Pyteomics documentation v4.7.3

idxml - idXML file reader

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idxml - idXML file reader

Summary

idXML is a format specified in the OpenMS project. It defines a list of peptide identifications.

This module provides a minimalistic way to extract information from idXML files. You can use the old functional interface (read()) or the new object-oriented interface (IDXML) to iterate over entries in <PeptideIdentification> elements. Note that each entry can contain more than one PSM (peptide-spectrum match). They are accessible with 'PeptideHit' key. IDXML objects also support direct indexing by element ID.

Data access

IDXML - a class representing a single idXML file. Other data access functions use this class internally.

read() - iterate through peptide-spectrum matches in an idXML file. Data from a single PSM group are converted to a human-readable dict. Basically creates an IDXML object and reads it.

chain() - read multiple files at once.

chain.from_iterable() - read multiple files at once, using an iterable of files.

DataFrame() - read idXML files into a pandas.DataFrame.

Target-decoy approach

filter() - read a chain of idXML files and filter to a certain FDR using TDA.

filter.chain() - chain a series of filters applied independently to several files.

filter.chain.from_iterable() - chain a series of filters applied independently to an iterable of files.

filter_df() - filter idXML files and return a pandas.DataFrame.

is_decoy() - determine if a “SpectrumIdentificationResult” should be consiudered decoy.

fdr() - estimate the false discovery rate of a set of identifications using the target-decoy approach.

qvalues() - get an array of scores and local FDR values for a PSM set using the target-decoy approach.

Deprecated functions

version_info() - get information about idXML version and schema. You can just read the corresponding attribute of the IDXML object.

get_by_id() - get an element by its ID and extract the data from it. You can just call the corresponding method of the IDXML object.

iterfind() - iterate over elements in an idXML file. You can just call the corresponding method of the IDXML object.

Dependencies

This module requires lxml.

pyteomics.openms.idxml.version_info(source)

Provide version information about the idXML file.

Note

This function is provided for backward compatibility only. It simply creates an IDXML instance and returns its version_info attribute.

Parameters:

source (str or file) – File name or file-like object.

Returns:

out – A (version, schema URL) tuple, both elements are strings or None.

Return type:

tuple

pyteomics.openms.idxml.fdr(psms=None, formula=1, is_decoy=None, ratio=1, correction=0, pep=None, decoy_prefix='DECOY_', decoy_suffix=None)

Estimate FDR of a data set using TDA or given PEP values. Two formulas can be used. The first one (default) is:

\[FDR = \frac{N_{decoy}}{N_{target} * ratio}\]

The second formula is:

\[FDR = \frac{N_{decoy} * (1 + \frac{1}{ratio})}{N_{total}}\]

Note

This function is less versatile than qvalues(). To obtain FDR, you can call qvalues() and take the last q-value. This function can be used (with correction = 0 or 1) when numpy is not available.

Parameters:

  • psms (iterable, optional) – An iterable of PSMs, e.g. as returned by read(). Not needed if is_decoy is an iterable.

  • formula (int, optional) – Can be either 1 or 2, defines which formula should be used for FDR estimation. Default is 1.

  • is_decoy (callable, iterable, or str, optional) –

    If callable, should accept exactly one argument (PSM) and return a truthy value if the PSM is considered decoy. Default is is_decoy(). If array-like, should contain float values for all given PSMs. If string, it is used as a field name (PSMs must be in a record array or a pandas.DataFrame).

    Warning

    The default function may not work with your files, because format flavours are diverse.

  • decoy_prefix (str, optional) – If the default is_decoy function works for you, this parameter specifies which protein name prefix to use to detect decoy matches. If you provide your own is_decoy, or if you specify decoy_suffix, this parameter has no effect. Default is “DECOY_”.

  • decoy_suffix (str, optional) – If the default is_decoy function works for you, this parameter specifies which protein name suffix to use to detect decoy matches. If you provide your own is_decoy, this parameter has no effect. Mutually exclusive with decoy_prefix.

  • pep (callable, iterable, or str, optional) –

    If callable, a function used to determine the posterior error probability (PEP). Should accept exactly one argument (PSM) and return a float. If array-like, should contain float values for all given PSMs. If string, it is used as a field name (PSMs must be in a record array or a pandas.DataFrame).

    Note

    If this parameter is given, then PEP values will be used to calculate FDR. Otherwise, decoy PSMs will be used instead. This option conflicts with: is_decoy, formula, ratio, correction.

  • ratio (float, optional) – The size ratio between the decoy and target databases. Default is 1. In theory, the “size” of the database is the number of theoretical peptides eligible for assignment to spectra that are produced by in silico cleavage of that database.

