Command-line reference#
Every command of the fasta-lake executable, generated from the code. The runner for a whole study, fasta-lake run, has its own page.
fasta-lake#
FASTA Lake: Sample-specific protein database construction for metaproteomics.
Usage:
Options:
Subcommands
- analyze-study: Export AnnData and run AlphaPeptTools QC, log2 PCA and optional replicate CV.
- annotate: Annotate selected proteins and inspect explicit annotation gaps.
- contaminants: Inspect or apply the contaminant database (v5.1).
- entrapment: Generate, inject and measure entrapment sequences.
- evidence-lake: Stage 1: Create evidence lake from peptide predictions.
- explore-study: EXPERIMENTAL: inspect annotated signal, coverage, diversity and CLR PCA.
- export: Prepare a FASTA for a specific search engine.
- extract-chunked: Build evidence in bounded reference pieces and merge before inference.
- extract-sample: Stage 2: Extract per-sample protein database.
- group-study: Group and quantify completed Sage searches (fasta-lake group-study --help).
- init: Generate an example fastalake.json configuration.
- lake-inspect: Query a lake provenance sidecar produced by lake-merge.
- lake-merge: Merge multiple source FASTAs into one lake with field-level annotation merge (v5.2).
- molecular: Prepare TPM inputs, select exact proteins and compare matched searches.
- network: Export peptide memberships and render experimental CKG network views.
- plan-resources: Show laptop planning choices without starting a workflow.
- quantify-study: Quantify completed study groups and retain peptide/ion support diagnostics.
- resources: Choose, size and download public reference databases and model weights.
- run: Run the whole study from an acquisition manifest (fasta-lake run --help).
- taxonomy: Export Unipept queries and plot its saved taxonomic assignments locally.
- validate: Validate a FASTA Lake JSON configuration file.
fasta-lake analyze-study#
Export AnnData and run AlphaPeptTools QC, log2 PCA and optional replicate CV.
Usage:
Options:
--groups DIRECTORY [required]
--out PATH [required]
--quantification DIRECTORY Completed quantify-study output; defaults to the
original group sums.
--metadata FILE TSV with one unique sample row per acquisition;
order is matched by name.
--replicate-column TEXT Metadata column defining replicate sets; blank
excludes.
--pca-samples FILE Optional sample roster, one acquisition
identifier per line.
--pca-features FILE Optional fixed group roster; all must be
complete within the PCA samples.
--help Show this message and exit.
fasta-lake annotate#
Annotate selected proteins and inspect explicit annotation gaps.
Usage:
Options:
Subcommands
- eggnog: Run eggNOG-mapper 2.1.12 with versioned inputs and complete coverage records.
- embed-unknown: Embed the recorded unknown roster; preserve every residue through windowing.
- study: Annotate a study's verified reporting representatives, with optional ESM-C.
fasta-lake annotate eggnog#
Run eggNOG-mapper 2.1.12 with versioned inputs and complete coverage records.
Usage:
Options:
--fasta FILE [required]
--out PATH [required]
--emapper FILE [required]
--emapper-python FILE
--data-dir DIRECTORY [required]
--threads INTEGER RANGE [default: 2; x>=1]
--sensitivity [sensitive|more-sensitive|very-sensitive]
[default: sensitive]
--tax-scope TEXT [default: auto]
--max-proteins INTEGER RANGE [default: 100000; x>=1]
--unknown-field [KEGG_ko|EC|GOs|PFAMs|COG_category|Description]
Unknown means no value in any selected
field; repeat to choose fields.
--embed-unknown After annotation, generate local ESM-C
vectors for its unknown proteins.
--model [esmc_300m|esmc_600m]
--checkpoint FILE Explicit local model weights; resources
download installs them separately.
--device [cpu|cuda]
--max-residues INTEGER RANGE [1<=x<=2046]
--help Show this message and exit.
fasta-lake annotate embed-unknown#
Embed the recorded unknown roster; preserve every residue through windowing.
