auxiliary  common functions and objects¶
Math¶
linear_regression_vertical()
 a wrapper for NumPy linear regression, minimizes the sum of squares of y errors.
linear_regression()
 alias forlinear_regression_vertical()
.
linear_regression_perpendicular()
 a wrapper for NumPy linear regression, minimizes the sum of squares of (perpendicular) distances between the points and the line.
TargetDecoy Approach¶
qvalues()
 estimate qvalues for a set of PSMs.
filter()
 filter PSMs to specified FDR level using TDA or given PEPs.
filter.chain()
 a chained version offilter()
.
fdr()
 estimate FDR in a set of PSMs using TDA or given PEPs.
Project infrastructure¶
PyteomicsError
 a pyteomicsspecific exception.
Helpers¶
Charge
 a subclass ofint
for charge states.
ChargeList
 a subclass oflist
for lists of charges.
print_tree()
 display the structure of a complex nesteddict
.
memoize()
 makes a memoization function decorator.
cvquery()
 traverse an arbitrarily nested dictionary looking for keys which arecvstr
instances, or objects with an attribute calledaccession
.

pyteomics.auxiliary.math.
linear_regression
(x, y=None, a=None, b=None)[source]¶ Alias of
linear_regression_vertical()
.

pyteomics.auxiliary.math.
linear_regression_perpendicular
(x, y=None)[source]¶ Calculate coefficients of a linear regression y = a * x + b. The fit minimizes perpendicular distances between the points and the line.
Requires
numpy
.Parameters:  x, y : array_like of float
1D arrays of floats. If y is omitted, x must be a 2D array of shape (N, 2).
Returns:  out : 4tuple of float
The structure is (a, b, r, stderr), where a – slope coefficient, b – free term, r – Peason correlation coefficient, stderr – standard deviation.

pyteomics.auxiliary.math.
linear_regression_vertical
(x, y=None, a=None, b=None)[source]¶ Calculate coefficients of a linear regression y = a * x + b. The fit minimizes vertical distances between the points and the line.
Requires
numpy
.Parameters:  x, y : array_like of float
1D arrays of floats. If y is omitted, x must be a 2D array of shape (N, 2).
 a : float, optional
If specified then the slope coefficient is fixed and equals a.
 b : float, optional
If specified then the free term is fixed and equals b.
Returns:  out : 4tuple of float
The structure is (a, b, r, stderr), where a – slope coefficient, b – free term, r – Peason correlation coefficient, stderr – standard deviation.

pyteomics.auxiliary.target_decoy.
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:
The second formula is:
Note
This function is less versatile than
qvalues()
. To obtain FDR, you can callqvalues()
and take the last qvalue. This function can be used (with correction = 0 or 1) whennumpy
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
If callable, should accept exactly one argument (PSM) and return a truthy value if the PSM is considered decoy. Default is
is_decoy()
. If arraylike, 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 apandas.DataFrame
). 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 arraylike, 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 qvalues do not exceed the “real” qvalues 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 : float
The estimation of FDR, (roughly) between 0 and 1.

pyteomics.auxiliary.target_decoy.
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:  positional args : iterables
Iterables to read PSMs from. All positional arguments are chained. The rest of the arguments must be named.
 fdr : float, keyword only, 0 <= fdr <= 1
Desired FDR level.
 key : callable / arraylike / iterable / str, keyword only
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 evalue 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 isFalse
. is_decoy : callable / arraylike / iterable / str, keyword only
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.
 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 offdr()
for math; basically, if remove_decoy isTrue
, 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 (seefdr()
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 qvalues do not exceed the “real” qvalues with 95% probability.
See this paper for further explanation.
 pep : callable / arraylike / 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 arraylike, 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 qvalues. 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 isTrue
.Note
The name for the parameter comes from the fact that it is internally passed to
qvalues()
. q_label : str, optional
Field name for qvalue 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 : iterator or
numpy.ndarray
orpandas.DataFrame

pyteomics.auxiliary.target_decoy.
qvalues
(*args, **kwargs)¶ Read args and return a NumPy array with scores and qvalues. qvalues are calculated either using TDA or based on provided values of PEP.
Requires
numpy
(and optionallypandas
).Parameters:  positional args : iterables
Iterables to read PSMs from. All positional arguments are chained. The rest of the arguments must be named.
 key : callable / arraylike / iterable / str, keyword only
If callable, a function used for sorting of PSMs. Should accept exactly one argument (PSM) and return a number (the smaller the better). If arraylike, 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 isFalse
. is_decoy : callable / arraylike / iterable / str, keyword only
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 arraylike, 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
). pep : callable / arraylike / 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 arraylike, 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 qvalues. 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 offdr()
for math; basically, if remove_decoy isTrue
, 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 (seefdr()
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 qvalues do not exceed the “real” qvalues with 95% probability.
See this paper for further explanation.
 q_label : str, optional
Field name for qvalue 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 qvalues. Default isFalse
. **kwargs : passed to the
chain()
function.
Returns:  out : numpy.ndarray
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 isTrue
)
 ‘score’:

pyteomics.auxiliary.target_decoy.
sigma_T
(psms, is_decoy, ratio=1)[source]¶ Calculates the standard error for the number of false positive target PSMs.
The formula is:
.. math ::
sigma(T) = sqrt{frac{(d + 1) cdot {p}}{(1  p)^{2}}} = sqrt{frac{d+1}{r^{2}} cdot (r+1)}This estimation is accurate for low FDRs. See the article for more details.

