Errors¶

Every error pyMzLib raises tells you whose problem it is, so you know whether to fix your call, retry later, or report a bug.

Exception	Whose problem	What to do
`UsageError`	Your call: a missing file, a malformed accession, a format without the view you asked for, an option without a value	Fix the call. Most are raised before any process starts.
`ServiceUnavailableError`	A remote service: PRIDE, UniProt or the Gene Ontology server was down, rate-limiting, timed out, or dropped the connection	Retry later. Not your bug, and not pyMzLib's.
`BridgeError`	mzLib: it read your input and failed, or rejected it. `error_type` is mzLib's own exception type, such as `MzLibException`	Read the message; it usually names the file and line. If it looks like a defect, report it.
`BridgeTimeoutError`	Time: the call ran past the `timeout` you gave	Give it longer, or a smaller input. pyMzLib will not guess whether the bridge was slow or stuck.
`ProjectNotFoundError`	The accession: PRIDE has no project by that name, or it has no files	Check the accession for a typo. Raised by `pymzlib.pride` only.
`BridgeNotFoundError`	The install: no bridge for this platform, or `PYMZLIB_BRIDGE` points at nothing	Reinstall the wheel; in a source checkout, build the bridge.

They nest, so you can catch as broadly or as narrowly as you like:

PyMzLibError                 every pyMzLib error
├── UsageError               your call
├── BridgeError              mzLib failed; .error_type says how
│   └── ServiceUnavailableError   a remote service failed: retry
├── BridgeTimeoutError
├── BridgeNotFoundError
└── pride.ProjectNotFoundError    no such PRIDE project

A typical pattern retries outages and reports everything else:

>>> import pymzlib
>>> try:
...     files = pymzlib.pride.list_files("PXD000001")
... except pymzlib.ServiceUnavailableError:
...     files = None          # PRIDE's problem; worth a retry
... except pymzlib.BridgeError as e:
...     raise SystemExit(f"{e.error_type}: {e}")
>>> len(files)
8

Every error, verb by verb¶

Each verb's spec lists the errors it can raise and when. They are collected here, so you can see in one place what a call can do wrong. The same tables appear on each verb's reference page. "Kind" is the bridge's language-neutral name for the error; "pyMzLib raises" is the Python exception.

`genes resolve` · `pymzlib.proteins.resolve_genes`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	neither or both of gtf and gene-set; a missing GTF, gene set or xref; any database-selection error proteins read raises
`correctness`	`BridgeError`	a GTF gene row without gene_id (InvalidDataException); an xref whose header is not Ensembl's nine columns; a compact gene table mzLib's reader refuses; a database mzLib cannot parse

Never raised: service_unavailable.

`isobaric kits` · `pymzlib.isobaric.kits`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	--kit blank, or not a name mzLib knows (the message lists the kits)
`correctness`	`BridgeError`	mzLib cannot build a kit from its embedded modifications (never at 0a808fec)

Never raised: service_unavailable.

`peptidoform convert` · `pymzlib.peptidoform.convert`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	no sequences on stdin; --from or --to not a registered format, or given without a value (the message lists the registered names); --mode not a SequenceConversionHandlingMode name; --threads 0 or below -1
`usage`	`UsageError`	--mode ThrowException and mzLib could not convert an input (the first in input order; the message names it and mzLib's reason)
`correctness`	`BridgeError`	mzLib threw something other than its SequenceConversionException (never seen at 0a808fec)

Never raised: service_unavailable.

`peptidoform fragments` · `pymzlib.peptidoform.fragments`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	accession missing or blank; UniProt answers 400 or 404 (no such entry); the entry holds no protein sequence; protease not in ProteaseDictionary; dissociation or terminus not an enum name; an integer option that is not an integer
`service_unavailable`	`ServiceUnavailableError`	UniProt unreachable by the bridge's own classification: a timeout (HttpClient 100 s), a socket or TLS failure, a request that never got a response, an HTTP 408, 429 or 5xx, or a body cut off in transit
`correctness`	`BridgeError`	any other UniProt status (e.g. 403); UniProt's ptmlist.txt or PSI-MOD.obo.xml missing from the bridge payload (FileNotFoundException: every protein would otherwise look unmodified or carry wrong charges); mzLib failing to parse the entry or to digest it

