plastid.util.scriptlib.argparsers module¶

This module contains classes that:

build argparse.ArgumentParser objects for various data types used in genomics

parse those arguments into useful file types

Arguments are grouped into the following sets:

Parameter/argument set

Parser building class

Generic parameters (e.g. for error reporting, logging)

BaseParser

Read alignments or count files

AlignmentParser

Genomic feature or mask annotations

AnnotationParser

Genomic sequence files

SequenceParser

Plotting parameters for charts

PlottingParser

Example¶

To use any of these in your own command line scripts, follow these steps:

Import one or more of the classes above:

>>> import argparse
>>> from plastid.util.scriptlib.argparsers import AnnotationParser

Use the first function to create an ArgumentParser, and supply this object as a parent when you build your script’s ArgumentParser:

>>> ap = AnnotationParser()

# create annotation file parser
>>> annotation_file_parser = ap.get_parser(disabled=["some_option_to_disable"])

# create my own parser, incorporating flags from annotation_file_parser
>>>> my_own_parser = argparse.ArgumentParser(parents=[annotation_file_parser])

# add script-specific arguments
>>> my_own_parer.add_argument("positional_argument",type=str)
>>> my_own_parser.add_argument("--foo",type=int,default=5,help="Some option")
>>> my_own_parser.add_argument("--bar",type=str,default="a string",help="Another option")

Then, use the second parse the arguments:

>>> args = parser.parse_args()

# get transcript objects from arguments
# this will be an iterator over |Transcripts|
>>> transcripts = ap.get_transcripts_from_args(args)

>>> pass # rest of your script

Your script will then be able process whatever sorts of annotation files that plastid currently supports.

See Also¶

argparse: Python documentation on argument parsing
plastid.bin: Source code of command-line scripts, for further examples

class plastid.util.scriptlib.argparsers.AlignmentParser(prefix='', disabled=None, input_choices=('BAM', 'bigwig', 'bowtie', 'wiggle'), groupname='alignment_options', allow_mapping=True)[source]¶

Bases: plastid.util.scriptlib.argparsers.Parser

Parser for files containing read alignments or quantitative data.

Checks for additional mapping rules and command-line arguments by checking the entrypoints plastid.mapping_rules and plastid.mapping_options

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
prefixstr, optional: string prefix to add to default argument options (Default: “”)
disabledlist, optional: list of parameter names that should be disabled from parser, without preceding dashes
input_choiceslist, optional: list of permitted alignment file type choices for input
allow_mappingbool, optional: Enable/disable user configuration of mapping rules (default: True)

Methods

`get_genome_array_from_args`(args[, printer])	Return a `GenomeArray`, `SparseGenomeArray` or `BAMGenomeArray` from arguments parsed by `get_alignment_file_parser()`
`get_parser`([title, description])	Return an `ArgumentParser` that opens alignment (BAM, or bowtie) or count (Wiggle, bedGraph) files.

get_genome_array_from_args(args, printer=None)[source]¶

Return a GenomeArray, SparseGenomeArray or BAMGenomeArray from arguments parsed by get_alignment_file_parser()

Parameters

argsargparse.Namespace: Arguments from the parser
printerfile-like, optional: A stream to which stderr-like info can be written (default: NullWriter)

Returns

GenomeArray, SparseGenomeArray, or BAMGenomeArray

get_parser(title='count & alignment file options', description='Open alignment or count files and optionally set mapping rules', **kwargs)[source]¶

Return an ArgumentParser that opens alignment (BAM, or bowtie) or count (Wiggle, bedGraph) files.

In the case of bowtie or BAM import, also parse arguments for mapping rules (e.g. fiveprime end mapping, threeprime end mapping, et c) and optional read length filters

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)
kwargskeyword arguments: Additional arguments to pass to Parser.get_parser()

Returns

argparse.ArgumentParser

class plastid.util.scriptlib.argparsers.AnnotationParser(prefix='', disabled=None, groupname='annotation_options', input_choices=('BED', 'BigBed', 'GTF2', 'GFF3'))[source]¶

Bases: plastid.util.scriptlib.argparsers.Parser

Parser for annotation files in various formats

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
prefixstr, optional: string prefix to add to default argument options (Default: “”)
disabledlist, optional: list of parameter names that should be disabled from parser, without preceding dashes
input_choiceslist, optional: list of permitted alignment file type choices for input
allow_mappingbool, optional: Enable/disable user configuration of mapping rules (default: True)