Usage:
Options:
--annotation DIRECTORY [required]
--out PATH [required]
--model [esmc_300m|esmc_600m] [default: esmc_300m]
--device [cpu|cuda] [default: cpu]
--threads INTEGER RANGE [default: 2; x>=1]
--max-residues INTEGER RANGE [default: 1024; 1<=x<=2046]
--checkpoint FILE Explicit local model weight file; analysis
never downloads weights.
--help Show this message and exit.
fasta-lake annotate study#
Annotate a study's verified reporting representatives, with optional ESM-C.
Usage:
Options:
--groups DIRECTORY [required]
--settings FILE [required]
--out PATH [required]
--help Show this message and exit.
fasta-lake contaminants#
Inspect or apply the contaminant database (v5.1).
FastaLake bundles a minimal contaminant accession list (keratins,
trypsin, BSA, caseins, IgGs, etc.). Proteins matching this list are
tagged with a CON_ prefix; downstream FDR accounting can exclude
them via fasta_lake.contaminants.exclude_contaminants().
Usage:
Options:
Subcommands
- list: List the bundled contaminant accessions.
- tag: Scan a FASTA, prefix CON_ on headers matching the contaminant list.
fasta-lake contaminants list#
List the bundled contaminant accessions.
Usage:
Options:
fasta-lake contaminants tag#
Scan a FASTA, prefix CON_ on headers matching the contaminant list.
Usage:
Options:
-i, --input PATH Input FASTA to scan and tag. [required]
-o, --output PATH New output FASTA with CON_-prefixed headers; existing
files are refused. [required]
--contaminant-db PATH Optional extra contaminant list (text: 1
accession/line, or FASTA).
-v, --verbose
--help Show this message and exit.
fasta-lake entrapment#
Generate, inject and measure entrapment sequences.
Entrapment gives an FDR estimate independent of target-decoy: sequences known to be absent from the sample are put into the database, and anything that matches them is a false discovery.
WHERE entrapment is injected decides WHAT is being measured. Four points exist, earliest (hardest to survive) first: prelake into the input lake BEFORE the cohort evidence filter. Faces every curation step: the fullest construction test. prebuild onto the clustered lake, then RE-CLUSTERED at 97%, so entrapment must also survive clustering. preselect onto the clustered lake, no re-clustering (DEFAULT). Must be nominated by the sample's own de novo peptides. appended onto the finished per-sample database AFTER parsimony, entering untested. Measures SEARCH error, not construction.
prebuild and preselect are NOT the same stage under two names. All are legitimate, none are the same quantity, so these commands record the stage in every output and refuse to pool across stages or classes.
PREFIXES are not uniform in this repo: ENTRAP_PFUR_/ENTRAP_SHUF_/..., but
also ENTRAPHUMAN_ (SIHUMIx) and ENTRAPNN_ (near-neighbour), which do NOT
match ENTRAP_. A wrong pattern scores entrapment as target and drives the FDP
to zero silently. The default pattern is the common denominator ENTRAP;
check any lake with fasta-lake entrapment prefixes <fasta>.
Typical run: fasta-lake entrapment classes fasta-lake entrapment generate --class shuffled --source lake.fasta \ -o entrap.fasta fasta-lake entrapment inject -d lake.fasta -e entrap.fasta \ -o augmented.fasta --class shuffled # ... run the pipeline on augmented.fasta, then search ... fasta-lake entrapment fdp --results-dir results/ --target-fasta lake.fasta \ -o fdp/
Usage:
Options:
Subcommands
- classes: List entrapment classes with their difficulty and interpretation.
- fdp: Compute the FDP from search results, with n, median, IQR and bootstrap CI.
- generate: Produce an entrapment FASTA, deterministically.
- inject: Concatenate entrapment into a database and write a manifest.
- prefixes: Report the entrapment prefixes actually present in a FASTA.
- prepare: Generate + inject entrapment as configured by a fastalake.json.
fasta-lake entrapment classes#
List entrapment classes with their difficulty and interpretation.
The classes do NOT measure the same thing. Read the caveats before comparing any two numbers produced with different classes.
Usage:
Options:
fasta-lake entrapment fdp#
Compute the FDP from search results, with n, median, IQR and bootstrap CI.