`pride download` · `pymzlib.pride.download`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	accession or dest missing or blank; category given but blank; ext given but naming no extension; names-from-stdin together with category or ext; names-from-stdin with no non-blank line on stdin
`usage`	`UsageError`	names-from-stdin naming a file the project's manifest does not contain (the message lists up to five). Raised AFTER the matching files have been downloaded: they are on disk when the error arrives.
`service_unavailable`	`ServiceUnavailableError`	the bridge's own classification (Program.ClassifyError; since mzLib 1.0.593 (#1350) PRIDE raises every transport failure as an HttpRequestException carrying the cause or the status, and messages name the file and host, never the URL): a timeout, a socket or TLS failure, an HTTP 408, 429 or 5xx on the manifest or a file, a body that delivered nothing for mzLib's BodyStallTimeout (2 min), or a body cut off in transit
`correctness`	`BridgeError`	a selected file has no HTTPS location (NotSupportedException; Aspera-only); a manifest file name that is not a bare leaf name (ArgumentException: refusing to write outside dest); any other HTTP status; a local disk failure while writing (a bare IOException, e.g. a full disk, is deliberately NOT treated as an outage)

`pride files` · `pymzlib.pride.list_files`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	accession missing or blank; page-size not an integer
`service_unavailable`	`ServiceUnavailableError`	the bridge's own classification (Program.ClassifyError; since mzLib 1.0.593 (#1350) PRIDE raises every transport failure as an HttpRequestException carrying the cause or the status, and messages name the file and host, never the URL): a timeout or cancellation, a socket failure, an HttpRequestException with no status but an inner cause (refused connection, DNS, TLS), an HTTP 408, 429 or 5xx, or a response body cut off in transit
`correctness`	`BridgeError`	any other HTTP status (e.g. 404), a paging contract violation (MzLibException: an identical page while total_records says more remain), the MaxPages backstop (an HttpRequestException mzLib composes with no status and no inner exception, which ClassifyHttpFailure deliberately does not excuse as an outage), or page-size <= 0 (mzLib's ArgumentOutOfRangeException; the bridge does not check it first)

`pride ftp-files` · `pymzlib.pride.list_ftp_files`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	accession missing or blank
`service_unavailable`	`ServiceUnavailableError`	the bridge's own classification (Program.ClassifyError; since mzLib 1.0.593 (#1350) PRIDE raises every transport failure as an HttpRequestException carrying the cause or the status, and messages name the file and host, never the URL): a timeout or cancellation, a socket failure, a request that never got a response (refused connection, DNS, TLS), an HTTP 408, 429 or 5xx on the project lookup or on any directory listing, or a body cut off in transit
`correctness`	`BridgeError`	no project has that accession, or it has no publication date to locate its directory (MzLibException; the bindings re-map it to their not-found error); a directory listing answering any other status; nesting deeper than 64 levels (MzLibException: the listing may be cyclic)

`pride search` · `pymzlib.pride.search`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	keyword missing or blank; keyword longer than 1000 characters; page-size not an integer or <= 0 (both checked by the bridge before mzLib)
`service_unavailable`	`ServiceUnavailableError`	the bridge's own classification (Program.ClassifyError; since mzLib 1.0.593 (#1350) PRIDE raises every transport failure as an HttpRequestException carrying the cause or the status, and messages name the file and host, never the URL): a timeout or cancellation, a socket failure, a request that never got a response (refused connection, DNS, TLS), an HTTP 408, 429 or 5xx, or a body cut off in transit
`correctness`	`BridgeError`	any other HTTP status; a paging contract violation (MzLibException: an identical page while total_records says more remain); the page limit (mzLib MaxPages) exceeded

`proteins annotate-go` · `pymzlib.proteins.annotate_go`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	a missing groups table, database, go.obo or category map; a FASTA database; out or categories-out not .tsv, naming an input, naming each other, or in a folder that does not exist; categories-out without category-map; a negative offset or limit. Every one is raised before any file is read.
`correctness`	`BridgeError`	the database cites a GO id the release lacks, without skip-unknown-go-ids (InvalidDataException naming every id); a go.obo mzLib cannot parse, including a truncated one whose edges name absent terms (InvalidDataException with the line); a category map it refuses; a group written twice with different members (InvalidDataException); a table or database it cannot parse

Never raised: service_unavailable.

