize. Some are detected before their reader ships. */
-type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'pir' | 'gff' | 'sam' | 'bam' | 'gfa' | 'unknown';
-/**
- * Detect the sequencing file format from its content. Returns 'unknown' when no signature
- * matches (empty input, or a leading line that is neither a known magic nor a recognized
- * text marker).
- */
-declare function detectFormat(bytes: Uint8Array): SeqFileFormat;
-
 /**
  * The common "a sequence with a name" record produced by every reader that extracts
  * sequences for downstream picking/export (GenBank, EMBL, Swiss-Prot, the alignment
@@ -38,6 +20,47 @@ interface SeqRecord {
 /** Build a {@link SeqRecord}, dropping an empty description so records compare cleanly. */
 declare function makeSeqRecord(id: string, description: string, sequence: string): SeqRecord;
 
+/**
+ * ACE (`.ace`) reader — assembly sequence extraction (Phrap/consed).
+ *
+ * An ACE file describes one or more contigs. Each contig is a `CO <name> <nBases> <nReads> …` line
+ * followed by the consensus sequence (wrapped over several lines), then per-read records
+ * `RD <readName> <nPaddedBases> …` each followed by that read's padded sequence. Other records
+ * (`AS`, `BQ`, `QA`, `AF`, `BS`, `DS`, `WA`, `CT`, `RT`, …) carry qualities/metadata and are skipped.
+ *
+ * This reader returns every sequence it finds, in file order:
+ *   - each contig consensus  → id `Contig<name>`, description `consensus`
+ *   - each read              → id `<readName>`,   description `read`
+ * The pad character `*` (an alignment gap in ACE) is kept verbatim — de-gapping is the caller's
+ * choice.
+ *
+ * A `CO`/`RD` header declares the block's exact base count, so the sequence is accumulated until that
+ * many residues are read (or a blank line ends it). This length-driven boundary — rather than
+ * "stop at the next two-letter tag" — avoids swallowing a following record and avoids truncating at a
+ * short residue line that merely looks like a tag (e.g. a line that is literally `BQ`/`CT`, both
+ * valid residues). Deliberately lenient (see AGENTS.md): never throws; a truncated final block is kept.
+ */
+
+declare function parseAce(input: string | Uint8Array): SeqRecord[];
+
+/**
+ * Content-based file-format detection.
+ *
+ * Sniffs the bytes, never the file extension: binary magic first (ABIF at offset 0, or at
+ * 128 behind a MacBinary preamble; SCF's ".scf" magic), then the first non-blank line for
+ * the text formats. Text signatures are matched on the leading line's content (a keyword
+ * like `LOCUS`, or the first character `>` / `;` / `@`), so a mislabeled or extension-less
+ * file still resolves.
+ */
+/** A format {@link detectFormat} can recognize. Some are detected before their reader ships. */
+type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'mega' | 'pir' | 'gff' | 'sam' | 'bam' | 'gfa' | 'pdb' | 'ace' | 'unknown';
+/**
+ * Detect the sequencing file format from its content. Returns 'unknown' when no signature
+ * matches (empty input, or a leading line that is neither a known magic nor a recognized
+ * text marker).
+ */
+declare function detectFormat(bytes: Uint8Array): SeqFileFormat;
+
 /**
  * EMBL / Swiss-Prot (UniProtKB) flat-file reader — sequence extraction only.
  *
@@ -213,7 +236,7 @@ declare function parseGff(input: string | Uint8Array): SeqRecord[];
  * Multiple-sequence-alignment readers — one aligned row = one record.
  *
  * Covers the common alignment formats: Clustal (`.aln`), Stockholm (`.sto`/`.stk`),
- * PHYLIP (`.phy`), NEXUS (`.nex`) and GCG/MSF (`.msf`). Each returns the alignment's rows
+ * PHYLIP (`.phy`), NEXUS (`.nex`), GCG/MSF (`.msf`) and MEGA (`.meg`). Each returns the alignment's rows
  * as {@link SeqRecord}s: `id` = the taxon/sequence name, `sequence` = that row **with its
  * gap characters preserved** (an aligned row is data; de-gapping is a caller's choice).
  * Only line spacing and wrap are removed. No description field — these formats don't carry
@@ -250,6 +273,37 @@ declare function parsePhylip(input: string | Uint8Array): SeqRecord[];
 declare function parseNexus(input: string | Uint8Array): SeqRecord[];
 /** Read a GCG/MSF (`.msf`) alignment (the sequence blocks after the header's `//`). */
 declare function parseMsf(input: string | Uint8Array): SeqRecord[];
+/**
+ * Read a MEGA (`.meg`) alignment / sequence set.
+ *
+ * MEGA files open with `#mega` (or `#MEGA`), carry `!Command …;` directives (Title/Format/…), then
+ * the sequences as `#Name residues` rows — interleaved (each name repeats per block) or with the
+ * residues wrapped onto following lines. Rows are accumulated by name. Gap `-` and the identity
+ * match-char `.` are kept verbatim (de-gapping is the caller's choice; note `.` means "same as the
+ * first sequence" in MEGA, like NEXUS). Deliberately lenient: never throws.
+ */
+declare function parseMega(input: string | Uint8Array): SeqRecord[];
+
+/**
+ * PDB (`.pdb`) reader — sequence extraction from `SEQRES` records.
+ *
+ * A PDB file lists each macromolecular chain's primary sequence in `SEQRES` records:
+ *   `SEQRES  <serNum> <chainID> <numRes>  <res1> <res2> … <res13>`
+ * with the residues as three-letter codes (13 per line, continued across records). This reader
+ * collects the SEQRES residues per chain, in file order, and maps the three-letter codes to the
+ * one-letter sequence: the 20 standard amino acids (+ SEC→U, PYL→O, the ambiguity codes B/Z/X),
+ * and nucleotides (DA/DC/DG/DT/DU and A/C/G/U/T/I/N). Anything unrecognized becomes `X`.
+ *   - id: the chain identifier (e.g. `A`).
+ *   - sequence: the chain's residues, one letter each (no gaps — SEQRES is the primary sequence).
+ *
+ * SEQRES is the declared sequence and is preferred. For a chain with no SEQRES record (common in
+ * coordinate-only files — predicted models, fragments), the sequence is reconstructed from the
+ * first model's `ATOM` records instead (one residue per chain + residue number), plus any `HETATM`
+ * whose residue is a recognized polymer/modified code (e.g. MSE selenomethionine) — solvent, ions
+ * and ligands are left out. Deliberately lenient (see AGENTS.md): never throws.
+ */
+
+declare function parsePdb(input: string | Uint8Array): SeqRecord[];
 
