emzed.table¶

the name of the new column.

either a list with the same length as table or an expression.

supported colum types are int, float, bool, MzType, RtType, str, PeakMap, Table, object. In case you want to use Python objects like lists or dicts, use column type 'object' instead.

is a format string as "%d" or or an executable string with python code. To suppress visibility set format_ = None. By default (not_specified) the method tries to determine a default format for the type.

to add column name at a defined position, one can specify its position left-wise to column insert_before via the name of an existing column, or an integer index (negative values allowed !).

to add column name at a defined position, one can specify its position right-wise to column insert_after.

new column name.

any of accepted types int, float, bool, MzType, RtType, str, PeakMap, Table.

target column type.

target column format. By default the default format for type_ is used.

insertion position for the new column.

insertion position for the new column.

name of added column. Default name is id.

to add column col_name at a defined position, one can specify its position via the name of an existing column, or an integer index (negative values allowed). setting insert_before and the insert_after at the same time is not allowed.

to add column col_name at a defined position, one can specify its position via the name of an existing column, or an integer index (negative values allowed). setting insert_before and the insert_after at the same time is not allowed.

start value for creating the ids. default value is 0.

column name to replace or create.

either a list with the same length as table or an expression.

target column type. If None and the column exists, the current column type is reused.

target column format. By default the existing format or the default format for type_ is used.

insertion position used when the column is created.

insertion position used when the column is created.

column name to replace or create.

scalar value assigned to all rows.

target column type. If None and the column exists, the current column type is reused.

target column format. By default the existing format or the default format for type_ is used.

insertion position used when the column is created.

insertion position used when the column is created.

list or tuple of values. Length must match.

any function accepting arguments *args. The return value can be used to compute another column.

function arguments. arguments can be column expressions like t['col_name'], or local or global variables accepted by the function.

since None represents a missing value, apply will not call function in case one of the arguments is None and will instead consider None as result. in case the function is able to consider such missing values, one must set ignore_nones to False.

Example: the following code

.. code-block:: python

def convert(v):
    return str(v) + "s"

t = emzed.to_table("a", [1, None, 5], int)
t.add_column("b", t.apply(replace_none, t.a), int)
t.add_column("c", t.apply(replace_none, t.a, ignore_nones=False), int)
print(t)

prints

.. parsed-literal::

a    b    c
int  int  int
---  ---  ---
1    1    1
-    -   -1
5    5    5

column names with values defining colapsing groups.

column name of the new column holding the collapsed sub-tables.

If specified the result will be a Table with a db file backend, else the result will be managed in memory.

emzed.Table

Example:

.. parsed-literal::

a   b   c
int int int
--- --- ---
  1   1   1
  1   1   2
  2   1   3
  2   2   4

print(t.collapse('a'))

results

.. parsed-literal::

a   collapsed
int emzed.Table
--- ---------------
1   <Table af3 ...>
2   <Table e9f ...>

If specified the result will be a Table with a db file backend, else the result will be managed in memory.

Indicate if an already existing database file should be overwritten.

emzed.Table.

list or tuple of strings.

list of types.

list of formats using format specifiers like "%.2f" If not specified emzed tries to guess appropriate formats based on column type and column name.

list of lists.

table title as string.

dictionary to manage user defined meta data.

path for the db backend, default is None to use the the in-memory db backend.

emzed.Table.

column names. either exact names or names containg wild cards like ? and *.

Example: Table t with colnames id, mz, mzmin, mzmax, sample_1k1, sample_1m1, sample_1k2

t.drop_columns('mz*', 'sample_1?1')

results t with columns id, sample_1k2

table with the same columns, types, and formats.

unused legacy argument kept for API compatibility.

unused legacy argument kept for API compatibility.

list or tuple with selected, existing column names.

second table for join.

column name to consider.

column name of other to consider in case it is different to col_name.

absolute tolerance for approximate equlity check.

relative tolerance for approximate equlity check.

optional additional join expression that must also match for a row pair to be included.

emzed.Table.

Performance: In case other is significantly larger than self, it is recommended to swap the tables.

The apprimate equality check for two numbers a and b is:

 abs(a - b) <= atol + rtol * abs(a)

So if you only need comparison based absolute tolerance you can set rtol to 0.0, and if you only need relative tolerance check you can set atol to 0.0.

second table for join.

column name to consider.

column name of other to consider in case it is different to col_name.

absolute tolerance for approximate equlity check.

relative tolerance for approximate equlity check.

optional additional join expression that must also match for a row pair to be included.

emzed.Table.

Performance: In case other is significantly larger than self, it is recommended to swap the tables.

The apprimate equality check for two numbers a and b is:

 abs(a - b) <= atol + rtol * abs(a)

So if you only need comparison based absolute tolerance you can set rtol to 0.0, and if you only need relative tolerance check you can set atol to 0.0.

expression like t.a < 0 or t.a <= t.b.

emzed.Table with filtered rows.

pandas data frame.

list of colum names, can be used to override data frame colum names.

list of colum types, if not provided emzed determines types from column contents and names.

list of colum formats, if not provided emzed determines formats from column contents and names.

emzed.Table.

existing column name or "_index".

You can use t[name] instead.

second table for join.