pyteomics.auxiliary.target_decoy.
sigma_fdr
(psms=None, formula=1, is_decoy=None, ratio=1)[source]¶ Calculates the standard error of FDR using the formula for negative binomial distribution. See
sigma_T()
for math. This estimation is accurate for low FDRs. See also the article for more details.

class
pyteomics.auxiliary.utils.
BinaryDataArrayTransformer
[source]¶ Bases:
object
A base class that provides methods for reading base64encoded binary arrays.
Attributes:  compression_type_map : dict
Maps compressor type name to decompression function
Methods
binary_array_record
Hold all of the information about a base64 encoded array needed to decode the array. decode_data_array
(self, source[, …])Decode a base64encoded, compressed bytestring into a numerical array. 
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature

class
binary_array_record
[source]¶ Bases:
pyteomics.auxiliary.utils.binary_array_record
Hold all of the information about a base64 encoded array needed to decode the array.
Attributes: compression
Alias for field number 1
data
Alias for field number 0
dtype
Alias for field number 2
key
Alias for field number 4
source
Alias for field number 3
Methods
count
()decode
(self)Decode data
into a numerical arrayindex
()Raises ValueError if the value is not present. 
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature

compression
¶ Alias for field number 1

count
()¶

data
¶ Alias for field number 0

dtype
¶ Alias for field number 2

index
()¶ Raises ValueError if the value is not present.

key
¶ Alias for field number 4

source
¶ Alias for field number 3

decode_data_array
(self, source, compression_type=None, dtype=<type 'numpy.float64'>)[source]¶ Decode a base64encoded, compressed bytestring into a numerical array.
Parameters:  source : bytes
A base64 string encoding a potentially compressed numerical array.
 compression_type : str, optional
The name of the compression method used before encoding the array into base64.
 dtype : type, optional
The data type to use to decode the binary array from the decompressed bytes.
Returns:  np.ndarray

pyteomics.auxiliary.utils.
memoize
(maxsize=1000)[source]¶ Make a memoization decorator. A negative value of maxsize means no size limit.

pyteomics.auxiliary.utils.
print_tree
(d, indent_str=' > ', indent_count=1)[source]¶ Read a nested dict (with strings as keys) and print its structure.

class
pyteomics.auxiliary.structures.
BasicComposition
(*args, **kwargs)[source]¶ Bases:
collections.defaultdict
,collections.Counter
A generic dictionary for compositions. Keys should be strings, values should be integers. Allows simple arithmetics.
Attributes: default_factory
Factory for default value called by __missing__().
Methods
clear
()elements
(self)Iterator over elements repeating each as many times as its count. get
()has_key
()items
()iteritems
()iterkeys
()itervalues
()keys
()most_common
(self[, n])List the n most common elements and their counts from the most common to the least. pop
()If key is not found, d is returned if given, otherwise KeyError is raised popitem
()2tuple; but raise KeyError if D is empty. setdefault
()subtract
(\*args, \*\*kwds)Like dict.update() but subtracts counts instead of replacing them. update
(\*args, \*\*kwds)Like dict.update() but add counts instead of replacing them. values
()viewitems
()viewkeys
()viewvalues
()copy fromkeys 
__init__
(self, *args, **kwargs)[source]¶ x.__init__(…) initializes x; see help(type(x)) for signature

clear
()¶

default_factory
¶ Factory for default value called by __missing__().

elements
(self)¶ Iterator over elements repeating each as many times as its count.
>>> c = Counter('ABCABC') >>> sorted(c.elements()) ['A', 'A', 'B', 'B', 'C', 'C']
# Knuth’s example for prime factors of 1836: 2**2 * 3**3 * 17**1 >>> prime_factors = Counter({2: 2, 3: 3, 17: 1}) >>> product = 1 >>> for factor in prime_factors.elements(): # loop over factors … product *= factor # and multiply them >>> product 1836
Note, if an element’s count has been set to zero or is a negative number, elements() will ignore it.

classmethod
fromkeys
(cls, iterable, v=None)¶ v defaults to None.

get
()¶

has_key
()¶

items
()¶

iteritems
()¶

iterkeys
()¶

itervalues
()¶

keys
()¶

most_common
(self, n=None)¶ List the n most common elements and their counts from the most common to the least. If n is None, then list all element counts.
>>> Counter('abcdeabcdabcaba').most_common(3) [('a', 5), ('b', 4), ('c', 3)]

pop
()¶ If key is not found, d is returned if given, otherwise KeyError is raised

popitem
()¶ 2tuple; but raise KeyError if D is empty.