`proteins classify-peptides` · `pymzlib.proteins.classify_peptides`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	no peptides; a peptide that is not non-empty A-Z (mzLib's ArgumentException, reclassified; the message names the peptide) - lower case and bracketed modifications included
`usage`	`UsageError`	on-error other than fail; any database-selection error proteins read raises; paths-stdin without the '--' line
`correctness`	`BridgeError`	a database mzLib cannot parse

Never raised: service_unavailable.

`proteins read` · `pymzlib.proteins.read`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	neither or both of path and paths-stdin; contaminant with paths-stdin; no paths on stdin; a blank or repeated path; a role other than target/contaminant; accessions-stdin with no accessions; paths-stdin with accessions-stdin but no '--' line
`usage`	`UsageError`	tables names something else; threads 0 or < -1; on-error not fail/skip; an option given without a value
`usage`	`UsageError`	a database not named .xml or a FASTA extension; a missing database (under skip: recorded in files[i].error with kind usage)
`correctness`	`BridgeError`	mzLib cannot parse a database (malformed XML); under skip, recorded with kind correctness

Never raised: service_unavailable.

`proteins update-go` · `pymzlib.proteins.update_go`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	the folder for go-obo does not exist
`service_unavailable`	`ServiceUnavailableError`	GO's PURL is unreachable, answers 408/429/5xx, or stalls for Loaders.GeneOntologyStallTimeout (2 min); any existing file is left untouched
`correctness`	`BridgeError`	a non-transient HTTP failure (e.g. 404); a downloaded file GeneOntologyGraph.Load refuses

`quant flashlfq` · `pymzlib.flashlfq.quantify`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	psms missing or blank; the PSM file not found; nothing on stdin; a stdin line with no path; a run that is not .mzML; an mzML not found; two runs sharing a base name; a design field that is not a non-negative integer
`usage`	`UsageError`	the PSM file names runs with no mzML on stdin (checked before any spectra are read; the message lists up to five); ppm, isotope-ppm, mbr-ppm or mbr-q not a number; threads not an integer
`correctness`	`BridgeError`	the PSM file is of a type mzLib cannot read as quantifiable results (MzLibException), or is malformed; an mzML fails to parse; the FlashLFQ engine fails

Never raised: service_unavailable.

`quant median-polish` · `pymzlib.flashlfq.median_polish`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	peptides missing or blank, or not found; the file empty; a required column (Sequence, Base Sequence, Protein Groups) missing; no Intensity_ columns; a sequence on two rows; an intensity cell that is not a number; a Detection Type_ cell that is not a FlashLFQ DetectionType name
`usage`	`UsageError`	a design line with no run name, a run named twice, or a replicate/fraction that is not a non-negative integer; design runs with no Intensity_ column; Intensity_ runs the design does not mention (a design must name every run and only those)
`correctness`	`BridgeError`	FlashLFQ's reconstruction or median polish fails

Never raised: service_unavailable.

`readers identify` · `pymzlib.readers.identify`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing, blank or not found; mzLib does not recognise the file type
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`usage`	`UsageError`	out with paths-stdin: identify returns no table

Never raised: service_unavailable.