Reports raw and conserved-corrected FDP together, and states how many samples were evaluable. A sample with no entrapment sequences in its searched database has an UNDEFINED FDP, not a zero, and is excluded rather than counted as 0.0.
Usage:
Options:
--results-dir PATH Directory of per-sample search results
(SAMPLE/results.sage.tsv or
SAMPLE/*/results.sage.tsv). [required]
-o, --output-dir PATH Output directory for the per-sample TSV and
the FDP record. [required]
--dataset TEXT Dataset/cohort name for the record.
--class TEXT Entrapment class. Read from the manifest
when present; an explicit value that
contradicts the manifest is refused.
--stage [prelake|prebuild|preselect|appended]
Injection stage. Read from the manifest when
present. Required if no manifest exists --
it will not be guessed.
--target-fasta PATH Target sequence space for the conserved-
peptide test. Every entrapment-attributed
peptide is checked for occurrence here (I/L
normalised, exact substring); those found
are genuinely conserved, not false
discoveries. Required for homologous classes
such as plant.
--no-conserved-check Skip the conserved-peptide correction and
report an explicitly UNCORRECTED FDP.
--normalize-il / --no-normalize-il
Treat I and L as equivalent when matching.
Default: on.
--q-threshold FLOAT FDR cutoff. Default 0.01.
--q-column TEXT FDR column. Default peptide_q.
--min-length INTEGER Peptide length floor. Default 9.
--entrap-prefix TEXT Header prefix identifying entrapment.
Defaults to what the manifest recorded, else
the class prefix. Set this when the run used
a non-standard convention such as
ENTRAPHUMAN_ or ENTRAPNN_ -- a wrong pattern
silently reports ~0% FDP.
--decoy-prefix TEXT Decoy tag, used only if the results have no
`label` column. SAGE writes rev_.
--db-pattern TEXT Glob (relative to a sample dir) for that
sample's searched FASTA, e.g.
'*_razor.fasta'. Enables per-sample database
partition sizes and the size-corrected
estimators.
--results-name TEXT Results filename, or
'<subdir>/results.sage.tsv' to choose one of
several entrapment runs inside a sample
directory.
--peptide-level Count distinct peptides instead of spectra.
--allow-mixed Permit pooling across injection stages or
classes. Produces a number that mixes
different quantities; use only deliberately.
--entrapment-seed INTEGER Seed for the bootstrap CI. Default 42.
--bootstrap-draws INTEGER Bootstrap draws. Default 2000.
-v, --verbose
--help Show this message and exit.
fasta-lake entrapment generate#
Produce an entrapment FASTA, deterministically.
Headers are tagged with the class prefix (ENTRAP_SHUF_, ENTRAP_PFUR_, ...) so downstream hits can be attributed. The same seed and input always produce a byte-identical file.
Usage:
Options:
--class TEXT Entrapment class (default: shuffled, the
recommended headline class). See `fasta-lake
entrapment classes`.
-i, --source PATH Source FASTA. Required for --class shuffled
(the sequences to shuffle -- normally the
lake you will inject into) and for classes
with no bundled default. Overrides the class
default.
-o, --output PATH Output entrapment FASTA. [required]
--entrapment-seed INTEGER Random seed; same seed gives a byte-
identical file. Default 42. Zero is
rejected.
-n, --n-proteins INTEGER Write only N proteins, chosen by seeded
subsample. Default: all.
--prefix TEXT Override the class header prefix (default:
the class's own).
--preserve-cleavage-sites / --no-preserve-cleavage-sites
Hold K/R in place when shuffling so tryptic
peptide lengths match the source. Default:
on.
-v, --verbose
--help Show this message and exit.
fasta-lake entrapment inject#
Concatenate entrapment into a database and write a manifest.
The manifest records the stage, the class, the seed, the entrapment:target ratio and the counts. Protein counts come from header lines only.
Usage:
Options:
-d, --database PATH Database to inject into. For the pre-
selection stages this is the lake that de
novo selection will run against; for
appended it is the finished per-sample
parsimony FASTA. [required]
-e, --entrapment PATH Entrapment FASTA from `entrapment generate`.