setdefault
()¶

subtract
(*args, **kwds)¶ Like dict.update() but subtracts counts instead of replacing them. Counts can be reduced below zero. Both the inputs and outputs are allowed to contain zero and negative counts.
Source can be an iterable, a dictionary, or another Counter instance.
>>> c = Counter('which') >>> c.subtract('witch') # subtract elements from another iterable >>> c.subtract(Counter('watch')) # subtract elements from another counter >>> c['h'] # 2 in which, minus 1 in witch, minus 1 in watch 0 >>> c['w'] # 1 in which, minus 1 in witch, minus 1 in watch 1

update
(*args, **kwds)¶ Like dict.update() but add counts instead of replacing them.
Source can be an iterable, a dictionary, or another Counter instance.
>>> c = Counter('which') >>> c.update('witch') # add elements from another iterable >>> d = Counter('watch') >>> c.update(d) # add elements from another counter >>> c['h'] # four 'h' in which, witch, and watch 4

values
()¶

viewitems
()¶

viewkeys
()¶

viewvalues
()¶

class
pyteomics.auxiliary.structures.
CVQueryEngine
[source]¶ Bases:
object
Traverse an arbitrarily nested dictionary looking for keys which are
cvstr
instances, or objects with an attribute calledaccession
.Methods
__call__
(self, data[, accession])If accession
isNone
, callsindex()
ondata
, otherwise callsquery()
withdata
andaccession
.index
(self, data)Construct a flat dict
whose keys are the accession numbers for all qualified keys indata
and whose values are the mapped values fromdata
.query
(self, data, accession)Search data
for a key with the accession numberaccession
.
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature


class
pyteomics.auxiliary.structures.
Charge
[source]¶ Bases:
int
A subclass of
int
. Can be constructed from strings in “N+” or “N” format, and the string representation of aCharge
is also in that format.Attributes: denominator
the denominator of a rational number in lowest terms
imag
the imaginary part of a complex number
numerator
the numerator of a rational number in lowest terms
real
the real part of a complex number
Methods
bit_length
()Number of bits necessary to represent self in binary. conjugate
()Returns self, the complex conjugate of any int. 
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature

bit_length
()¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6

conjugate
()¶ Returns self, the complex conjugate of any int.

denominator
¶ the denominator of a rational number in lowest terms

imag
¶ the imaginary part of a complex number

numerator
¶ the numerator of a rational number in lowest terms

real
¶ the real part of a complex number

class
pyteomics.auxiliary.structures.
ChargeList
(*args, **kwargs)[source]¶ Bases:
list
Just a list of :py:class:`Charge`s. When printed, looks like an enumeration of the list contents. Can also be constructed from such strings (e.g. “2+, 3+ and 4+”).
Methods
append
()L.append(object) – append object to end count
()extend
()L.extend(iterable) – extend list by appending elements from the iterable index
()Raises ValueError if the value is not present. insert
()L.insert(index, object) – insert object before index pop
()Raises IndexError if list is empty or index is out of range. remove
()L.remove(value) – remove first occurrence of value. reverse
()L.reverse() – reverse IN PLACE sort
()L.sort(cmp=None, key=None, reverse=False) – stable sort IN PLACE; cmp(x, y) > 1, 0, 1 
__init__
(self, *args, **kwargs)[source]¶ x.__init__(…) initializes x; see help(type(x)) for signature

append
()¶ L.append(object) – append object to end

count
()¶

extend
()¶ L.extend(iterable) – extend list by appending elements from the iterable

index
()¶ Raises ValueError if the value is not present.

insert
()¶ L.insert(index, object) – insert object before index

pop
()¶ Raises IndexError if list is empty or index is out of range.

remove
()¶ L.remove(value) – remove first occurrence of value. Raises ValueError if the value is not present.

reverse
()¶ L.reverse() – reverse IN PLACE

sort
()¶ L.sort(cmp=None, key=None, reverse=False) – stable sort IN PLACE; cmp(x, y) > 1, 0, 1


exception
pyteomics.auxiliary.structures.
PyteomicsError
(msg, *values)[source]¶ Bases:
exceptions.Exception
Exception raised for errors in Pyteomics library.
Attributes:  message : str
Error message.

pyteomics.auxiliary.structures.
clear_unit_cv_table
()[source]¶ Clear the modulelevel unit name and controlled vocabulary accession table.