  • correction (int or float, optional) –

    Possible values are 0, 1 and 2, or floating point numbers between 0 and 1.

    0 (default): no correction;

    1: enable “+1” correction. This accounts for the probability that a false positive scores better than the first excluded decoy PSM;

    2: this also corrects that probability for finite size of the sample, so the correction will be slightly less than “+1”.

    If a floating point number is given, then instead of the expectation value for the number of false PSMs, the confidence value is used. The value of correction is then interpreted as desired confidence level. E.g., if correction=0.95, then the calculated q-values do not exceed the “real” q-values with 95% probability.

    See this paper for further explanation.

    Note

    Requires numpy, if correction is a float or 2.

    Note

    Correction is only needed if the PSM set at hand was obtained using TDA filtering based on decoy counting (as done by using filter() without correction).

Returns:

out – The estimation of FDR, (roughly) between 0 and 1.

Return type:

float

pyteomics.openms.idxml.qvalues(*args, **kwargs)

Read args and return a NumPy array with scores and q-values. q-values are calculated either using TDA or based on provided values of PEP.

Requires numpy (and optionally pandas).

Parameters:

  • args (positional) – Files to read PSMs from. All positional arguments are treated as files. The rest of the arguments must be named.

  • key (callable / array-like / iterable / str, keyword only, optional) –

    If callable, a function used for sorting of PSMs. Should accept exactly one argument (PSM) and return a number (the smaller the better). If array-like, should contain scores for all given PSMs. If string, it is used as a field name (PSMs must be in a record array or a DataFrame).

    Warning

    The default function may not work with your files, because format flavours are diverse.

  • reverse (bool, keyword only, optional) – If True, then PSMs are sorted in descending order, i.e. the value of the key function is higher for better PSMs. Default is False.

  • is_decoy (callable / array-like / iterable / str, keyword only, optional) –

    If callable, a function used to determine if the PSM is decoy or not. Should accept exactly one argument (PSM) and return a truthy value if the PSM should be considered decoy. If array-like, should contain boolean values for all given PSMs. If string, it is used as a field name (PSMs must be in a record array or a DataFrame).

    Warning

    The default function may not work with your files, because format flavours are diverse.

  • decoy_prefix (str, optional) – If the default is_decoy function works for you, this parameter specifies which protein name prefix to use to detect decoy matches. If you provide your own is_decoy, or if you specify decoy_suffix, this parameter has no effect. Default is “DECOY_”.

  • decoy_suffix (str, optional) – If the default is_decoy function works for you, this parameter specifies which protein name suffix to use to detect decoy matches. If you provide your own is_decoy, this parameter has no effect. Mutually exclusive with decoy_prefix.

  • pep (callable / array-like / iterable / str, keyword only, optional) –

    If callable, a function used to determine the posterior error probability (PEP). Should accept exactly one argument (PSM) and return a float. If array-like, should contain float values for all given PSMs. If string, it is used as a field name (PSMs must be in a record array or a DataFrame).

    Note

    If this parameter is given, then PEP values will be used to calculate q-values. Otherwise, decoy PSMs will be used instead. This option conflicts with: is_decoy, remove_decoy, formula, ratio, correction. key can still be provided. Without key, PSMs will be sorted by PEP.

  • remove_decoy (bool, keyword only, optional) –

    Defines whether decoy matches should be removed from the output. Default is False.

    Note

    If set to False, then by default the decoy PSMs will be taken into account when estimating FDR. Refer to the documentation of fdr() for math; basically, if remove_decoy is True, then formula 1 is used to control output FDR, otherwise it’s formula 2. This can be changed by overriding the formula argument.

  • formula (int, keyword only, optional) – Can be either 1 or 2, defines which formula should be used for FDR estimation. Default is 1 if remove_decoy is True, else 2 (see fdr() for definitions).

  • ratio (float, keyword only, optional) – The size ratio between the decoy and target databases. Default is 1. In theory, the “size” of the database is the number of theoretical peptides eligible for assignment to spectra that are produced by in silico cleavage of that database.

  • correction (int or float, keyword only, optional) –

    Possible values are 0, 1 and 2, or floating point numbers between 0 and 1.

    0 (default): no correction;

    1: enable “+1” correction. This accounts for the probability that a false positive scores better than the first excluded decoy PSM;

    2: this also corrects that probability for finite size of the sample, so the correction will be slightly less than “+1”.

    If a floating point number is given, then instead of the expectation value for the number of false PSMs, the confidence value is used. The value of correction is then interpreted as desired confidence level. E.g., if correction=0.95, then the calculated q-values do not exceed the “real” q-values with 95% probability.

