pluto.tools.TableReader¶

class pluto.tools.TableReader(filename, comment_char='#', delimiter='\t')[source]¶

Handler for reading a table with comments

Allows for parsing file attributes and rows without loading the whole file into memory

Note

Input file must have column headers!

Parameters

filename (str) – path to input file
comment_char (str) – comment character for the file
delimiter (str) – file field delimiter

Examples

Example usage:

table_reader = TableReader(input_maf_file)
comment_lines = table_reader.comment_lines
fieldnames = table_reader.get_fieldnames()
records = [ rec for rec in table_reader.read() ]

__init__(filename, comment_char='#', delimiter='\t')[source]¶

Parameters

filename (str) – path to input file
comment_char (str) – comment character for the file
delimiter (str) – file field delimiter

Examples

Example usage:

table_reader = TableReader(input_maf_file)
comment_lines = table_reader.comment_lines
fieldnames = table_reader.get_fieldnames()
records = [ rec for rec in table_reader.read() ]

Methods

`__init__`(filename[, comment_char, delimiter])	param filename path to input file
`count`()	Return the total number of records in the table
`get_fieldnames`()	returns the list of fieldnames for the table
`get_reader`(fin)	returns the csv.DictReader for the table rows, skipping the comments
`read`()	iterable to get the record rows from the table, skipping the comments