class
pyteomics.auxiliary.structures.
cvstr
[source]¶ Bases:
str
A helper class to associate a controlled vocabullary accession number with an otherwise plain
str
objectMethods
capitalize
()Return a copy of the string S with only its first character capitalized. center
()Return S centered in a string of length width. count
()Return the number of nonoverlapping occurrences of substring sub in string S[start:end]. decode
()Decodes S using the codec registered for encoding. encode
()Encodes S using the codec registered for encoding. endswith
()Return True if S ends with the specified suffix, False otherwise. expandtabs
()Return a copy of S where all tab characters are expanded using spaces. find
()Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. format
()Return a formatted version of S, using substitutions from args and kwargs. index
()Like S.find() but raise ValueError when the substring is not found. isalnum
()Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise. isalpha
()Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise. isdigit
()Return True if all characters in S are digits and there is at least one character in S, False otherwise. islower
()Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise. isspace
()Return True if all characters in S are whitespace and there is at least one character in S, False otherwise. istitle
()Return True if S is a titlecased string and there is at least one character in S, i.e. isupper
()Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise. join
()Return a string which is the concatenation of the strings in the iterable. ljust
()Return S leftjustified in a string of length width. lower
()Return a copy of the string S converted to lowercase. lstrip
()Return a copy of the string S with leading whitespace removed. partition
(sep)Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. replace
()Return a copy of string S with all occurrences of substring old replaced by new. rfind
()Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. rindex
()Like S.rfind() but raise ValueError when the substring is not found. rjust
()Return S rightjustified in a string of length width. rpartition
(sep)Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. rsplit
()Return a list of the words in the string S, using sep as the delimiter string, starting at the end of the string and working to the front. rstrip
()Return a copy of the string S with trailing whitespace removed. split
()Return a list of the words in the string S, using sep as the delimiter string. splitlines
()Return a list of the lines in S, breaking at line boundaries. startswith
()Return True if S starts with the specified prefix, False otherwise. strip
()Return a copy of the string S with leading and trailing whitespace removed. swapcase
()Return a copy of the string S with uppercase characters converted to lowercase and vice versa. title
()Return a titlecased version of S, i.e. translate
()Return a copy of the string S, where all characters occurring in the optional argument deletechars are removed, and the remaining characters have been mapped through the given translation table, which must be a string of length 256 or None. upper
()Return a copy of the string S converted to uppercase. zfill
()Pad a numeric string S with zeros on the left, to fill a field of the specified width. 
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature

capitalize
()¶ Return a copy of the string S with only its first character capitalized.

center
()¶ Return S centered in a string of length width. Padding is done using the specified fill character (default is a space)

count
()¶ Return the number of nonoverlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.

decode
()¶ Decodes S using the codec registered for encoding. encoding defaults to the default encoding. errors may be given to set a different error handling scheme. Default is ‘strict’ meaning that encoding errors raise a UnicodeDecodeError. Other possible values are ‘ignore’ and ‘replace’ as well as any other name registered with codecs.register_error that is able to handle UnicodeDecodeErrors.

encode
()¶ Encodes S using the codec registered for encoding. encoding defaults to the default encoding. errors may be given to set a different error handling scheme. Default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that is able to handle UnicodeEncodeErrors.

endswith
()¶ Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.

expandtabs
()¶ Return a copy of S where all tab characters are expanded using spaces. If tabsize is not given, a tab size of 8 characters is assumed.

find
()¶ Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return 1 on failure.

format
()¶ Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{‘ and ‘}’).

index
()¶ Like S.find() but raise ValueError when the substring is not found.

isalnum
()¶ Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise.

isalpha
()¶ Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise.

isdigit
()¶ Return True if all characters in S are digits and there is at least one character in S, False otherwise.

islower
()¶ Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise.

isspace
()¶ Return True if all characters in S are whitespace and there is at least one character in S, False otherwise.

istitle
()¶ Return True if S is a titlecased string and there is at least one character in S, i.e. uppercase characters may only follow uncased characters and lowercase characters only cased ones. Return False otherwise.

isupper
()¶ Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise.

join
()¶ Return a string which is the concatenation of the strings in the iterable. The separator between elements is S.

ljust
()¶ Return S leftjustified in a string of length width. Padding is done using the specified fill character (default is a space).

lower
()¶ Return a copy of the string S converted to lowercase.

lstrip
()¶ Return a copy of the string S with leading whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

partition
(sep) > (head, sep, tail)¶ Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return S and two empty strings.

replace
()¶ Return a copy of string S with all occurrences of substring old replaced by new. If the optional argument count is given, only the first count occurrences are replaced.

rfind
()¶ Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return 1 on failure.

rindex
()¶ Like S.rfind() but raise ValueError when the substring is not found.

rjust
()¶ Return S rightjustified in a string of length width. Padding is done using the specified fill character (default is a space)

rpartition
(sep) > (head, sep, tail)¶ Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return two empty strings and S.

rsplit
()¶ Return a list of the words in the string S, using sep as the delimiter string, starting at the end of the string and working to the front. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator.

rstrip
()¶ Return a copy of the string S with trailing whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

split
()¶ Return a list of the words in the string S, using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator and empty strings are removed from the result.

splitlines
()¶ Return a list of the lines in S, breaking at line boundaries. Line breaks are not included in the resulting list unless keepends is given and true.

startswith
()¶ Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.