    See this paper for further explanation.

  • q_label (str, optional) – Field name for q-value in the output. Default is 'q'.

  • score_label (str, optional) – Field name for score in the output. Default is 'score'.

  • decoy_label (str, optional) – Field name for the decoy flag in the output. Default is 'is decoy'.

  • pep_label (str, optional) – Field name for PEP in the output. Default is 'PEP'.

  • full_output (bool, keyword only, optional) – If True, then the returned array has PSM objects along with scores and q-values. Default is False.

  • **kwargs (passed to the chain() function.)

Returns:

out – A sorted array of records with the following fields:

  • ’score’: np.float64

  • ’is decoy’: np.bool_

  • ’q’: np.float64

  • ’psm’: np.object_ (if full_output is True)

Return type:

numpy.ndarray

pyteomics.openms.idxml.chain(*sources, **kwargs)

Chain IDXML for several sources into a single iterable. Positional arguments should be sources like file names or file objects. Keyword arguments are passed to the IDXML function.

Parameters:

  • sources (Iterable) – Sources for creating new sequences from, such as paths or file-like objects

  • kwargs (Mapping) – Additional arguments used to instantiate each sequence

chain.from_iterable(files, **kwargs)

Chain read() for several files. Keyword arguments are passed to the read() function.

Parameters:

files – Iterable of file names or file objects.

pyteomics.openms.idxml.filter(*args, **kwargs)

Read args and yield only the PSMs that form a set with estimated false discovery rate (FDR) not exceeding fdr.

Requires numpy and, optionally, pandas.

Parameters:

  • args (positional) – Files to read PSMs from. All positional arguments are treated as files. The rest of the arguments must be named.

  • fdr (float, keyword only, 0 <= fdr <= 1) – Desired FDR level.

  • key (callable / array-like / iterable / str, keyword only, optional) –

    A function used for sorting of PSMs. Should accept exactly one argument (PSM) and return a number (the smaller the better). The default is a function that tries to extract e-value from the PSM.

    Warning

    The default function may not work with your files, because format flavours are diverse.

  • reverse (bool, keyword only, optional) – If True, then PSMs are sorted in descending order, i.e. the value of the key function is higher for better PSMs. Default is False.

  • is_decoy (callable / array-like / iterable / str, keyword only, optional) –

    A function used to determine if the PSM is decoy or not. Should accept exactly one argument (PSM) and return a truthy value if the PSM should be considered decoy.

    Warning

    The default function may not work with your files, because format flavours are diverse.

  • decoy_prefix (str, optional) – If the default is_decoy function works for you, this parameter specifies which protein name prefix to use to detect decoy matches. If you provide your own is_decoy, or if you specify decoy_suffix, this parameter has no effect. Default is “DECOY_”.

  • decoy_suffix (str, optional) – If the default is_decoy function works for you, this parameter specifies which protein name suffix to use to detect decoy matches. If you provide your own is_decoy, this parameter has no effect. Mutually exclusive with decoy_prefix.

  • remove_decoy (bool, keyword only, optional) –

    Defines whether decoy matches should be removed from the output. Default is True.

    Note

    If set to False, then by default the decoy PSMs will be taken into account when estimating FDR. Refer to the documentation of fdr() for math; basically, if remove_decoy is True, then formula 1 is used to control output FDR, otherwise it’s formula 2. This can be changed by overriding the formula argument.

  • formula (int, keyword only, optional) – Can be either 1 or 2, defines which formula should be used for FDR estimation. Default is 1 if remove_decoy is True, else 2 (see fdr() for definitions).

  • ratio (float, keyword only, optional) – The size ratio between the decoy and target databases. Default is 1. In theory, the “size” of the database is the number of theoretical peptides eligible for assignment to spectra that are produced by in silico cleavage of that database.

  • correction (int or float, keyword only, optional) –

    Possible values are 0, 1 and 2, or floating point numbers between 0 and 1.

    0 (default): no correction;

    1: enable “+1” correction. This accounts for the probability that a false positive scores better than the first excluded decoy PSM;

    2: this also corrects that probability for finite size of the sample, so the correction will be slightly less than “+1”.

    If a floating point number is given, then instead of the expectation value for the number of false PSMs, the confidence value is used. The value of correction is then interpreted as desired confidence level. E.g., if correction=0.95, then the calculated q-values do not exceed the “real” q-values with 95% probability.

    See this paper for further explanation.