[required]
-o, --output PATH Augmented FASTA to write. [required]
--stage [prelake|prebuild|preselect|appended]
Injection stage, earliest first: prelake
(before the evidence filter), prebuild (re-
clustered with the lake), preselect
(default; clustered lake, no re-clustering),
appended (after parsimony). The first three
measure database-construction error and
differ by how much curation entrapment
survived; appended measures search error.
Recorded in the manifest so the result
cannot be misread later.
--class TEXT Entrapment class, recorded in the manifest
along with its difficulty and
interpretation.
--entrapment-seed INTEGER Seed used to generate the entrapment, for
the manifest.
--entrap-prefix TEXT Header prefix identifying entrapment.
Defaults to the class prefix, or ENTRAP when
no class is given. Recorded in the manifest
and reused by `entrapment fdp`.
--manifest PATH Manifest path (default:
entrapment_manifest.json beside output).
--no-checksums Skip SHA-256 of the inputs.
-v, --verbose
--help Show this message and exit.
fasta-lake entrapment prefixes#
Report the entrapment prefixes actually present in a FASTA.
Use this before computing an FDP on a database you did not build. A matcher configured for the wrong convention scores every entrapment record as target and drives the FDP toward zero, silently, with the run completing normally.
Usage:
Options:
--candidate TEXT Substring identifying an entrapment tag. Default ENTRAP.
--json Emit as JSON.
--help Show this message and exit.
fasta-lake entrapment prepare#
Generate + inject entrapment as configured by a fastalake.json.
This is the config-driven form of generate followed by inject. It is a
no-op when entrapment.enabled is false.
Usage:
Options:
-c, --config PATH FastaLake JSON config with an `entrapment` section.
[required]
-d, --database PATH Database to inject into (the lake de novo selection
runs against). [required]
-o, --output-dir PATH Directory for entrapment.fasta,
augmented_database.fasta and the manifest.
[required]
-v, --verbose
--help Show this message and exit.
fasta-lake evidence-lake#
Stage 1: Create evidence lake from peptide predictions.
Usage:
Options:
-d, --database PATH [required]
-p, --predictions PATH [required]
-o, --output PATH [required]
-s, --source-tag TEXT
--normalize-il / --no-normalize-il
--top-percent FLOAT
--output-hits PATH
-t, --threads INTEGER
-v, --verbose
--help Show this message and exit.
fasta-lake explore-study#
EXPERIMENTAL: inspect annotated signal, coverage, diversity and CLR PCA.
Usage:
Options:
--matrix FILE [required]
--annotations FILE [required]
--out PATH [required]
--level TEXT One declared annotation level, such as KO, EC
or genus. [required]
--metadata FILE
--group-column TEXT Explicitly request one-way PERMANOVA for this
metadata column.
--block-column TEXT Restrict label permutations to donor/repeated-
measure blocks.
--permutations INTEGER RANGE [default: 999; x>=1]
--seed INTEGER RANGE [default: 0; x>=0]
--backend [numpy|numba] [default: numpy]
--help Show this message and exit.
fasta-lake export#
Prepare a FASTA for a specific search engine.
Each engine has specific requirements: sage — adds GN= tags, no decoys (SAGE generates internal decoys) diann — gene name as first word of description (DIA-NN requirement) msfragger — adds GN= tags + reversed decoy sequences (rev_ prefix)
Usage:
Options:
-i, --input PATH Input inference FASTA from FastaLake
[required]
-o, --output PATH Engine-ready output FASTA [required]
-e, --engine [sage|diann|msfragger]
Target search engine [required]
--canonical PATH SwissProt FASTA for gene resolution (DIA-NN)
-v, --verbose
--help Show this message and exit.
fasta-lake extract-chunked#
Build evidence in bounded reference pieces and merge before inference.
Usage:
Options:
--database FILE [required]
--predictions PATH [required]
--out PATH [required]
--chunk-mib INTEGER RANGE Reference piece target in MiB; complete
records are never split. [default: 256;
x>=1]
--chunk-records INTEGER RANGE [default: 500000; x>=1]
--top-fraction FLOAT RANGE Rank predictions per sample before matching.
