识别网 export

gmeta net build turns profiler output into the 国家致病菌识别网 "混合样本" submission workbook.

The output

Two sheets per workbook:

混合样本 — the template-exact eight columns:

样本名称	属中文名	属序列数	属相对丰度	种中文名	种序列数	种基因组覆盖度	种相对丰度

样本名称 is written only on each sample's first row (template style); abundances are percent strings (48.23%), coverage is a 0–100 float.

审核明细 — latin names, TaxID, accession, reference path/length, mean depth, 1x coverage: everything the submission sheet intentionally omits.

Examples

# kraken2 kreports, auto-detected
gmeta net build kraken/*.report -o 识别网上报.xlsx --split-dir result/

# mixed tools in one batch — each file sniffed independently
gmeta net build kraken/a.report centrifuge/b.txt kmcp/c.tsv -o 识别网上报.xlsx

# with 种基因组覆盖度
gmeta net build kraken/*.report \
  --reads-dir raw_reads --manifest ref_genome_manifest.csv \
  -o 识别网上报.xlsx --split-dir result/ --details coverage_details.tsv

Semantics per profiler

Profiler	属序列数 source	种相对丰度 source
kraken2 kreport	genus clade row (real counts)	kreport percentage
centrifuge native	genus rows in the report	abundance column
kaiju (+--kaiju-genus)	genus kaiju2table	percent column
metaphlan	g__ rows	relative_abundance
kmcp	species aggregation (per-reference format)	percentage (aggregated)

When a profiler has no genus rows (kmcp, kaiju without the genus table), genus counts are aggregated from that genus' species rows — the honest estimate the format allows.

Missing references leave the coverage cell blank and print the taxids; the rows themselves are still emitted.

Options

Flag	Meaning
--profiler	force the format (auto/kraken2/bracken/centrifuge/kaiju/metaphlan/kmcp/sylph)
--kaiju-genus	kaiju2table genus table for real genus counts
--top	species rows per sample (default 10)
--reads-dir + --reads-pattern	raw reads for coverage
--manifest / --ref-dir	reference genomes
--split-dir	one workbook per sample
--details	extra coverage TSV
--per-species	independent per-reference alignment (exact, slower)
--min-depths	coverage thresholds (default 1,5,10)
--preset	minimap2 read preset: sr / map-ont / map-pb