`readers read-features` · `pymzlib.readers.read_features`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file or directory not found; mzLib does not recognise the file type (the message points at readers formats)
`usage`	`UsageError`	offset, limit or out given with no value; offset or limit < 0; non-integer value; out resolves to the same file as path
`usage`	`UsageError`	the file has no ms1_features view
`correctness`	`BridgeError`	mzLib recognises the file and fails to parse it
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`readers read-matches` · `pymzlib.readers.read_matches`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file or directory not found; mzLib does not recognise the file type (the message points at readers formats)
`usage`	`UsageError`	offset, limit or out given with no value; offset or limit < 0; non-integer value; out resolves to the same file as path
`usage`	`UsageError`	the file has no spectral_match view
`correctness`	`BridgeError`	mzLib recognises the file and fails to parse it
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`readers read-occupancy` · `pymzlib.readers.read_occupancy`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file or directory not found; mzLib does not recognise the file type (the message points at readers formats)
`usage`	`UsageError`	offset, limit or out given with no value; offset or limit < 0; non-integer value; out resolves to the same file as path
`usage`	`UsageError`	the file is not a MetaMorpheus protein-group table
`correctness`	`BridgeError`	mzLib cannot parse the table (MzLibException). A single malformed cell does NOT fail the read: it is named in failed_fields and gives no rows
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`readers read-protein-groups` · `pymzlib.readers.read_protein_groups`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file or directory not found; mzLib does not recognise the file type (the message points at readers formats)
`usage`	`UsageError`	offset, limit or out given with no value; offset or limit < 0; non-integer value; out resolves to the same file as path
`usage`	`UsageError`	the file is not a MetaMorpheus protein-group table (the message names what it is and points at read-records)
`correctness`	`BridgeError`	mzLib cannot parse the table (MzLibException)
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`readers read-quantified-peptides` · `pymzlib.readers.read_quantified_peptides`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file or directory not found; mzLib does not recognise the file type (the message points at readers formats)
`usage`	`UsageError`	offset, limit or out given with no value; offset or limit < 0; non-integer value; out resolves to the same file as path
`usage`	`UsageError`	the file is not a FlashLFQ peptide table
`correctness`	`BridgeError`	mzLib cannot parse the table (MzLibException)
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`readers read-records` · `pymzlib.readers.read_records`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file or directory not found
`usage`	`UsageError`	mzLib does not recognise the file type (the message points at readers formats)
`usage`	`UsageError`	offset, limit or out given with no value; offset or limit < 0; non-integer value; out resolves to the same file as path
`correctness`	`BridgeError`	the file is recognised but mzLib fails to parse it; the error type is mzLib's own (e.g. HeaderValidationException, MzLibException)
`correctness`	`BridgeError`	a vendor format that cannot load on this platform surfaces as its real failure (Bruker/timsTOF native DLLs are Windows x64 only)
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	with paths-stdin, inputs of more than one record type: refused before any file is parsed, naming the groups, whatever on-error says
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`readers read-results` · `pymzlib.readers.read_results`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file or directory not found; mzLib does not recognise the file type (the message points at readers formats)
`usage`	`UsageError`	offset, limit or out given with no value; offset or limit < 0; non-integer value; out resolves to the same file as path
`usage`	`UsageError`	the file has no quantifiable view (the message names the views it does have)
`correctness`	`BridgeError`	mzLib recognises the file and fails to parse it
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`readers read-spectra` · `pymzlib.readers.read_spectra`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; file not found; the file is not one of the seven spectra types (the message names the views it does have)
`usage`	`UsageError`	ms-order, offset, limit or out given with no value; ms-order < 1; offset or limit < 0; non-integer value
`usage`	`UsageError`	out resolves to the same file as path
`correctness`	`BridgeError`	a vendor format that cannot load on this platform surfaces as its real failure (Bruker/timsTOF native DLLs are Windows x64 only)
`usage`	`UsageError`	paths-stdin with path, offset or limit; paths-stdin with a value; no paths on stdin; a repeated path; threads 0 or below -1; on-error not fail or skip; on-error skip with a single path; out naming an input
`usage`	`UsageError`	with on-error fail, an input that is missing or not this view: the usage error of that input, prefixed 'Input ()'
`correctness`	`BridgeError`	with on-error fail, mzLib failing to parse an input: that input's own error type, message prefixed 'Input ()'
`usage`	`UsageError`	out (with path or paths-stdin) whose extension is not .tsv, any case, including none (PYB-1); checked before any input is opened
`usage`	`UsageError`	the answer is too large to return as one JSON document (PYB-3 part 1; measured: past the ~1.07 G-character .NET string ceiling, not RAM). Message: 'this read (N records) is too large to return as one document; use --limit/--offset or --out', N the parsed record_count

Never raised: service_unavailable.