If None this method returns a table with the row wise cross product of both tables. else this expression is used to filter rows from this cross product.

emzed.Table.

Example:

if you have two table t1 and t2 as

.. parsed-literal::

id   mz
int  float
---  -----
  0  100.0
  1  200.0
  2  300.0

and

.. parsed-literal::

id   mz     rt
int  float  float
---  -----  -----
  0  100.0   10.0
  1  110.0   20.0
  2  200.0   30.0

Then the result of t1.join(t2, t1.mz.in_range(t2.mz - 20.0, t2.mz + 20.0)) is

.. parsed-literal::

id   mz     id__0  mz__0  rt__0
int  float  int    float  float
---  -----  -----  -----  -----
  0  100.0      0  100.0   10.0
  0  100.0      1  110.0   20.0
  1  200.0      2  200.0   30.0

If you do not provide an expression, this method returns the full cross product.

Second table for join.

If None this method returns a table with the row wise cross product of both tables. Else this expression is used to filter rows from this cross product, whereby all rows of the left table are kept.

emzed.Table.

If we take the example from join

Then t1.left_join(t2, t1.mz.in_range(t2.mz - 20.0, t2.mz + 20.0)) results:

.. parsed-literal::

id   mz     id__0  mz__0  rt__0
int  float  int    float  float
---  -----  -----  -----  -----
  0  100.0      0  100.0   10.0
  0  100.0      1  110.0   20.0
  1  200.0      2  200.0   30.0
  3  300.0      -      -      -

path to file.

emzed.Table.

path to csv file.

list of colum names, if not provided first line of csv file is used instead.

list of colum types, if not provided emzed determines types from column contents and names.

list of colum formats, if not provided emzed determines formats from column contents and names.

csv delimiter character.

cells with '-' are interpreted as None (missing value). types. In case - should be handled as a string with the single character "-" one must set this argument to False.

emzed.Table.

path to file.

list of column names, if not provided first line of .xlsx or .xls file is used instead.

list of colum types, if not provided emzed determines types from column contents and names.

list of colum formats, if not provided emzed determines formats from column contents and names.

emzed.Table.

path to file.

emzed.Table.

Maximum number of rows to display. If the table is longer only head and tail of the table are shown. The missing part is denoted with "...".

If specified the width of columns can be restricted.

file object to redirect printing, e.g. to a file.

the name of the exisiting column.

you can use a list with the same length as table or an expression.

supported colum types are int, float, bool, MzType, RtType, str, PeakMap, Table, object. In case you want to use Python objects like lists or dicts, use column type 'object' instead.

is a format string as "%d" or or an executable string with python code. To suppress visibility set format_ = None. By default (not_specified) the method tries to determine a default format for the type.

The column keeps its existing position in the table.

existing column name.

any of accepted types int, float, bool, MzType, RtType, str, PeakMap, Table.

target column type. If None, the current column type is used.

target column format. By default the existing format or the default format for type_ is used.

path describing target location.

If set to True an existing file will be overwritten, else an exception will be thrown.

specifies path of the file. The path must end with .csv.

Alias for sep. Default value is set to Excel dialect ';'.

If True, formatted values will be stored. Note, format settings can lead to information loss, i.e. if column format value is set to .2f% only the first 2 decimal places will be saved.

if True, missing values are written as - when as_printed is enabled.

If set to True an existing file will be overwritten, else an exception will be thrown.

specifies path of the file. The path must end with .xls or .xlsx.

column name.

accepted column format (see add_column).

None.

column name.

accepted column type (see add_column).

None.

title string stored with the table metadata.

one or more column names as separate arguments.

either bool or list/tuple of bools of same number as specified column names.

emzed.Table.

column names with values defining split groups.

a list of sub_tables

Example: If we have a table t as

.. parsed-literal::

a   b   c
int int int
--- --- ---
  1   1   1
  1   1   2
  2   1   3
  2   2   4

sub_tables = t.splitBy("a") results 3 subtables

sub_tables[0]

.. parsed-literal::

a   b   c
int int int
--- --- ---
  1   1   1
  1   1   2

sub_tables[1]

.. parsed-literal::

a   b   c
int int int
--- --- ---
  2   1   3

and subtables[2]

.. parsed-literal::

a   b   c
int int int
--- --- ---
  2   2   4

column names with values defining split groups.

a generator object of subtables

refering to example table split_by:

sub_tables=t.split_by_iter("a")

print(next(sub_tables))

results

.. parsed-literal::

a   b   c
int int int
--- --- ---
  1   1   1
  1   1   2

hence the first sub_table of t, corresponding to sub_tables[0] in split_by example. split_by_iter can be more memory efficient than split_by.

list or tuple of Tables. All tables must have the same colum names with same types and formats.

If specified the result will be a Table with a db file backend, else the result will be managed in memory.

Indicate if an already existing database file should be overwritten.

emzed.Table.

list or tuple of column names.

list of common postfixes.

Examples: Assuming a Table with columns ['rt', 'rtmin', 'rtmax', 'rt1', 'rtmin1'].

t.supported_postfixes(['rt'])

returns ['', 'min', 'max', '1', 'min1']

t.supported_postfixes(['rt', 'rtmin'])

returns ['', '1']

t.supported_postfixes(['rt', 'rtmax'])

returns ['']