Methods

`get_genome_hash_from_args`(args[, printer])	Return a `GenomeHash` of regions from command-line arguments
`get_parser`([title, description])	Return an `ArgumentParser` that opens annotation files.
`get_segmentchains_from_args`(args[, printer, ...])	Return a generator of `SegmentChain` objects from arguments parsed by `get_annotation_file_parser()`
`get_transcripts_from_args`(args[, printer, ...])	Return a generator of `Transcript` objects from arguments parsed by `get_annotation_file_parser()`

get_genome_hash_from_args(args, printer=None)[source]¶

Return a GenomeHash of regions from command-line arguments

Parameters

argsargparse.Namespace: Namespace object from get_mask_file_parser()
printerfile-like: A stream to which stderr-like info can be written (Default: NullWriter)

Returns

GenomeHash: Hashed data structure of masked genomic regions

See also

get_mask_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

get_parser(title='annotation file options (one or more annotation files required)', description='Open one or more genome annotation files', **kwargs)[source]¶

Return an ArgumentParser that opens annotation files.

Parameters

titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)
kwargskeyword arguments: Additional arguments to pass to Parser.get_parser()

Returns

argparse.ArgumentParser

get_segmentchains_from_args(args, printer=None, return_type=None, require_sort=False)[source]¶

Return a generator of SegmentChain objects from arguments parsed by get_annotation_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_annotation_file_parser()
printerfile-like, optional: A stream to which stderr-like info can be written (Default: NullWriter)
return_typeSegmentChain or subclass, optional: Type of object to return (Default: Transcript)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: SegmentChain objects, either in order of appearance (if input was a BED, BigBed, or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was GTF2 or GFF3).

See also

get_annotation_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

get_transcripts_from_args(args, printer=None, return_type=None, require_sort=False)[source]¶

Return a generator of Transcript objects from arguments parsed by get_annotation_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_annotation_file_parser()
printerfile-like, optional: A stream to which stderr-like info can be written (Default: NullWriter)
return_typeSegmentChain or subclass, optional: Type of object to return (Default: Transcript)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: Transcript objects, either in order of appearance (if input was a BED, BigBed, or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was GTF2 or GFF3).

See also

get_annotation_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

class plastid.util.scriptlib.argparsers.BaseParser(groupname='base_options', prefix='', disabled=None)[source]¶

Bases: plastid.util.scriptlib.argparsers.Parser

Parser basic options

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
prefixstr, optional: string prefix to add to default argument options (Default: “”)
disabledlist, optional: list of parameter names that should be disabled from parser, without preceding dashes

Methods

get_parser([title, description])

Return an ArgumentParser

get_base_ops_from_args

get_base_ops_from_args(args)[source]¶

get_parser(title=None, description=None)[source]¶

Return an ArgumentParser

Parameters

titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)

Returns

argparse.ArgumentParser

class plastid.util.scriptlib.argparsers.MaskParser(prefix='mask_', disabled=None, groupname='mask_options', input_choices=('BED', 'BigBed', 'GTF2', 'GFF3', 'PSL'))[source]¶

Bases: plastid.util.scriptlib.argparsers.AnnotationParser

Create a parser for masking genomic features given in an annotation file

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
prefixstr, optional: string prefix to add to default argument options (Default: “”)
disabledlist, optional: list of parameter names that should be disabled from parser, without preceding dashes
input_choiceslist, optional: list of permitted alignment file type choices for input
allow_mappingbool, optional: Enable/disable user configuration of mapping rules (default: True)

Methods

`get_genome_hash_from_args`(args[, printer])	Return a `GenomeHash` of regions from command-line arguments
`get_parser`([title, description])	Return an `ArgumentParser` that opens annotation files as masks alignment (BAM or bowtie) or count (Wiggle, bedGraph) files.
`get_segmentchains_from_args`(args[, printer, ...])	Return a generator of `SegmentChain` objects from arguments parsed by `get_annotation_file_parser()`
`get_transcripts_from_args`(args[, printer, ...])	Return a generator of `Transcript` objects from arguments parsed by `get_annotation_file_parser()`

get_genome_hash_from_args(args, printer=None)¶

Return a GenomeHash of regions from command-line arguments

Parameters

argsargparse.Namespace: Namespace object from get_mask_file_parser()
printerfile-like: A stream to which stderr-like info can be written (Default: NullWriter)

Returns

GenomeHash: Hashed data structure of masked genomic regions

See also

get_mask_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

get_parser(title='mask file options (optional)', description='Add mask file(s) that annotate regions that should be excluded from analyses\n(e.g. repetitive genomic regions).', **kwargs)[source]¶

Return an ArgumentParser that opens annotation files as masks alignment (BAM or bowtie) or count (Wiggle, bedGraph) files.

