Module sequencing 

Sequence-based species identification for Mycobacteriaceae.

Generation of species identification databases

The database sequences are flagged as type material using the INSD Collaboration type_material qualifier. Type material ties formal species names to physical specimens (culture collections for prokaryotes, museum or herbarium specimens for eukaryotes), as annotated in the NCBI Taxonomy Database.

See fn fetch_myco_sequences() in build.rs for details on how the sequences were fetched from NCBI at build time.

myco_erm41.fasta is generated at build time but unused; erm41 identification uses per-subspecies references (erm41_abscessus_ATCC_19977.fasta, erm41_bolletii_CIP_108541.fasta, erm41_massiliense_CCUG_48898.fasta) instead.

Re-exports

pub use batch::SampleSusceptibilityRecord;

Modules

batch

bed

erm41

hsp65

ntfy_notify

pnca

rpob

rrl

rrs

serde_helpers

tb_data

Structs

Ab1Channels

Parsed channel intensity data from an AB1 chromatogram.

Erm41ViewState

Chromatogram display parameters for the erm(41) region.

GappedAlignment

Alignment result from align_to_ref: gapped strings plus reference start position.

RrlNtmViewState

Chromatogram display parameters for the rrl / NTM macrolide-resistance region.

SeqData

Top-level result for a processed AB1 read.

SeqIdHit

Best-hit result from aligning an AB1 read against the reference sequences.

SusceptibilityCalls

Susceptibility calls derived from AB1 capillary sequencing, keyed by gene target.

Constants

ACC_GASTRI 🔒

ACC_KANSASII 🔒

ACC_MARINUM 🔒

ACC_ULCERANS 🔒

DESC_ABSCESSUS

DESC_BOLLETII

DESC_MASSILIENSE

ERM41_ANCHOR_L 🔒

ERM41_ANCHOR_R 🔒

ERM41_FWD_END 🔒

ERM41_FWD_START 🔒

KANSASII_GASTRI_ACCS 🔒

MARINUM_ULCERANS_ACCS 🔒

MIN_PNCA_REF_LEN 🔒

MIN_RPOB_REF_LEN 🔒

MIN_RRL_REF_LEN 🔒

MIN_RRS_REF_LEN 🔒

MIN_SEQ_ID_IDENTITY

PDF_COL_HEADERS 🔒

PDF_COL_X 🔒

PDF_MARGIN_B 🔒

PDF_MARGIN_L 🔒

PDF_MARGIN_T 🔒

PDF_PAGE_H 🔒

PDF_PAGE_W 🔒

PDF_ROW_H 🔒

PDF_TABLE_W 🔒

PNCA_FWD_END 🔒

PNCA_FWD_START 🔒

REF_ERM41_ABSCESSUS 🔒

REF_ERM41_BOLLETII 🔒

REF_ERM41_MASSILENSE 🔒

REF_MYCO_HSP65 🔒

hsp65 / groEL2 reference sequences — Mycobacteriaceae type strains, fetched from NCBI at build time.

REF_MYCO_RPOB 🔒

rpoB reference sequences — Mycobacteriaceae type strains, fetched from NCBI at build time.

REF_MYCO_RRL 🔒

23S rRNA (rrl) reference sequences — Mycobacteriaceae type strains, fetched from NCBI at build time.

REF_MYCO_RRS 🔒

16S rRNA (rrs) reference sequences — Mycobacteriaceae type strains, fetched from NCBI at build time.

REF_PNCA 🔒

pncA CDS + 50bp upstream promoter flank for each M. tuberculosis complex member with a distinct reference sequence, fetched from NCBI at build time (see pnca module docs). Concatenated into one multi-FASTA so identify_sequence_pnca() can search all of them via parse_multi_fasta, the same way identify_sequence_rrl_ntm() searches REF_MYCO_RRL.

RRL_ANCHOR_L 🔒

RRL_ANCHOR_R 🔒

Functions

align_to_ref

Align query (Sanger read) against reference (gene sequence) using semiglobal Smith-Waterman (free reference end-gaps, full query placed within reference).

base_at_ref_pos

Return the query base at a given reference position, or None if the position is outside the aligned region or the query has a deletion ('-') there.

build_report_pdf

Build a landscape A4 PDF report from AB1 scan records. Filtered to gene-identified records with identity ≥ MIN_SEQ_ID_IDENTITY, same as the CSV output, and to samples no older than report_max_age_days (see TBConfig::report_max_age_days).

dedup_substring_same_desc 🔒

Within each description group, remove entries whose sequence (uppercased) is a contiguous substring of a longer entry that shares the same description. Longer entries survive; the shorter entries are redundant for alignment purposes because the aligner will find the same best position inside the longer reference.

format_pairwise_alignment 🔒

parse_ab1_quality

Tries edited quality scores (PCON tag 2) first, falling back to raw (PCON tag 1). Each byte is a Phred quality score corresponding to the base at the same index in PBAS.

parse_ab1_sequence

Tries the edited basecalls (PBAS tag 2) first, falling back to raw basecalls (PBAS tag 1).

parse_fasta_seq 🔒

Parse a FASTA string, returning just the sequence bytes (ignores header).

parse_multi_fasta 🔒

Parse a multi-FASTA string into (accession, description, sequence) tuples.

pdf_current_date 🔒

pdf_days_to_ymd 🔒

pdf_hline 🔒

pdf_sus 🔒

pdf_truncate 🔒

pdf_write_row 🔒

reverse_complement

scan_window 🔒

trim_start_end

Trim a basecall sequence to the amplicon region defined by a primer pair.

trim_to_min_quality

Trim leading and trailing low-quality bases using a sliding-window average.