  • pep (callable / array-like / iterable / str, keyword only, optional) –

    If callable, a function used to determine the posterior error probability (PEP). Should accept exactly one argument (PSM) and return a float. If array-like, should contain float values for all given PSMs. If string, it is used as a field name (PSMs must be in a record array or a DataFrame).

    Note

    If this parameter is given, then PEP values will be used to calculate q-values. Otherwise, decoy PSMs will be used instead. This option conflicts with: is_decoy, remove_decoy, formula, ratio, correction. key can still be provided. Without key, PSMs will be sorted by PEP.

  • full_output (bool, keyword only, optional) –

    If True, then an array of PSM objects is returned. Otherwise, an iterator / context manager object is returned, and the files are parsed twice. This saves some RAM, but is ~2x slower. Default is True.

    Note

    The name for the parameter comes from the fact that it is internally passed to qvalues().

  • q_label (str, optional) – Field name for q-value in the output. Default is 'q'.

  • score_label (str, optional) – Field name for score in the output. Default is 'score'.

  • decoy_label (str, optional) – Field name for the decoy flag in the output. Default is 'is decoy'.

  • pep_label (str, optional) – Field name for PEP in the output. Default is 'PEP'.

  • **kwargs (passed to the chain() function.)

Returns:

out

Return type:

iterator or numpy.ndarray or pandas.DataFrame

filter.chain(*files, **kwargs)

Chain filter() for several files. Positional arguments should be file names or file objects. Keyword arguments are passed to the filter() function.

filter.chain.from_iterable(*files, **kwargs)

Chain filter() for several files. Keyword arguments are passed to the filter() function.

Parameters:

files – Iterable of file names or file objects.

pyteomics.openms.idxml.DataFrame(*args, **kwargs)[source]

Read idXML files into a pandas.DataFrame.

Requires pandas.

Warning

Only the first ‘PeptideHit’ element is considered in every ‘PeptideIdentification’.

Parameters:

  • *args – Passed to chain()

  • **kwargs – Passed to chain()

  • sep (str or None, keyword only, optional) – Some values related to PSMs (such as protein information) are variable-length lists. If sep is a str, they will be packed into single string using this delimiter. If sep is None, they are kept as lists. Default is None.

Returns:

out

Return type:

pandas.DataFrame

class pyteomics.openms.idxml.IDXML(*args, **kwargs)[source]

Bases: IndexedXML

Parser class for idXML files.

__init__(*args, **kwargs)[source]

Create an indexed XML parser object.

Parameters:

  • source (str or file) – File name or file-like object corresponding to an XML file.

  • read_schema (bool, optional) – Defines whether schema file referenced in the file header should be used to extract information about value conversion. Default is False.

  • iterative (bool, optional) – Defines whether an ElementTree object should be constructed and stored on the instance or if iterative parsing should be used instead. Iterative parsing keeps the memory usage low for large XML files. Default is True.

  • use_index (bool, optional) – Defines whether an index of byte offsets needs to be created for elements listed in indexed_tags. This is useful for random access to spectra in mzML or elements of mzIdentML files, or for iterative parsing of mzIdentML with retrieve_refs=True. If True, build_id_cache is ignored. If False, the object acts exactly like XML. Default is True.

  • indexed_tags (container of bytes, optional) – If use_index is True, elements listed in this parameter will be indexed. Empty set by default.

build_byte_index()

Build up an index of offsets for elements.

Returns:

out

Return type:

TagSpecificXMLByteIndex

build_id_cache()

Construct a cache for each element in the document, indexed by id attribute

build_tree()

Build and store the ElementTree instance for the underlying file

clear_id_cache()

Clear the element ID cache

clear_tree()

Remove the saved ElementTree.

get_by_id(elem_id, id_key=None, element_type=None, **kwargs)

Retrieve the requested entity by its id. If the entity is a spectrum described in the offset index, it will be retrieved by immediately seeking to the starting position of the entry, otherwise falling back to parsing from the start of the file.

Parameters:

  • elem_id (str) – The id value of the entity to retrieve.

  • id_key (str, optional) – The name of the XML attribute to use for lookup. Defaults to self._default_id_attr.

Return type:

dict

iterfind(path, **kwargs)

Parse the XML and yield info on elements with specified local name or by specified “XPath”.

Parameters:

  • path (str) – Element name or XPath-like expression. The path is very close to full XPath syntax, but local names should be used for all elements in the path. They will be substituted with local-name() checks, up to the (first) predicate. The path can be absolute or “free”. Please don’t specify namespaces.

  • **kwargs (passed to self._get_info_smart().)