strip
()¶ Return a copy of the string S with leading and trailing whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

swapcase
()¶ Return a copy of the string S with uppercase characters converted to lowercase and vice versa.

title
()¶ Return a titlecased version of S, i.e. words start with uppercase characters, all remaining cased characters have lowercase.

translate
()¶ Return a copy of the string S, where all characters occurring in the optional argument deletechars are removed, and the remaining characters have been mapped through the given translation table, which must be a string of length 256 or None. If the table argument is None, no translation is applied and the operation simply removes the characters in deletechars.

upper
()¶ Return a copy of the string S converted to uppercase.

zfill
()¶ Pad a numeric string S with zeros on the left, to fill a field of the specified width. The string S is never truncated.


class
pyteomics.auxiliary.structures.
unitfloat
[source]¶ Bases:
float
Attributes: Methods
as_integer_ratio
()Return a pair of integers, whose ratio is exactly equal to the original float and with a positive denominator. conjugate
()Return self, the complex conjugate of any float. fromhex
()Create a floatingpoint number from a hexadecimal string. hex
()Return a hexadecimal representation of a floatingpoint number. is_integer
()Return True if the float is an integer. 
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature

as_integer_ratio
() > (int, int)¶ Return a pair of integers, whose ratio is exactly equal to the original float and with a positive denominator. Raise OverflowError on infinities and a ValueError on NaNs.
>>> (10.0).as_integer_ratio() (10, 1) >>> (0.0).as_integer_ratio() (0, 1) >>> (.25).as_integer_ratio() (1, 4)

conjugate
()¶ Return self, the complex conjugate of any float.

fromhex
()¶ Create a floatingpoint number from a hexadecimal string. >>> float.fromhex(‘0x1.ffffp10’) 2047.984375 >>> float.fromhex(‘0x1p1074’) 4.9406564584124654e324

hex
()¶ Return a hexadecimal representation of a floatingpoint number. >>> (0.1).hex() ‘0x1.999999999999ap4’ >>> 3.14159.hex() ‘0x1.921f9f01b866ep+1’

imag
¶ the imaginary part of a complex number

is_integer
()¶ Return True if the float is an integer.

real
¶ the real part of a complex number


class
pyteomics.auxiliary.structures.
unitint
[source]¶ Bases:
int
Attributes: denominator
the denominator of a rational number in lowest terms
imag
the imaginary part of a complex number
numerator
the numerator of a rational number in lowest terms
real
the real part of a complex number
Methods
bit_length
()Number of bits necessary to represent self in binary. conjugate
()Returns self, the complex conjugate of any int. 
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature

bit_length
()¶ Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6

conjugate
()¶ Returns self, the complex conjugate of any int.

denominator
¶ the denominator of a rational number in lowest terms

imag
¶ the imaginary part of a complex number

numerator
¶ the numerator of a rational number in lowest terms

real
¶ the real part of a complex number

class
pyteomics.auxiliary.structures.
unitstr
[source]¶ Bases:
str
Methods
capitalize
()Return a copy of the string S with only its first character capitalized. center
()Return S centered in a string of length width. count
()Return the number of nonoverlapping occurrences of substring sub in string S[start:end]. decode
()Decodes S using the codec registered for encoding. encode
()Encodes S using the codec registered for encoding. endswith
()Return True if S ends with the specified suffix, False otherwise. expandtabs
()Return a copy of S where all tab characters are expanded using spaces. find
()Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. format
()Return a formatted version of S, using substitutions from args and kwargs. index
()Like S.find() but raise ValueError when the substring is not found. isalnum
()Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise. isalpha
()Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise. isdigit
()Return True if all characters in S are digits and there is at least one character in S, False otherwise. islower
()Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise. isspace
()Return True if all characters in S are whitespace and there is at least one character in S, False otherwise. istitle
()Return True if S is a titlecased string and there is at least one character in S, i.e. isupper
()Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise. join
()Return a string which is the concatenation of the strings in the iterable. ljust
()Return S leftjustified in a string of length width. lower
()Return a copy of the string S converted to lowercase. lstrip
()Return a copy of the string S with leading whitespace removed. partition
(sep)Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. replace
()Return a copy of string S with all occurrences of substring old replaced by new. rfind
()Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. rindex
()Like S.rfind() but raise ValueError when the substring is not found. rjust
()Return S rightjustified in a string of length width. rpartition
(sep)Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. rsplit
()Return a list of the words in the string S, using sep as the delimiter string, starting at the end of the string and working to the front. rstrip
()Return a copy of the string S with trailing whitespace removed. split
()Return a list of the words in the string S, using sep as the delimiter string. splitlines
()Return a list of the lines in S, breaking at line boundaries. startswith
()Return True if S starts with the specified prefix, False otherwise. strip
()Return a copy of the string S with leading and trailing whitespace removed. swapcase
()Return a copy of the string S with uppercase characters converted to lowercase and vice versa. title
()Return a titlecased version of S, i.e. translate
()Return a copy of the string S, where all characters occurring in the optional argument deletechars are removed, and the remaining characters have been mapped through the given translation table, which must be a string of length 256 or None. upper
()Return a copy of the string S converted to uppercase. zfill
()Pad a numeric string S with zeros on the left, to fill a field of the specified width. 
__init__
¶ x.__init__(…) initializes x; see help(type(x)) for signature

capitalize
()¶ Return a copy of the string S with only its first character capitalized.