Parameters

titlestr, optional

title for option group (used in command-line help screen)

descriptionstr, optional

description of parser (used in command-line help screen)

arglistlist, optional

If not None, arguments in this list will be added to parser. Otherwise, arguments will be taken from self.arguments.

The list should be a list of tuples of (‘argument_name’,dict_of_options), where argument_name is a string, and dict_of_options a dictionary of keyword arguments to pass to argparse.ArgumentParser.add_argument().

Returns

argparse.ArgumentParser

get_segmentchains_from_args(args, printer=None, return_type=None, require_sort=False)¶

Return a generator of SegmentChain objects from arguments parsed by get_annotation_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_annotation_file_parser()
printerfile-like, optional: A stream to which stderr-like info can be written (Default: NullWriter)
return_typeSegmentChain or subclass, optional: Type of object to return (Default: Transcript)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: SegmentChain objects, either in order of appearance (if input was a BED, BigBed, or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was GTF2 or GFF3).

See also

get_annotation_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

get_transcripts_from_args(args, printer=None, return_type=None, require_sort=False)¶

Return a generator of Transcript objects from arguments parsed by get_annotation_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_annotation_file_parser()
printerfile-like, optional: A stream to which stderr-like info can be written (Default: NullWriter)
return_typeSegmentChain or subclass, optional: Type of object to return (Default: Transcript)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: Transcript objects, either in order of appearance (if input was a BED, BigBed, or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was GTF2 or GFF3).

See also

get_annotation_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

class plastid.util.scriptlib.argparsers.Parser(groupname=None, prefix='', disabled=None, **kwargs)[source]¶

Bases: object

Base class for argument parser factories used below

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
prefixstr, optional: string prefix to add to default argument options (Default: “”)
disabledlist, optional: list of parameter names that should be disabled from parser, without preceding dashes

Methods

get_parser([parser, groupname, arglist, ...])

Create an populate argparse.ArgumentParser with arguments

get_parser(parser=None, groupname=None, arglist=None, title=None, description=None, **kwargs)[source]¶

Create an populate argparse.ArgumentParser with arguments

Parameters

parserargparse.ArgumentParser or None, optional

If None, a new parser will be created, and arguments will be added to it. If not None, arguments will be added to parser. (Default: None)

groupnamestr or None, optional

If not None, default to self.groupname. If either groupname or self.groupname is not None, an option group with this name will be added to parser, and arguments added to that groupname instead of the main argument group of parser. In this case, title and description will be applied to the option group instead of to parser. Default : None)

arglistlist, optional

If not None, arguments in this list will be added to parser. Otherwise, arguments will be taken from self.arguments.

The list should be a list of tuples of (‘argument_name’,dict_of_options), where argument_name is a string, and dict_of_options a dictionary of keyword arguments to pass to argparse.ArgumentParser.add_argument().

titlestr, optional

Optional title for parser

descriptionstr, optional

Optional description for parser

kwargskeyword arguments

Additional arguments passed during creation of argparse.ArgumentParser

Returns

argparse.ArgumentParser

class plastid.util.scriptlib.argparsers.PlottingParser(groupname='plotting_options', prefix='', disabled=None)[source]¶

Bases: plastid.util.scriptlib.argparsers.Parser

Parser for plotting options

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
prefixstr, optional: string prefix to add to default argument options (Default: “”)
disabledlist, optional: list of parameter names that should be disabled from parser, without preceding dashes

Methods

`get_colors_from_args`(args, num_colors)	Return a list of colors from arguments parsed by a parser from `get_plotting_parser()`
`get_figure_from_args`(args, **kwargs)	Return a `matplotlib.figure.Figure` following arguments from `get_plotting_parser()`
`get_parser`([title, description])	Return an `ArgumentParser` to control plotting
`set_style_from_args`(args)	Parse style information, if present on system and defined in args

get_colors_from_args(args, num_colors)[source]¶

Return a list of colors from arguments parsed by a parser from get_plotting_parser()

If a matplotlib colormap is specified in args.figcolors, colors will be generated from that map.