[default: 0.3; 0<x<=1]
--min-length INTEGER RANGE [default: 9; x>=1]
--max-length INTEGER RANGE [default: 50; x>=1]
--normalize-il / --no-normalize-il
[default: normalize-il]
--threads INTEGER RANGE [default: 1; x>=1]
--output-hits Also retain and merge all peptide hit rows.
--keep-pieces Keep selected piece FASTAs/tables after
merging; uses additional disk.
--help Show this message and exit.
fasta-lake extract-sample#
Stage 2: Extract per-sample protein database.
With -c/--config and entrapment.enabled: true, entrapment is injected into
the database before extraction (stage pre-selection), which is what makes an
entrapment hit a measurement of database-construction error rather than of
search error.
Usage:
Options:
-d, --database PATH [required]
-p, --predictions PATH [required]
-o, --output PATH [required]
-s, --source-tag TEXT
--normalize-il / --no-normalize-il
--output-hits PATH
-t, --threads INTEGER
-c, --config PATH FastaLake JSON config. When
`entrapment.enabled` is true and the stage
is pre-selection, entrapment is generated
and injected into --database first, so
entrapment competes for de novo nomination
exactly like a real sequence. A manifest is
written next to the augmented lake.
--entrapment-dir PATH Where to put the augmented lake and manifest
(default: <output>.entrapment/).
-v, --verbose
--help Show this message and exit.
fasta-lake group-study#
Group and quantify completed Sage searches (fasta-lake group-study --help).
Usage:
fasta-lake init#
Generate an example fastalake.json configuration.
Usage:
Options:
--template [minimal|clinical|metaproteomics|full]
Config template type
--help Show this message and exit.
fasta-lake lake-inspect#
Query a lake provenance sidecar produced by lake-merge.
Usage:
Options:
--accession TEXT Show record for a specific accession.
--conflicts-only Only show conflicting records.
--duplicates Only show records where ≥2 sources contributed the exact
same sequence (byte-identical collapse).
--summary Print aggregate counts instead of records.
--limit INTEGER Max records to print (default 20).
--help Show this message and exit.
fasta-lake lake-merge#
Merge multiple source FASTAs into one lake with field-level annotation merge (v5.2).
Example:
fasta-lake lake-merge \
--source SP=swissprot.fasta \
--source TR=trembl.fasta \
--source UH=uhgp.fasta \
-o lake.fasta --embed-sources
Usage:
Options:
--source TAG=PATH Source FASTA, e.g. --source SP=swissprot.fasta.
Repeatable. [required]
-o, --out-fasta PATH [required]
-p, --out-provenance PATH Output JSONL sidecar path. Defaults to <out-
fasta>.provenance.jsonl
--mode [merge|priority-win] merge = v5.2 field-level merge (default).
priority-win = legacy behaviour for regression
checks.
--priority TEXT Comma-separated tag priority, e.g. UH,SP,TR.
Default: SP,TR,UH,GM,GENCODE,GNOMAD,NCBI
--embed-sources Append [FLlake:sources=...] to FASTA headers
(opt-in).
--compress Gzip the provenance sidecar.
-v, --verbose
--help Show this message and exit.
fasta-lake molecular#
Prepare TPM inputs, select exact proteins and compare matched searches.
Usage:
Options:
Subcommands
- add: Keep a final de novo FASTA and append DNA/RNA/metabolite-supported proteins.
- compare: Compare exact proteins, accepted peptides and LFQ in two matched Sage searches.
- increments: List gained/lost peptide and protein support against one complete reference.
- prepare-source: Check and copy specimen inputs into a new portable source directory.
- select: Build a standalone molecular FASTA with an optional common background.
- validate-source: Check source hashes, gene agreement, annotation links and declared scope.
fasta-lake molecular add#
Keep a final de novo FASTA and append DNA/RNA/metabolite-supported proteins.
Usage:
Options:
--baseline FILE [required]
--source FILE [required]
--specimen TEXT Specimen matching the source manifest.
[required]
--out PATH [required]
--background FILE Identical target-only host/contaminant
background for compared arms.