center
()¶ Return S centered in a string of length width. Padding is done using the specified fill character (default is a space)

count
()¶ Return the number of nonoverlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.

decode
()¶ Decodes S using the codec registered for encoding. encoding defaults to the default encoding. errors may be given to set a different error handling scheme. Default is ‘strict’ meaning that encoding errors raise a UnicodeDecodeError. Other possible values are ‘ignore’ and ‘replace’ as well as any other name registered with codecs.register_error that is able to handle UnicodeDecodeErrors.

encode
()¶ Encodes S using the codec registered for encoding. encoding defaults to the default encoding. errors may be given to set a different error handling scheme. Default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that is able to handle UnicodeEncodeErrors.

endswith
()¶ Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.

expandtabs
()¶ Return a copy of S where all tab characters are expanded using spaces. If tabsize is not given, a tab size of 8 characters is assumed.

find
()¶ Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return 1 on failure.

format
()¶ Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{‘ and ‘}’).

index
()¶ Like S.find() but raise ValueError when the substring is not found.

isalnum
()¶ Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise.

isalpha
()¶ Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise.

isdigit
()¶ Return True if all characters in S are digits and there is at least one character in S, False otherwise.

islower
()¶ Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise.

isspace
()¶ Return True if all characters in S are whitespace and there is at least one character in S, False otherwise.

istitle
()¶ Return True if S is a titlecased string and there is at least one character in S, i.e. uppercase characters may only follow uncased characters and lowercase characters only cased ones. Return False otherwise.

isupper
()¶ Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise.

join
()¶ Return a string which is the concatenation of the strings in the iterable. The separator between elements is S.

ljust
()¶ Return S leftjustified in a string of length width. Padding is done using the specified fill character (default is a space).

lower
()¶ Return a copy of the string S converted to lowercase.

lstrip
()¶ Return a copy of the string S with leading whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

partition
(sep) > (head, sep, tail)¶ Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return S and two empty strings.

replace
()¶ Return a copy of string S with all occurrences of substring old replaced by new. If the optional argument count is given, only the first count occurrences are replaced.

rfind
()¶ Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return 1 on failure.

rindex
()¶ Like S.rfind() but raise ValueError when the substring is not found.

rjust
()¶ Return S rightjustified in a string of length width. Padding is done using the specified fill character (default is a space)

rpartition
(sep) > (head, sep, tail)¶ Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return two empty strings and S.

rsplit
()¶ Return a list of the words in the string S, using sep as the delimiter string, starting at the end of the string and working to the front. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator.

rstrip
()¶ Return a copy of the string S with trailing whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

split
()¶ Return a list of the words in the string S, using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator and empty strings are removed from the result.

splitlines
()¶ Return a list of the lines in S, breaking at line boundaries. Line breaks are not included in the resulting list unless keepends is given and true.

startswith
()¶ Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.

strip
()¶ Return a copy of the string S with leading and trailing whitespace removed. If chars is given and not None, remove characters in chars instead. If chars is unicode, S will be converted to unicode before stripping

swapcase
()¶ Return a copy of the string S with uppercase characters converted to lowercase and vice versa.

title
()¶ Return a titlecased version of S, i.e. words start with uppercase characters, all remaining cased characters have lowercase.

translate
()¶ Return a copy of the string S, where all characters occurring in the optional argument deletechars are removed, and the remaining characters have been mapped through the given translation table, which must be a string of length 256 or None. If the table argument is None, no translation is applied and the operation simply removes the characters in deletechars.

upper
()¶ Return a copy of the string S converted to uppercase.

zfill
()¶ Pad a numeric string S with zeros on the left, to fill a field of the specified width. The string S is never truncated.


class
pyteomics.auxiliary.file_helpers.
ChainBase
(*sources, **kwargs)[source]¶ Bases:
object
Chain
sequence_maker()
for several sources into a single iterable. Positional arguments should be sources like file names or file objects. Keyword arguments are passed to thesequence_maker()
function.Attributes:  sources :
Iterable
Sources for creating new sequences from, such as paths or filelike objects
 kwargs :
Mapping
Additional arguments used to instantiate each sequence
Methods
map
(self[, target, processes, …])Execute the target
function over entries of this object across up toprocesses
processes.from_iterable next sequence_maker 
__init__
(self, *sources, **kwargs)[source]¶ x.__init__(…) initializes x; see help(type(x)) for signature