Otherwise, if a stylesheet is specified, colors will be fetched from the stylesheet’s color cycle.

Otherwise, colors will be chosen from the default color cycle specified matplotlibrc.

Parameters

argsargparse.Namespace: Namespace object from get_plotting_parser()
num_colorsint: Number of colors to fetch

Returns

list: List of matplotlib colors

get_figure_from_args(args, **kwargs)[source]¶

Return a matplotlib.figure.Figure following arguments from get_plotting_parser()

A new figure is created with parameters specified in args. If these are not found, values found in **kwargs will instead be used. If these are not found, we fall back to matplotlibrc values.

Parameters

argsargparse.Namespace: Namespace object from get_plotting_parser()
kwargskeyword arguments: Fallback arguments for items not defined in args, plus any other keyword arguments.

Returns

matplotlib.figure.Figure: Matplotlib figure

get_parser(title='Plotting options', description=None)[source]¶

Return an ArgumentParser to control plotting

Parameters

titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)

Returns

argparse.ArgumentParser

set_style_from_args(args)[source]¶

Parse style information, if present on system and defined in args

Parameters

argsargparse.Namespace: Namespace object from get_plotting_parser()

class plastid.util.scriptlib.argparsers.PrefixNamespaceWrapper(namespace, prefix)[source]¶

Bases: object

Wrapper class to facilitate processing of Namespace objects created by get_alignment_file_parser() or get_annotation_file_parser() with non-empty prefix values, as if no prefix had been used.

See also

get_annotation_file_parser
get_alignment_file_parser
get_genome_array_from_args
get_transcripts_from_args

Attributes

namespaceNamespace: Result of calling argparse.ArgumentParser.parse_args()
prefixstr: Prefix that will be prepended to names of attributes of self.namespace before they are fetched. Must match prefix that was used in creation of the argparse.ArgumentParser that created self.namespace

class plastid.util.scriptlib.argparsers.SequenceParser(groupname='sequence_options', prefix='', disabled=None, input_choices=('fasta', 'fastq', 'twobit', 'genbank', 'embl'))[source]¶

Bases: plastid.util.scriptlib.argparsers.AnnotationParser

Parser for sequence files

Parameters

groupnamestr, optional: Name of argument group. If not None, an argument group with the specified name will be created and added to the parser. If not, arguments will be in the main group.
prefixstr, optional: string prefix to add to default argument options (Default: “”)
disabledlist, optional: list of parameter names that should be disabled from parser, without preceding dashes
input_choiceslist, optional: list of permitted alignment file type choices for input

Methods

`get_genome_hash_from_args`(args[, printer])	Return a `GenomeHash` of regions from command-line arguments
`get_parser`([title, description])	Return an `ArgumentParser` that opens sequence files
`get_segmentchains_from_args`(args[, printer, ...])	Return a generator of `SegmentChain` objects from arguments parsed by `get_annotation_file_parser()`
`get_seqdict_from_args`(args[, index, printer])	Retrieve a dictionary-like object of sequences
`get_transcripts_from_args`(args[, printer, ...])	Return a generator of `Transcript` objects from arguments parsed by `get_annotation_file_parser()`

get_genome_hash_from_args(args, printer=None)¶

Return a GenomeHash of regions from command-line arguments

Parameters

argsargparse.Namespace: Namespace object from get_mask_file_parser()
printerfile-like: A stream to which stderr-like info can be written (Default: NullWriter)

Returns

GenomeHash: Hashed data structure of masked genomic regions

See also

get_mask_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

get_parser(title='sequence options', description='', **kwargs)[source]¶

Return an ArgumentParser that opens sequence files

Parameters

titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)
kwargskeyword arguments: Additional arguments to pass to Parser.get_parser()

Returns

argparse.ArgumentParser

See also

get_seqdict_from_args: function that parses the Namespace returned by this ArgumentParser

get_segmentchains_from_args(args, printer=None, return_type=None, require_sort=False)¶

Return a generator of SegmentChain objects from arguments parsed by get_annotation_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_annotation_file_parser()
printerfile-like, optional: A stream to which stderr-like info can be written (Default: NullWriter)
return_typeSegmentChain or subclass, optional: Type of object to return (Default: Transcript)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: SegmentChain objects, either in order of appearance (if input was a BED, BigBed, or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was GTF2 or GFF3).