`sdrf assess` · `pymzlib.sdrf.assess`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	as for sdrf validate (path / paths-stdin / threads / on-error rules, missing or repeated files)
`correctness`	`BridgeError`	mzLib cannot read a document

Never raised: service_unavailable.

`sdrf design` · `pymzlib.sdrf.design`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or the file does not exist
`usage`	`UsageError`	--out without a value, or not ending in .tsv (checked before the SDRF is read)
`usage`	`UsageError`	--condition-columns without a value, or with a blank name
`correctness`	`BridgeError`	mzLib cannot parse the SDRF at all, or the --out directory cannot be written

Never raised: service_unavailable.

`sdrf lint` · `pymzlib.sdrf.lint`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	stdin empty; a blank path; a file not found; some lines labelled and some not
`correctness`	`BridgeError`	mzLib cannot read one of the documents

Never raised: service_unavailable.

`sdrf parse-age` · `pymzlib.sdrf.parse_ages`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	stdin empty
`correctness`	`BridgeError`	never expected: TryParse does not throw

Never raised: service_unavailable.

`sdrf pool` · `pymzlib.sdrf.pool`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	stdin empty; a blank path; a file not found; some lines labelled and some not
`usage`	`UsageError`	offset or limit negative or not an integer
`correctness`	`BridgeError`	mzLib cannot read one of the documents

Never raised: service_unavailable.

`sdrf read` · `pymzlib.sdrf.read`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	path missing or blank; offset or limit negative or not an integer
`correctness`	`BridgeError`	mzLib cannot read the file (MzLibException for an empty or missing file)

Never raised: service_unavailable.

`sdrf samples` · `pymzlib.sdrf.samples`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	as for sdrf validate
`correctness`	`BridgeError`	mzLib cannot read a document

Never raised: service_unavailable.

`sdrf validate` · `pymzlib.sdrf.validate`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	neither or both of path and paths-stdin; stdin empty under paths-stdin; a repeated path
`usage`	`UsageError`	a file not found (under fail, checked before any document is read)
`usage`	`UsageError`	threads 0 or below -1 or not an integer; on-error not fail or skip, or given without a value; on-error skip with path
`correctness`	`BridgeError`	mzLib cannot read a document (MzLibException for an empty file); under fail, the lowest input position's failure is raised

Never raised: service_unavailable.

`stats adjust` · `pymzlib.stats.adjust`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	stdin empty; a line that is not a number (other than blank, NA, NaN); a p-value outside [0, 1] (mzLib's refusal, reclassified)
`correctness`	`BridgeError`	never expected

Never raised: service_unavailable.

`stats fit` · `pymzlib.stats.fit`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	responses or design missing, blank or not found; a table empty, header-only or with too few columns; a row whose field count differs from its header; an empty or repeated feature id, sample or coefficient name; a response cell that is not a number (other than blank, NA, NaN); a design cell that is not a finite number
`usage`	`UsageError`	the design's samples are not exactly the responses' sample columns (both differences are named); no coefficient on stdin, one named twice, or one not in the design; --spline-basis without --trend, or below 1; --threads 0 or below -1
`usage`	`UsageError`	mzLib refuses the input: the design is not of full column rank, or fewer than 2 features could be fitted, so no variance prior exists (mzLib's ArgumentException, reclassified)
`correctness`	`BridgeError`	never expected

Never raised: service_unavailable.

`stats meta` · `pymzlib.stats.meta`¶

Kind	pyMzLib raises	When
`usage`	`UsageError`	stdin empty; a line without exactly 3 tab-separated fields; an empty feature name; an estimate that is not a finite number; a standard error that is not finite and positive (mzLib's refusal, reclassified, naming the feature); --confidence not strictly between 0 and 1, or given without a value
`correctness`	`BridgeError`	never expected

Never raised: service_unavailable.