--dna-percent FLOAT Top percent of positive available DNA genes;
zero disables. [default: 1.0]
--rna-percent FLOAT Top percent of positive available RNA genes;
zero disables. [default: 0]
--dna-absolute FLOAT Strict DNA TPM threshold; requires dna-
percent=0.
--rna-absolute FLOAT Strict RNA TPM threshold; requires rna-
percent=0.
--rank-rounding [floor|ceil] [default: floor]
--metabolites Also select through positive compounds and
direct reaction/KO links.
--help Show this message and exit.
fasta-lake molecular compare#
Compare exact proteins, accepted peptides and LFQ in two matched Sage searches.
Usage:
Options:
--left DIRECTORY [required]
--right DIRECTORY [required]
--out PATH [required]
--left-label TEXT [default: metaG]
--right-label TEXT [default: de_novo]
--peptide-q FLOAT [default: 0.01]
--protein-q FLOAT
--compress-tables Write overlap tables as gzip TSV.
--help Show this message and exit.
fasta-lake molecular increments#
List gained/lost peptide and protein support against one complete reference.
Usage:
Options:
--left DIRECTORY [required]
--right DIRECTORY [required]
--reference FILE Full declared target reference including the shared
host background. [required]
--host-reference FILE
--out PATH [required]
--left-label TEXT [default: de_novo]
--right-label TEXT [default: with_molecular]
--peptide-q FLOAT [default: 0.01]
--protein-q FLOAT
--help Show this message and exit.
fasta-lake molecular prepare-source#
Check and copy specimen inputs into a new portable source directory.
Usage:
Options:
--out PATH [required]
--specimen TEXT [required]
--reference-id TEXT [required]
--reference-scope [complete|available]
Available explicitly reports genes without
sequences and excludes them. [default:
complete]
--tpm FILE [required]
--proteins FILE [required]
--provenance FILE [required]
--alternate-proteins FILE
--annotations FILE
--metabolites FILE
--compound-links FILE
--help Show this message and exit.
fasta-lake molecular select#
Build a standalone molecular FASTA with an optional common background.
Usage:
Options:
--source FILE [required]
--specimen TEXT Specimen matching the source manifest.
[required]
--out PATH [required]
--background FILE Identical target-only host/contaminant
background for compared arms.
--dna-percent FLOAT Top percent of positive available DNA genes;
zero disables. [default: 0.0]
--rna-percent FLOAT Top percent of positive available RNA genes;
zero disables. [default: 0]
--dna-absolute FLOAT Strict DNA TPM threshold; requires dna-
percent=0.
--rna-absolute FLOAT Strict RNA TPM threshold; requires rna-
percent=0.
--rank-rounding [floor|ceil] [default: floor]
--metabolites Also select through positive compounds and
direct reaction/KO links.
--help Show this message and exit.
fasta-lake molecular validate-source#
Check source hashes, gene agreement, annotation links and declared scope.
Usage:
Options:
fasta-lake network#
Export peptide memberships and render experimental CKG network views.
Usage:
Options:
Subcommands
- eggnog: Attach eggNOG annotations by exact protein sequence; retain unknowns.
- export: Export complete accepted memberships from a group-study result.
- render: Create an experimental CKG report from a completed export.
fasta-lake network eggnog#
Attach eggNOG annotations by exact protein sequence; retain unknowns.
Usage:
Options:
--bundle DIRECTORY [required]
--annotation PATH Completed FastaLake annotation folder or native
eggNOG output. [required]
--fasta FILE Study representatives.fasta or a recorded
search FASTA. [required]
--query-fasta FILE Original annotation queries; required only for
native eggNOG output.
--out PATH [required]
--field TEXT Annotation namespace; repeat for multiple
namespaces. [default: KEGG_ko, EC, GOs, PFAMs]
--max-records INTEGER RANGE [default: 100000; x>=1]
--help Show this message and exit.
fasta-lake network export#
Export complete accepted memberships from a group-study result.
Usage:
Options:
--groups DIRECTORY [required]
--out PATH [required]
--max-rows INTEGER RANGE [default: 1000000; x>=1]
--max-edges INTEGER RANGE [default: 1000000; x>=1]
--help Show this message and exit.
fasta-lake network render#
Create an experimental CKG report from a completed export.
