coalispr.bedgraph_analyze.store¶

Module for dealing with file storage and retrieval to and from BNY.

to do: Change saving format to TSV using command parameter.

Attributes¶

logger

Functions¶

`config_from_newdirs`(exp, path)	Create storage folders during the initialization step `coalispr init`.
`get_unselected_folderpath`()	Return path to folder with written bam files for unselected reads that
`store_chromosome_data`(name, plusdata, minusdata, tag)	Binarize binned bedgraph dataframes for easy access.
`store_processed_chrindexes`(name, chrnam, plusdata, ...)	Binarize chromosomal indexfile tuples for easy access.
`save_average_table`(df, name, kind, samples)	Save averaged count tables with given keywords in the folder/filename.
`retrieve_merged`([tag])	Retrieve the merged experimental data.
`retrieve_processed_files`(name, tag[, notag])	Retrieve experimental data from binary files.
`retrieve_merged_unselected`()	Returns merged unselected data, organized per binned chromosome.
`get_inputtotals`([kind])	Returns total input counts for 'kind' of sequence from saved files.
`has_been_run`(options[, backup])	Check folders for possibility to contine with options.
`backup_binary_to_tsv`([data_only, merged_only])	Convert binary bedgraph-data to text; skip indexes-only files.
`binary_from_backup_tsv`()	Restore binary bedgraph-data from text files. This will replace
`rename_in_data_tsv`(names_old_new)	Replace sample names in data files.
`rename_unselected`(names_old_new)	Replace sample in file names
`rename_in_count_tsv`(names_old_new)	Replace sample names in count files.
`rename_in_expfile`(names_old_new)	Replace sample names in experiment file EXPFILE.
`print_memory_usage_merged`()	Show pandas memory usage of merged data frames.

Module Contents¶

coalispr.bedgraph_analyze.store.logger¶

coalispr.bedgraph_analyze.store.config_from_newdirs(exp, path)¶

Create storage folders during the initialization step coalispr init.

Returns:: Paths to storage folders linked to new experiment EXP.
Return type:: Path

coalispr.bedgraph_analyze.store.get_unselected_folderpath()¶: Return path to folder with written bam files for unselected reads that have been retrieved during counting of UNSPECIFIC reads.

coalispr.bedgraph_analyze.store.store_chromosome_data(name, plusdata, minusdata, tag, notag=False, suffix=BNY, otherpath=None)¶

Binarize binned bedgraph dataframes for easy access.

Parameters:

name (str) – Name for file to be stored.
plusdata (object) – Data for plus strand.
minusdata (object) – Data for minus strand.
tag (str) – Flag TAG to indicate kind of aligned-reads, TAGUNCOLL or TAGCOLL.
notag (bool) – Flag to indicate whether ‘tag’ needs an argument.
suffix (str) – Suffix indicating file format and used to select function name for storing dataframes by pandas.
otherpath (Path) – Path to storage location if different from default _get_store_path().

Returns:

Prints message upon completion of function

Return type:

None

coalispr.bedgraph_analyze.store.store_processed_chrindexes(name, chrnam, plusdata, minusdata, tag)¶

Binarize chromosomal indexfile tuples for easy access.

Parameters:

name (str) – Name for file to be stored.
chrnam (str) – Name of chromosome for which data are stored.
plusdata (object) – Data for plus strand of chromosome chrnam.
minusdata (object) – Data for minus strand of chromosome chrnam.
tag (str) – Flag to indicate kind of aligned-reads, TAGUNCOLL or TAGCOLL.

Returns:

Prints message upon completion of function.

Return type:

None

coalispr.bedgraph_analyze.store.save_average_table(df, name, kind, samples)¶

Save averaged count tables with given keywords in the folder/filename.

Parameters:

name (str) – Name of filename for output table to save; is equal to figure name.
kind (str (default: SPECIFIC)) – What type of counted reads to use, i.e. SPECIFIC or UNSPECIFIC.
samples (list) – List of library samples used for averaging dataframe.

coalispr.bedgraph_analyze.store.retrieve_merged(tag=TAG)¶

Retrieve the merged experimental data.

Parameters:: tag (str) – Flag TAG to indicate kind of aligned-reads, TAGUNCOLL or TAGCOLL.
Returns:: A tuple of dicts, one for each strand, with pandas dataframes, one for each chromosome, with columns of bedgraph values summed per BINSET for each sample.
Return type:: dict of pandas.DataFrames, dict of pandas.DataFrames

coalispr.bedgraph_analyze.store.retrieve_processed_files(name, tag, notag=False)¶

Retrieve experimental data from binary files.

Defines internal class FileTooShortWarning(Exception)

Parameters:

name (str) – Name for file
tag (str) – Flag TAG to indicate kind of aligned-reads, TAGUNCOLL or TAGCOLL.
notag (bool) – Flag to indicate whether ‘tag’ needs an argument.

Raises:

FileTooShortWarning – Raised when stored file has no significant size; previous file writing was inadequate.

Returns:

A tuple of dicts, one for each strand, with data structures, one for each chromosome.

Return type:

dict, dict

coalispr.bedgraph_analyze.store.retrieve_merged_unselected()¶: Returns merged unselected data, organized per binned chromosome.

coalispr.bedgraph_analyze.store.get_inputtotals(kind=TAGUNCOLL)¶

Returns total input counts for ‘kind’ of sequence from saved files.

Parameters:: kind (str) – Type of reads, TAGUNCOLL (all reads) or TAGCOLL (unique cDNAs).

coalispr.bedgraph_analyze.store.has_been_run(options, backup=False)¶

Check folders for possibility to contine with options.

Parameters:: options (list) – List of keys to find folders to check

coalispr.bedgraph_analyze.store.backup_binary_to_tsv(data_only=False, merged_only=False)¶

Convert binary bedgraph-data to text; skip indexes-only files.

Returns:: Prints message upon completion of function
Return type:: None

coalispr.bedgraph_analyze.store.binary_from_backup_tsv()¶

Restore binary bedgraph-data from text files. This will replace original STOREBINARY contents.

Returns:: Prints message upon completion of function
Return type:: None

coalispr.bedgraph_analyze.store.rename_in_data_tsv(names_old_new)¶

Replace sample names in data files.

Parameters:: names_old_new (list of tuples: [(old_name1, new_name1),) – (old_name2, new_name2),]
Return type:: boolean expressing completion.

coalispr.bedgraph_analyze.store.rename_unselected(names_old_new)¶

Replace sample in file names

Parameters:: names_old_new (list of tuples: [(old_name1, new_name1),) – (old_name2, new_name2),]
Return type:: boolean expressing completion.

coalispr.bedgraph_analyze.store.rename_in_count_tsv(names_old_new)¶

Replace sample names in count files.

Parameters:: names_old_new (list of tuples: [(old_name1, new_name1),) – (old_name2, new_name2),]
Returns:: Flag expressing completion.
Return type:: boolean

coalispr.bedgraph_analyze.store.rename_in_expfile(names_old_new)¶

Replace sample names in experiment file EXPFILE.

Parameters:: names_old_new (list of tuples: [(old_name1, new_name1),) – (old_name2, new_name2),]
Return type:: boolean expressing completion.

coalispr.bedgraph_analyze.store.print_memory_usage_merged()¶

Show pandas memory usage of merged data frames.

Returns:: Floats describing (in MBs) memory usage of reference, TAGCOLL or TAGUNCOLL datasets in Pandas.
Return type:: floats