Parsers

Predefined parsers

class BedParser

Standard Full BED Parser of 10 Columns

class ANNParser

Annotation Parser, 6 columns

class BasicParser

Parser for Chr, Start, Stop only (no Strand)

class NarrowPeakParser

Narrow Peaks Parser. 10 columns

class RnaSeqParser

Standard Full BED Parser of 10 Columns

class BedScoreParser

Standard Full BED Parser of 10 Columns

Customizable parser

All the parsers in PyGMQL extend the RegionParser

class RegionParser(gmql_parser=None, chrPos=None, startPos=None, stopPos=None, strandPos=None, otherPos=None, delimiter='t', coordinate_system='0-based', schema_format='del', parser_name='parser')

Creates a custom region dataset

Parameters:

• chrPos – position of the chromosome column
• startPos – position of the start column
• stopPos – position of the stop column
• strandPos – (optional) position of the strand column. Default is None
• otherPos – (optional) list of tuples of the type [(pos, attr_name, typeFun), …]. Default is None
• delimiter – (optional) delimiter of the columns of the file. Default ” “
• coordinate_system – can be {‘0-based’, ‘1-based’, ‘default’}. Default is ‘0-based’
• schema_format – (optional) type of file. Can be {‘tab’, ‘gtf’, ‘vcf’, ‘del’}. Default is ‘del’
• parser_name – (optional) name of the parser. Default is ‘parser’

get_gmql_parser()

Gets the Scala implementation of the parser

Returns:a Java Object

static parse_strand(strand)

Defines how to parse the strand column

Parameters:strand – a string representing the strand Returns:the parsed result

parse_regions(path)

Given a file path, it loads it into memory as a Pandas dataframe

Parameters:path – file path Returns:a Pandas Dataframe

get_attributes()

Returns the unordered list of attributes

Returns:list of strings

get_ordered_attributes()

Returns the ordered list of attributes

Returns:list of strings

get_types()

Returns the unordered list of data types

Returns:list of data types

get_name_type_dict()

Returns a dictionary of the type {‘column_name’: data_type, …}

Returns:dict

get_ordered_types()

Returns the ordered list of data types

Returns:list of data types