Errors¶

Every error, verb by verb¶

genes resolve · pymzlib.proteins.resolve_genes¶

isobaric kits · pymzlib.isobaric.kits¶

peptidoform convert · pymzlib.peptidoform.convert¶

peptidoform fragments · pymzlib.peptidoform.fragments¶

pride download · pymzlib.pride.download¶

pride files · pymzlib.pride.list_files¶

pride ftp-files · pymzlib.pride.list_ftp_files¶

pride search · pymzlib.pride.search¶

proteins annotate-go · pymzlib.proteins.annotate_go¶

proteins classify-peptides · pymzlib.proteins.classify_peptides¶

proteins read · pymzlib.proteins.read¶

proteins update-go · pymzlib.proteins.update_go¶

quant flashlfq · pymzlib.flashlfq.quantify¶

quant median-polish · pymzlib.flashlfq.median_polish¶

readers identify · pymzlib.readers.identify¶

readers read-features · pymzlib.readers.read_features¶

readers read-matches · pymzlib.readers.read_matches¶

readers read-occupancy · pymzlib.readers.read_occupancy¶

readers read-protein-groups · pymzlib.readers.read_protein_groups¶

readers read-quantified-peptides · pymzlib.readers.read_quantified_peptides¶

readers read-records · pymzlib.readers.read_records¶

readers read-results · pymzlib.readers.read_results¶

readers read-spectra · pymzlib.readers.read_spectra¶

sdrf assess · pymzlib.sdrf.assess¶

sdrf design · pymzlib.sdrf.design¶

sdrf lint · pymzlib.sdrf.lint¶

sdrf parse-age · pymzlib.sdrf.parse_ages¶

sdrf pool · pymzlib.sdrf.pool¶

sdrf read · pymzlib.sdrf.read¶

sdrf samples · pymzlib.sdrf.samples¶

sdrf validate · pymzlib.sdrf.validate¶

stats adjust · pymzlib.stats.adjust¶

stats fit · pymzlib.stats.fit¶

stats meta · pymzlib.stats.meta¶

`genes resolve` · `pymzlib.proteins.resolve_genes`¶

`isobaric kits` · `pymzlib.isobaric.kits`¶

`peptidoform convert` · `pymzlib.peptidoform.convert`¶

`peptidoform fragments` · `pymzlib.peptidoform.fragments`¶

`pride download` · `pymzlib.pride.download`¶

`pride files` · `pymzlib.pride.list_files`¶

`pride ftp-files` · `pymzlib.pride.list_ftp_files`¶

`pride search` · `pymzlib.pride.search`¶

`proteins annotate-go` · `pymzlib.proteins.annotate_go`¶

`proteins classify-peptides` · `pymzlib.proteins.classify_peptides`¶

`proteins read` · `pymzlib.proteins.read`¶

`proteins update-go` · `pymzlib.proteins.update_go`¶

`quant flashlfq` · `pymzlib.flashlfq.quantify`¶

`quant median-polish` · `pymzlib.flashlfq.median_polish`¶

`readers identify` · `pymzlib.readers.identify`¶

`readers read-features` · `pymzlib.readers.read_features`¶

`readers read-matches` · `pymzlib.readers.read_matches`¶

`readers read-occupancy` · `pymzlib.readers.read_occupancy`¶

`readers read-protein-groups` · `pymzlib.readers.read_protein_groups`¶

`readers read-quantified-peptides` · `pymzlib.readers.read_quantified_peptides`¶

`readers read-records` · `pymzlib.readers.read_records`¶

`readers read-results` · `pymzlib.readers.read_results`¶

`readers read-spectra` · `pymzlib.readers.read_spectra`¶

`sdrf assess` · `pymzlib.sdrf.assess`¶

`sdrf design` · `pymzlib.sdrf.design`¶

`sdrf lint` · `pymzlib.sdrf.lint`¶

`sdrf parse-age` · `pymzlib.sdrf.parse_ages`¶

`sdrf pool` · `pymzlib.sdrf.pool`¶

`sdrf read` · `pymzlib.sdrf.read`¶

`sdrf samples` · `pymzlib.sdrf.samples`¶

`sdrf validate` · `pymzlib.sdrf.validate`¶

`stats adjust` · `pymzlib.stats.adjust`¶

`stats fit` · `pymzlib.stats.fit`¶

`stats meta` · `pymzlib.stats.meta`¶