map
(self, target=None, processes=1, queue_timeout=4, args=None, kwargs=None, **_kwargs)[source]¶ Execute the
target
function over entries of this object across up toprocesses
processes.Results will be returned out of order.
Parameters:  target :
Callable
, optional The function to execute over each entry. It will be given a single object yielded by the wrapped iterator as well as all of the values in
args
andkwargs
 processes : int, optional
The number of worker processes to use. If negative, the number of processes will match the number of available CPUs.
 queue_timeout : float, optional
The number of seconds to block, waiting for a result before checking to see if all workers are done.
 args :
Sequence
, optional Additional positional arguments to be passed to the target function
 kwargs :
Mapping
, optional Additional keyword arguments to be passed to the target function
 **_kwargs
Additional keyword arguments to be passed to the target function
Yields:  object
The work item returned by the target function.
 target :
 sources :

class
pyteomics.auxiliary.file_helpers.
FileReader
(source, **kwargs)[source]¶ Bases:
pyteomics.auxiliary.file_helpers.IteratorContextManager
Abstract class implementing context manager protocol for file readers.
Methods
next reset

class
pyteomics.auxiliary.file_helpers.
FileReadingProcess
(reader_spec, target_spec, qin, qout, args_spec, kwargs_spec)[source]¶ Bases:
multiprocessing.process.Process
Process that does a share of distributed work on entries read from file. Reconstructs a reader object, parses an entries from given indexes, optionally does additional processing, sends results back.
The reader class must support the
__getitem__()
dictlike lookup.Attributes: Methods
is_alive
(self)Return whether process is alive join
(self[, timeout])Wait until child process terminates start
(self)Start child process terminate
(self)Terminate process; sends SIGTERM signal or uses TerminateProcess() is_done run 
__init__
(self, reader_spec, target_spec, qin, qout, args_spec, kwargs_spec)[source]¶ x.__init__(…) initializes x; see help(type(x)) for signature

daemon
¶ Return whether process is a daemon

exitcode
¶ Return exit code of process or None if it has yet to stop

ident
¶ Return identifier (PID) of process or None if it has yet to start

is_alive
(self)¶ Return whether process is alive

join
(self, timeout=None)¶ Wait until child process terminates

pid
¶ Return identifier (PID) of process or None if it has yet to start

start
(self)¶ Start child process

terminate
(self)¶ Terminate process; sends SIGTERM signal or uses TerminateProcess()


class
pyteomics.auxiliary.file_helpers.
IndexSavingMixin
(*args, **kwargs)[source]¶ Bases:
pyteomics.auxiliary.file_helpers.NoOpBaseReader
Common interface for
IndexSavingXML
andIndexSavingTextReader
.Methods
prebuild_byte_offset_file
(cls, path)Construct a new XML reader, build its byte offset index and write it to file write_byte_offsets
(self)Write the byte offsets in _offset_index
to the file at_byte_offset_filename

__init__
(self, *args, **kwargs)¶ x.__init__(…) initializes x; see help(type(x)) for signature


class
pyteomics.auxiliary.file_helpers.
IndexSavingTextReader
(source, **kwargs)[source]¶ Bases:
pyteomics.auxiliary.file_helpers.IndexSavingMixin
,pyteomics.auxiliary.file_helpers.IndexedTextReader
Attributes:  default_index
 delimiter
 index
 label
Methods
prebuild_byte_offset_file
(cls, path)Construct a new XML reader, build its byte offset index and write it to file write_byte_offsets
(self)Write the byte offsets in _offset_index
to the file at_byte_offset_filename
build_byte_index get_by_id get_by_ids get_by_index get_by_index_slice get_by_indexes get_by_key_slice next reset 
__init__
(self, source, **kwargs)¶ x.__init__(…) initializes x; see help(type(x)) for signature

classmethod
prebuild_byte_offset_file
(cls, path)¶ Construct a new XML reader, build its byte offset index and write it to file
Parameters:  path : str
The path to the file to parse

reset
(self)¶ Resets the iterator to its initial state.

write_byte_offsets
(self)¶ Write the byte offsets in
_offset_index
to the file at_byte_offset_filename

class
pyteomics.auxiliary.file_helpers.
IndexedReaderMixin
(*args, **kwargs)[source]¶ Bases:
pyteomics.auxiliary.file_helpers.NoOpBaseReader
Common interface for
IndexedTextReader
andIndexedXML
.Attributes:  default_index
 index
Methods
get_by_id get_by_ids get_by_index get_by_index_slice get_by_indexes get_by_key_slice 
__init__
(self, *args, **kwargs)¶ x.__init__(…) initializes x; see help(type(x)) for signature

class
pyteomics.auxiliary.file_helpers.
IndexedTextReader
(source, **kwargs)[source]¶ Bases:
pyteomics.auxiliary.file_helpers.IndexedReaderMixin
,pyteomics.auxiliary.file_helpers.FileReader
Abstract class for text file readers that keep an index of records for random access. This requires reading the file in binary mode.
Attributes:  default_index
 delimiter
 index
 label
Methods
build_byte_index get_by_id get_by_ids get_by_index get_by_index_slice get_by_indexes get_by_key_slice next reset 
__init__
(self, source, **kwargs)[source]¶ x.__init__(…) initializes x; see help(type(x)) for signature

reset
(self)¶ Resets the iterator to its initial state.