 /**
  * PIR / NBRF (`.pir`) reader — sequence extraction.
@@ -309,4 +363,34 @@ declare function parseBam(bytes: Uint8Array): SeqRecord[];
 
 declare function parseSam(input: string | Uint8Array): SeqRecord[];
 
-export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseBam, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGfa, parseGff, parseMsf, parseNexus, parsePhylip, parsePir, parseSam, parseStockholm, parseSwissprot };
+/**
+ * SCF (`.scf`) reader — the called base sequence from a Staden chromatogram trace.
+ *
+ * SCF (Standard Chromatogram Format) is a binary trace file. Only the **called bases** are
+ * extracted here (the trace samples/qualities are ignored — this library reads sequences):
+ *
+ *   Header (128 bytes, big-endian). The fields this reader uses:
+ *     off  field
+ *       0  magic ".scf"
+ *      12  bases          (uint32 — number of called bases)
+ *      24  bases_offset   (uint32 — start of the bases section)
+ *      36  version[4]     (ASCII, e.g. "2.00" / "3.00")
+ *      28  comments_size  (uint32)
+ *      32  comments_offset(uint32)
+ *
+ *   Bases section — two layouts by version:
+ *     • v3.x (column/SoA): peak indices (bases×uint32), then prob_A/C/G/T (bases bytes each),
+ *       then the **base characters** (bases bytes), then spare (bases×3). So the characters begin
+ *       at `bases_offset + bases*8`.
+ *     • v2.x (interleaved/AoS): `bases` records of 12 bytes each — peak_index(uint32),
+ *       prob_A/C/G/T(4), **base char(1)**, spare(3). The character of record i is at
+ *       `bases_offset + i*12 + 8`.
+ *
+ * The record id comes from a `NAME=` field in the comments section when present, else `"scf"`.
+ * Deliberately lenient (see AGENTS.md): never throws; returns `[]` for a truncated/unreadable
+ * file, and best-effort (whatever bases fit) for one truncated mid-section.
+ */
+
+declare function parseScf(input: string | Uint8Array): SeqRecord[];
+
+export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseAce, parseBam, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGfa, parseGff, parseMega, parseMsf, parseNexus, parsePdb, parsePhylip, parsePir, parseSam, parseScf, parseStockholm, parseSwissprot };

package/dist/index.js

@@ -1,14 +1,14 @@
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