coalispr.resources.utilities¶

Attributes¶

logger

Functions¶

`bins_sum`(df[, level])	Sum bin-values to get bin totals.
`chrom_region`(chrnam, region)	Create label for chromosome region.
`chrxtra`()	Check for presence extra DNA and annotations.
`clean_dict`(adict)	Remove empty items from a dictionary.
`doneon`()	Return date of function called (for saving files).
`get_skip`()	Provide a value of fragment size skipped during counting,
`get_string_info`(df)	Return a string for logging info, bypassing standard out.
`get_tsvpath`()	Return location of folder with TSV files
`get_ylabel`(label[, strand, spaces])	Return formatted label for y-axis of count plots.
`is_all_zero`(df)	Is this a dataframe with only 0 values?
`joinall`(labels[, conn])	Return string of words from list or dict of labels.
`joiner`([symb])	Quote list-items when joined to string. Add start and end ' to calling
`merg`(df1, df2)	Merge bedgraphs for each chr on intervals with hits.
`percentaged`(df)	Turn dataframe values into percentages of column totals.
`remove_odds`(termodds)	Prevent spaces or odd symbols in filename string.
`replace_dot`(termdot)	Remove dots from file name.
`replacelist`(linestring, names_old_new)	Replace sections in a string, pathname, print line etc.
`replacelist_list`(listofitems, names_old_new)	Replace items in a list.
`thisfunc`([n])	Return name of current or calling function for logging.
`timer`(func)	Print the time needed to run the decorated function.

Module Contents¶

coalispr.resources.utilities.logger¶

coalispr.resources.utilities.bins_sum(df, level=BINN)¶

Sum bin-values to get bin totals.

Parameters:

df (pandas.DataFrame) – Dataframe with bins that constitute a level to be converted.
level (str) – Column header with indices to be grouped (default=**BINN**).

Return type:

pandas.DataFrame

coalispr.resources.utilities.chrom_region(chrnam, region)¶

Create label for chromosome region.

Parameters:

chrnam (str) – Chromosome name.
region (tuple) – Tuple of coordinates.

coalispr.resources.utilities.chrxtra()¶: Check for presence extra DNA and annotations.

coalispr.resources.utilities.clean_dict(adict)¶

Remove empty items from a dictionary.

Parameters:: adict (dict) – Dictionary

coalispr.resources.utilities.doneon()¶: Return date of function called (for saving files).

coalispr.resources.utilities.get_skip()¶

Provide a value of fragment size skipped during counting, which depends on BINSTEP and MIRNAPKBUF.

Returns:: A value representing an extra margin to expand read segment with a single peak beyond 0.
Return type:: int

coalispr.resources.utilities.get_string_info(df)¶

Return a string for logging info, bypassing standard out.

Parameters:: df (pandas.DataFrame) – Dataframe to get info for.

coalispr.resources.utilities.get_tsvpath()¶: Return location of folder with TSV files

coalispr.resources.utilities.get_ylabel(label, strand=COMBI, spaces=0)¶

Return formatted label for y-axis of count plots.

Parameters:

label (str) – Read kind name to retrieve a label for configured in CNTLABELS.
strand (str) – One of COMBI, MUNR or CORB to indicate strand counted reads map to.
spaces (int) – Number of spaces to start second line with.

coalispr.resources.utilities.is_all_zero(df)¶

Is this a dataframe with only 0 values?

Parameters:: df (pandas.DataFrame) – Dataframe to get info for.
Returns:: Flag to indicate whether all values are 0.
Return type:: bool

coalispr.resources.utilities.joinall(labels, conn="', '")¶

Return string of words from list or dict of labels.

Parameters:

labels (list or dict) – List/Dictionary of lists of words to be joined.
conn (str) – Connector linking the words from labels.

coalispr.resources.utilities.joiner(symb=None)¶: Quote list-items when joined to string. Add start and end ‘ to calling format function {no control of ‘/” when using ‘repr’ by including !r}.

coalispr.resources.utilities.merg(df1, df2)¶

Merge bedgraphs for each chr on intervals with hits.

All rows/columns need to be combined; this creates duplicate columns with adapted names when non-unique columns are merged.

Parameters:

df1 (pandas.DataFrame) – Dataframes to merge
df2 (pandas.DataFrame) – Dataframes to merge

Returns:

Merged dataframe.

Return type:

pandas.DataFrame

coalispr.resources.utilities.percentaged(df)¶

Turn dataframe values into percentages of column totals.

Parameters:: df (pandas.DataFrame) – Dataframe with raw counts
Return type:: pandas.DataFrame

coalispr.resources.utilities.remove_odds(termodds)¶

Prevent spaces or odd symbols in filename string.

Parameters:: termodds (str) – String with possibly symbols or spaces in filename.
Returns:: Lower case name without odds; not to be confused with extension.
Return type:: str

coalispr.resources.utilities.replace_dot(termdot)¶

Remove dots from file name.

Parameters:: termdot (str) – String with possibly dots (‘.’) in filename (excluding extension).
Returns:: Name without dot(s); not to be confused with extension.
Return type:: str

coalispr.resources.utilities.replacelist(linestring, names_old_new)¶

Replace sections in a string, pathname, print line etc.

Parameters:

linestring (str) – String with particular sections to be replaced.
names_old_new (list of tuples) – Contents of listed tuples: (search-string, replacement).

Returns:

String after replacement.

Return type:

str

coalispr.resources.utilities.replacelist_list(listofitems, names_old_new)¶

Replace items in a list.

Parameters:

listofitems (list) – List with particular items to be changed.
names_old_new (list of tuples) – Contents of listed tuples: (search-string, replacement).

Returns:

List with items including those that have been replaced.

Return type:

list

coalispr.resources.utilities.thisfunc(n=0)¶

Return name of current or calling function for logging.

from: https://stackoverflow.com/questions/5067604/determine-function-name-from-within-that-function-without-using-traceback

https://docs.quantifiedcode.com/python-anti-patterns/correctness/assigning_a_lambda_to_a_variable.html

https://docs.quantifiedcode.com/python-anti-patterns/correctness/accessing_a_protected_member_from_outside_the_class.html

Parameters:: n (int) – For current func name, specify 0 or no argument. For name of caller of current func, specify 1. For name of caller of caller of current func, specify 2. etc.
Returns:: Name of function containing call.
Return type:: str

coalispr.resources.utilities.timer(func)¶: Print the time needed to run the decorated function. from: https://realpython.com/primer-on-python-decorators/