class
pyteomics.auxiliary.file_helpers.
OffsetIndex
(*args, **kwargs)[source]¶ Bases:
collections.OrderedDict
,pyteomics.auxiliary.file_helpers.WritableIndex
An augmented OrderedDict that formally wraps getting items by index
Attributes: index_sequence
Keeps a cached copy of the
items()
sequence stored as atuple
to avoid repeatedly copying the sequence over many method calls.
Methods
clear
(self)copy
(self)from_index
(self, index[, include_value])Get an entry by its integer index in the ordered sequence of this mapping. from_slice
(self, spec[, include_value])Get a slice along index in the ordered sequence of this mapping. fromkeys
(cls, iterable[, value])If not specified, the value defaults to None. get
()has_key
()items
(self)iteritems
(self)od.iteritems > an iterator over the (key, value) pairs in od iterkeys
(self)itervalues
(self)od.itervalues > an iterator over the values in od keys
(self)popitem
(self[, last])Pairs are returned in LIFO order if last is true or FIFO order if false. setdefault
(self, key[, default])update
(\*args, \*\*kwds)If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v values
(self)viewitems
(self)viewkeys
(self)viewvalues
(self)between find load pop save sort 
__init__
(self, *args, **kwargs)[source]¶ Initialize an ordered dictionary. The signature is the same as regular dictionaries, but keyword arguments are not recommended because their insertion order is arbitrary.

clear
(self)¶

copy
(self)¶

from_index
(self, index, include_value=False)[source]¶ Get an entry by its integer index in the ordered sequence of this mapping.
Parameters:  index: int
The index to retrieve.
 include_value: bool
Whether to return both the key and the value or just the key. Defaults to
False
.
Returns:  object:
If
include_value
isTrue
, a tuple of (key, value) atindex
else just the key atindex
.

from_slice
(self, spec, include_value=False)[source]¶ Get a slice along index in the ordered sequence of this mapping.
Parameters:  spec: slice
The slice over the range of indices to retrieve
 include_value: bool
Whether to return both the key and the value or just the key. Defaults to
False
Returns:  list:
If
include_value
isTrue
, a tuple of (key, value) atindex
else just the key atindex
for eachindex
inspec

classmethod
fromkeys
(cls, iterable, value=None)¶ If not specified, the value defaults to None.

get
()¶

has_key
()¶

index_sequence
¶ Keeps a cached copy of the
items()
sequence stored as atuple
to avoid repeatedly copying the sequence over many method calls.Returns:

items
(self)¶

iteritems
(self)¶ od.iteritems > an iterator over the (key, value) pairs in od

iterkeys
(self)¶

itervalues
(self)¶ od.itervalues > an iterator over the values in od

keys
(self)¶

pop
(self, *args, **kwargs)[source]¶ value. If key is not found, d is returned if given, otherwise KeyError is raised.

popitem
(self, last=True)¶ Pairs are returned in LIFO order if last is true or FIFO order if false.

setdefault
(self, key, default=None)¶

update
(*args, **kwds)¶ If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v

values
(self)¶

viewitems
(self)¶

viewkeys
(self)¶

viewvalues
(self)¶

class
pyteomics.auxiliary.file_helpers.
TableJoiner
(*sources, **kwargs)[source]¶ Bases:
pyteomics.auxiliary.file_helpers.ChainBase
Methods
map
(self[, target, processes, …])Execute the target
function over entries of this object across up toprocesses
processes.concatenate from_iterable next sequence_maker 
__init__
(self, *sources, **kwargs)¶ x.__init__(…) initializes x; see help(type(x)) for signature

map
(self, target=None, processes=1, queue_timeout=4, args=None, kwargs=None, **_kwargs)¶ Execute the
target
function over entries of this object across up toprocesses
processes.Results will be returned out of order.
Parameters:  target :
Callable
, optional The function to execute over each entry. It will be given a single object yielded by the wrapped iterator as well as all of the values in
args
andkwargs
 processes : int, optional
The number of worker processes to use. If negative, the number of processes will match the number of available CPUs.
 queue_timeout : float, optional
The number of seconds to block, waiting for a result before checking to see if all workers are done.
 args :
Sequence
, optional Additional positional arguments to be passed to the target function
 kwargs :
Mapping
, optional Additional keyword arguments to be passed to the target function
 **_kwargs
Additional keyword arguments to be passed to the target function
Yields:  object
The work item returned by the target function.
 target :


class
pyteomics.auxiliary.file_helpers.
TimeOrderedIndexedReaderMixin
(*args, **kwargs)[source]¶ Bases:
pyteomics.auxiliary.file_helpers.IndexedReaderMixin
Attributes:  default_index
 index
 time
Methods
get_by_id get_by_ids get_by_index get_by_index_slice get_by_indexes get_by_key_slice