keggtools.utils#

Basic utils for HTTP requests, parsing and rendering.

Classes#

ColorGradient

Create color gradient.

Functions#

`is_valid_gene_name`(value)	Check if gene identifer is valid. String must match "<org>:<number>".
`is_valid_hex_color`(value)	Check if string is a valid hex color.
`is_valid_pathway_name`(value)	Check if combined pathway identifer is valid. String must match "path:<org><number>".
`is_valid_pathway_number`(value)	Check if pathway number has correct 5 digit format.
`is_valid_pathway_org`(value)	Check if organism identifier is valid.
`merge_entrez_geneid`(diffexp[, gene_column, ...])	Use pybiomart to merge entrez gene id to differential expression dataframe.
`msig_to_kegg_id`()	Load dataframe to map canonical pathway id of MSigDB to KEGG pathway id.
`parse_tsv`(data)	Parse .tsv file from string.
`parse_tsv_to_dict`(data[, col_keys, col_values])	Parse .tsv file from string and build dict from first two columns. Other columns are ignored.
`parse_xml`(xml_object_or_string)	Returns XML Element object from string or XML Element.

Module Contents#

class keggtools.utils.ColorGradient(start, stop, steps=100)#

Create color gradient.

Parameters:

start (tuple)
stop (tuple)
steps (int)

get_list()#

Get gradient color as list.

Returns:: Returns list of hexadecimal color strings with a gradient.
Return type:: List[str]

start: tuple#

steps: int = 100#

stop: tuple#

static to_css(color)#

Convert color tuple to CSS rgb color string.

Parameters:: color (tuple) – RGB color tuple containing 3 integers
Returns:: Color as CSS string (e.g. “rgb(0, 0, 0)”).
Return type:: str

static to_hex(color)#

Convert color tuple to hex color string.

Parameters:: color (tuple) – RGB color tuple containing 3 integers.
Returns:: Hexadecimal color string (e.g. “#000000”).
Return type:: str

keggtools.utils.is_valid_gene_name(value)#

Check if gene identifer is valid. String must match “<org>:<number>”.

Parameters:: value (str) – String value to check.
Returns:: Returns True if value matches format of gene name.
Return type:: bool

keggtools.utils.is_valid_hex_color(value)#

Check if string is a valid hex color.

Parameters:: value (str) – String value to check.
Returns:: Returns True if value is valid hexadecimal color string.
Return type:: bool

keggtools.utils.is_valid_pathway_name(value)#

Check if combined pathway identifer is valid. String must match “path:<org><number>”.

Parameters:: value (str) – String value to check.
Returns:: Returns True if value matches format of pathway name.
Return type:: bool

keggtools.utils.is_valid_pathway_number(value)#

Check if pathway number has correct 5 digit format.

Parameters:: value (str) – String value to check.
Returns:: Returns True if value has the correct format of pathway number.
Return type:: bool

keggtools.utils.is_valid_pathway_org(value)#

Check if organism identifier is valid.

Parameters:: value (str) – String value to check.
Returns:: Returns True if value is a valid organism code.
Return type:: bool

keggtools.utils.merge_entrez_geneid(diffexp, gene_column='names', dataset_name='hsapiens_gene_ensembl', symbol_source='hgnc_symbol', entrez_source='entrezgene_id', use_cache=True)#

Use pybiomart to merge entrez gene id to differential expression dataframe.

Parameters:

diffexp (pandas.DataFrame) – Pandas dataframe containing to differential expression data.
gene_column (str) – Name of column in differential expression dataframe that contains to gene symbol.
dataset_name (str) – Biomart dataset to use for conversion.
symbol_source (str) – Biomart source dataset for gene symbol.
entrez_source (str) – Biomart source dataset for entrez id.
use_cache (bool) – Use cache for pybioart requests. Defaults to True.

Returns:

Returns differential expression dataframe with merged column for entrez id.

Return type:

pandas.DataFrame

keggtools.utils.msig_to_kegg_id()#

Load dataframe to map canonical pathway id of MSigDB to KEGG pathway id.

Returns:: Dataframe containing MSigDB id and KEGG pathway id.
Return type:: pandas.DataFrame
Raises:: AssertionError – If mapping file does not exist.

keggtools.utils.parse_tsv(data)#

Parse .tsv file from string.

Parameters:: data (str) – Tsv string to parse into list.
Returns:: List of items.
Return type:: list

keggtools.utils.parse_tsv_to_dict(data, col_keys=0, col_values=1)#

Parse .tsv file from string and build dict from first two columns. Other columns are ignored.

Parameters:

data (str) – Tsv string to parse.
col_keys (int) – Number of colum to parse as dict keys (0-index).
col_values (int) – Number of colum to parse as dict values (0-index).

Returns:

Dict of two tsv columns.

Return type:

Dict[str, str]

keggtools.utils.parse_xml(xml_object_or_string)#

Returns XML Element object from string or XML Element.

Parameters:

xml_object_or_string (str | xml.etree.ElementTree.Element) – Input parameter to check.
xml_object_or_string

Returns:

XML element instance.

Return type:

xml.etree.ElementTree.Element