Returns:

out

Return type:

iterator

reset()

Resets the iterator to its initial state.

pyteomics.openms.idxml.filter_df(*args, **kwargs)[source]

Read idXML files or DataFrames and return a DataFrame with filtered PSMs. Positional arguments can be idXML files or DataFrames.

Requires pandas.

Warning

Only the first ‘PeptideHit’ element is considered in every ‘PeptideIdentification’.

Parameters:

  • key (str / iterable / callable, keyword only, optional) – Peptide identification score. Default is ‘score’. You will probably need to change it.

  • is_decoy (str / iterable / callable, keyword only, optional) – Default is ‘is decoy’.

  • *args – Passed to auxiliary.filter() and/or DataFrame().

  • **kwargs – Passed to auxiliary.filter() and/or DataFrame().

Returns:

out

Return type:

pandas.DataFrame

pyteomics.openms.idxml.get_by_id(source, elem_id, **kwargs)[source]

Parse source and return the element with id attribute equal to elem_id. Returns None if no such element is found.

Note

This function is provided for backward compatibility only. If you do multiple get_by_id() calls on one file, you should create an IDXML object and use its get_by_id() method.

Parameters:

  • source (str or file) – A path to a target mzIdentML file of the file object itself.

  • elem_id (str) – The value of the id attribute to match.

Returns:

out

Return type:

dict or None

pyteomics.openms.idxml.is_decoy(psm, prefix=None)[source]

Given a PSM dict, return True if it is marked as decoy, and False otherwise.

Parameters:

  • psm (dict) – A dict, as yielded by read().

  • prefix (ignored)

Returns:

out

Return type:

bool

pyteomics.openms.idxml.iterfind(source, path, **kwargs)[source]

Parse source and yield info on elements with specified local name or by specified “XPath”.

Note

This function is provided for backward compatibility only. If you do multiple iterfind() calls on one file, you should create an IDXML object and use its iterfind() method.

Parameters:

  • source (str or file) – File name or file-like object.

  • path (str) – Element name or XPath-like expression. Only local names separated with slashes are accepted. An asterisk (*) means any element. You can specify a single condition in the end, such as: "/path/to/element[some_value>1.5]" Note: you can do much more powerful filtering using plain Python. The path can be absolute or “free”. Please don’t specify namespaces.

  • recursive (bool, optional) – If False, subelements will not be processed when extracting info from elements. Default is True.

  • retrieve_refs (bool, optional) – If True, additional information from references will be automatically added to the results. The file processing time will increase. Default is False.

  • iterative (bool, optional) – Specifies whether iterative XML parsing should be used. Iterative parsing significantly reduces memory usage and may be just a little slower. When retrieve_refs is True, however, it is highly recommended to disable iterative parsing if possible. Default value is True.

  • read_schema (bool, optional) – If True, attempt to extract information from the XML schema mentioned in the IDXML header (default). Otherwise, use default parameters. Disable this to avoid waiting on slow network connections or if you don’t like to get the related warnings.

  • build_id_cache (bool, optional) – Defines whether a cache of element IDs should be built and stored on the created IDXML instance. Default value is the value of retrieve_refs.

Returns:

out

Return type:

iterator

pyteomics.openms.idxml.read(source, **kwargs)[source]

Parse source and iterate through peptide-spectrum matches.

Note

This function is provided for backward compatibility only. It simply creates an IDXML instance using provided arguments and returns it.

Parameters:

  • source (str or file) – A path to a target IDXML file or the file object itself.

  • recursive (bool, optional) – If False, subelements will not be processed when extracting info from elements. Default is True.

  • retrieve_refs (bool, optional) – If True, additional information from references will be automatically added to the results. The file processing time will increase. Default is True.

  • iterative (bool, optional) – Specifies whether iterative XML parsing should be used. Iterative parsing significantly reduces memory usage and may be just a little slower. When retrieve_refs is True, however, it is highly recommended to disable iterative parsing if possible. Default value is True.

  • read_schema (bool, optional) – If True, attempt to extract information from the XML schema mentioned in the IDXML header (default). Otherwise, use default parameters. Disable this to avoid waiting on slow network connections or if you don’t like to get the related warnings.

  • build_id_cache (bool, optional) –

    Defines whether a cache of element IDs should be built and stored on the created IDXML instance. Default value is the value of retrieve_refs.

    Note

    This parameter is ignored when use_index is True (default).

  • use_index (bool, optional) – Defines whether an index of byte offsets needs to be created for the indexed elements. If True (default), build_id_cache is ignored.

  • indexed_tags (container of bytes, optional) – Defines which elements need to be indexed. Empty set by default.

Returns:

out – An iterator over the dicts with PSM properties.

Return type:

IDXML

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