Usage:
Options:
--bundle DIRECTORY [required]
--out PATH [required]
--annotations DIRECTORY Checked network eggnog output to show in the
evidence view.
--ckg-python FILE Python executable from a compatible CKG
environment. [required]
--ckg-source DIRECTORY Optional CKG source checkout to use with that
environment.
--max-nodes INTEGER RANGE Limit the view; complete exported evidence is
retained. [default: 150; x>=2]
--max-edges INTEGER RANGE [default: 300; x>=1]
--help Show this message and exit.
fasta-lake plan-resources#
Show laptop planning choices without starting a workflow.
Usage:
Options:
--memory-budget-gib FLOAT
--memory-fraction FLOAT [default: 0.35]
--cpu-fraction FLOAT [default: 0.5]
--threads INTEGER RANGE [x>=1]
--chunk-mib INTEGER RANGE [x>=1]
--help Show this message and exit.
fasta-lake quantify-study#
Quantify completed study groups and retain peptide/ion support diagnostics.
Usage:
Options:
--groups DIRECTORY [required]
--out PATH [required]
--method [sum|directlfq] Quantify the same fixed study-group assignments.
[default: sum]
--threads INTEGER RANGE [default: 1; x>=1]
--skip-qc Explicitly omit automatic QC/PCA for a core-only
installation.
--help Show this message and exit.
fasta-lake resources#
Choose, size and download public reference databases and model weights.
Usage:
Options:
Subcommands
- download: Show the plan, then explicitly download one chosen resource; do not unpack.
- list: Show installed choices and dated sizes; this command is offline.
- plan: Show release, download bytes and disk needs without downloading data.
- unpack: Unpack archives into a new directory within an explicit disk budget.
fasta-lake resources download#
Show the plan, then explicitly download one chosen resource; do not unpack.
Usage:
Options:
--directory PATH [required]
--resume Resume an unchanged interrupted resource.
--help Show this message and exit.
fasta-lake resources list#
Show installed choices and dated sizes; this command is offline.
Usage:
Options:
fasta-lake resources plan#
Show release, download bytes and disk needs without downloading data.
Usage:
Options:
fasta-lake resources unpack#
Unpack archives into a new directory within an explicit disk budget.
Usage:
Options:
--directory PATH [required]
--max-gib FLOAT RANGE Maximum expanded disk bytes in GiB; original archives
also occupy disk. [x>0; required]
--help Show this message and exit.
fasta-lake run#
Run the whole study from an acquisition manifest (fasta-lake run --help).
Usage:
fasta-lake taxonomy#
Export Unipept queries and plot its saved taxonomic assignments locally.
Usage:
Options:
Subcommands
- prepare: Write canonical peptides for Unipept pept2lca --all --equate.
- prepare-reference: Experimental: export a selected FASTA for Unipept's native index builder.
- report: Render upstream sunburst/treemap/tree with explicit counts, signal and citations.
fasta-lake taxonomy prepare#
Write canonical peptides for Unipept pept2lca --all --equate.
Usage:
Options:
fasta-lake taxonomy prepare-reference#
Experimental: export a selected FASTA for Unipept's native index builder.
Usage:
Options:
--fasta FILE [required]
--out PATH [required]
--taxonomy-map FILE Explicit accession/ncbi_taxon_id TSV; unmapped
proteins stay unresolved.
--max-proteins INTEGER RANGE [default: 100000; x>=1]
--help Show this message and exit.
fasta-lake taxonomy report#
Render upstream sunburst/treemap/tree with explicit counts, signal and citations.
Usage:
Options:
--groups DIRECTORY [required]
--unipept-output FILE [required]
--out PATH [required]
--database TEXT Reference/version reported by the selected
Unipept server. [required]
--equate-il Declare that Unipept was run with --equate
(required).
--host-taxon-id INTEGER RANGE [default: 9606; x>=1]
--contaminant-peptides FILE Optional explicit reference: one unmodified
peptide per line.
--help Show this message and exit.
fasta-lake validate#
Validate a FASTA Lake JSON configuration file.
Usage:
Options: