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pyNBS.gene_conversion_tools
gene_conversion_tools is a module that contains functions for constructing the Cancer Subnetwork and mapping gene names to HGNC symbols.
This module contains the following functions:
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exclude_id: This function is used to determine if id to be input is a valid gene name. A valid gene name should not contain parentheses or quotations or whitespace. -
get_identifier_without_prefix: Remove the naming system prefix, if there is one. -
query_constructor: Construct string for bach query to MyGene.Info v3.0.0 API -
query_batch: Function for posting batch query to MyGene.info v3.0.0 API -
construct_query_map_table: Construct matched queries maps -
filter_query_edgelist: Filter edgelist to remove all genes that contain invalid query names. This function is only required if there are any invalid genes found byquery_constructor -
convert_edgelist: Convert network edge lists. Third column is for weights if desired to pass weights forward. -
convert_custom_namelist:Sometimes each node needs to be converted by its best match if there are multiple names per node. This function uses the match_table constructed earlier to convert genes to either symbol or entrez format only. -
filter_converted_edgelist: Filter converted edge lists -
write_edgelist: Write edgelist to file.