coalispr.resources.utilities¶

Attributes¶

`logger`
`TEST`
`binary_read`
`binary_write`

Functions¶

`bins_sum`(df[, level])	Sum bin-values to get bin totals.
`check_newpath`(p)
`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_bnypath`()	Return location of folder with BNY files
`get_count_folder`(kind)	Return folder name for stored count 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.
`include_test`()	Include test command for profiling functions
`is_all_zero`(df)	Is this a dataframe with only 0 values?
`is_backedup`(pathtofile[, moveit])	Create a backup of file or directory or link, return success.
`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.
`multi_process`(func, keys)	Generalized multi_processor function for counting reads.
`percentaged`(df)	Turn dataframe values into percentages of column totals.
`read_bny`(filenam, kwargs)	Reader of tabbed binary files, returns dataframe.
`read_tsv`(filenam[, kwargs])	Reader of tabbed csv files, returns dataframe.
`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.
`write_bny`(df, filenam[, kwargs])	Writer of binary files from dataframe.
`write_suffix`(suffix, df, filenam[, kwargs])	Select and write file based on suffix
`write_tsv`(df, filenam[, kwargs])	Writer of tabbed csv files from dataframe.

Module Contents¶

coalispr.resources.utilities.logger¶

coalispr.resources.utilities.TEST = False¶

coalispr.resources.utilities.binary_read¶

coalispr.resources.utilities.binary_write¶

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.check_newpath(p)¶

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_bnypath()¶: Return location of folder with BNY files

coalispr.resources.utilities.get_count_folder(kind)¶

Return folder name for stored count files

Parameters:: kind (str) – Kind of reads: UNSPECIFIC or SPECIFIC

Notes

TAGBAM: str (bam): Flag to indicate sort of aligned-reads, TAGCOLL or TAGUNCOLL, used to obtain bam-alignments.
TAGSEG: str (segments): Flag to indicate sort of aligned-reads, TAGCOLL or TAGUNCOLL, used to obtain segment definitions.
LOG2BG: int (over): Exponent to set threshold above which read signals are considered; part of folder name with stored count files.
UNSPECLOG10: float (unspec): Exponent to set difference between SPECIFIC and UNSPECIFIC reads; part of folder name with stored count files.
gaps: int: Region tolerated between peaks of mapped reads to form a contiguous segment, USEGAPS or UNSPCGAPS.

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.include_test()¶: Include test command for profiling functions

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.is_backedup(pathtofile, moveit=True)¶

Create a backup of file or directory or link, return success.

Parameters:¶

pathtofile: Path: Path to object to be overwritten/replaced with a new version with the same name.
moveit: bool: Flag to indicate to rename and move file (default) or copy it.

returns:: Flag to indicate backup process went through.
rtype:: 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.multi_process(func, keys)¶

Generalized multi_processor function for counting reads.

Parameters:

func (function) – Name of function to run in separate process.
keys (list) – List of keys - SHORT names, each leading to one alignment file to be counted in a separate process.

Returns:

collected_objects – Collection of objects generated by fusing outcomes of each process.

Return type:

list

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.read_bny(filenam, kwargs)¶

Reader of tabbed binary files, returns dataframe.

Parameters:

filenam (Path or str) – Input binary file
kwargs (dict) – Additional parameters

coalispr.resources.utilities.read_tsv(filenam, kwargs=None)¶

Reader of tabbed csv files, returns dataframe.

Parameters:

filenam (Path or str) – Input text file
kwargs (dict) – Additional parameters fitting pd.to_csv; omit comment and sep

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/

coalispr.resources.utilities.write_bny(df, filenam, kwargs=None)¶

Writer of binary files from dataframe.

Parameters:

df (pd.DataFrame) – Dataframe to save.
filnam (Path or str) – Output binary file.
kwargs (dict) – Additional parameters fitting pd.to_<format>;

coalispr.resources.utilities.write_suffix(suffix, df, filenam, kwargs=None)¶: Select and write file based on suffix

coalispr.resources.utilities.write_tsv(df, filenam, kwargs=None)¶

Writer of tabbed csv files from dataframe.

Parameters:

df (pd.DataFrame) – Dataframe to save
filnam (Path or str) – Output path for tabbed text file
kwargs (dict) – Additional parameters, apart from ‘comment’, ‘sep’, ‘quoting’, ‘quotingchar’, or ‘escapechar’, fitting pd.to_csv.