See also

get_annotation_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

get_seqdict_from_args(args, index=True, printer=None)[source]¶

Retrieve a dictionary-like object of sequences

Parameters

argsargparse.Namespace: Namespace object from get_sequence_file_parser()
indexbool, optional: If sequence format is anything other than twobit, open with lazily-evaluating Bio.SeqIO.index() instead of Bio.SeqIO.to_dict() (Default: True)
printerfile-like: A stream to which stderr-like info can be written (Default: NullWriter)

Returns

dict-like: Dictionary-like object mapping chromosome names to Bio.SeqRecord.SeqRecord-like objects

get_transcripts_from_args(args, printer=None, return_type=None, require_sort=False)¶

Return a generator of Transcript objects from arguments parsed by get_annotation_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_annotation_file_parser()
printerfile-like, optional: A stream to which stderr-like info can be written (Default: NullWriter)
return_typeSegmentChain or subclass, optional: Type of object to return (Default: Transcript)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: Transcript objects, either in order of appearance (if input was a BED, BigBed, or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was GTF2 or GFF3).

See also

get_annotation_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

plastid.util.scriptlib.argparsers.get_alignment_file_parser(input_choices=('BAM', 'bigwig', 'bowtie', 'wiggle'), disabled=None, prefix='', title='count & alignment file options', description='Open alignment or count files and optionally set mapping rules', map_desc='For BAM or bowtie files, one of the mutually exclusive read mapping functions\nis required:\n', return_subparsers=False)[source]¶

plastid.util.scriptlib.argparsers.get_annotation_file_parser(input_choices=['BED', 'BigBed', 'GTF2', 'GFF3'], disabled=[], prefix='', title='annotation file options (one or more annotation files required)', description='Open one or more genome annotation files', return_subparsers=False)[source]¶

Return an ArgumentParser that opens annotation files from BED, BigBed, GTF2, or GFF3 formats

Parameters

input_choiceslist, optional: list of permitted alignment file type choices. (Default: ‘[“BED”,”BigBed”,”GTF2”,”GFF3”]’). ‘PSL’_ may also be added
disabledlist, optional: list of parameter names that should be disabled from parser without preceding dashes
prefixstr, optional: string prefix to add to default argument options (Default: ‘’)
titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)
return_subparsersbool, optional: if True, additionally return a dictionary of subparser option groups, to which additional options may be added (Default: False)

Returns

argparse.ArgumentParser

See also

get_transcripts_from_args: function that parses the Namespace returned by this ArgumentParser

plastid.util.scriptlib.argparsers.get_colors_from_args(args, num_colors)[source]¶

Return a list of colors from arguments parsed by a parser from get_plotting_parser()

If a matplotlib colormap is specified in args.figcolors, colors will be generated from that map.

Otherwise, if a stylesheet is specified, colors will be fetched from the stylesheet’s color cycle.

Otherwise, colors will be chosen from the default color cycle specified matplotlibrc.

Parameters

argsargparse.Namespace: Namespace object from get_plotting_parser()
num_colorsint: Number of colors to fetch

Returns

list: List of matplotlib colors

plastid.util.scriptlib.argparsers.get_figure_from_args(args, **kwargs)[source]¶

Return a matplotlib.figure.Figure following arguments from get_plotting_parser()

A new figure is created with parameters specified in args. If these are not found, values found in **kwargs will instead be used. If these are not found, we fall back to matplotlibrc values.

Parameters

argsargparse.Namespace: Namespace object from get_plotting_parser()
kwargskeyword arguments: Fallback arguments for items not defined in args, plus any other keyword arguments.

Returns

matplotlib.figure.Figure: Matplotlib figure

plastid.util.scriptlib.argparsers.get_genome_array_from_args(args, prefix='', disabled=None, printer=None)[source]¶

Return a GenomeArray, SparseGenomeArray or BAMGenomeArray from arguments parsed by get_alignment_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_alignment_file_parser()
prefixstr, optional: string prefix to add to default argument options (Default: “”) Must be same prefix that was added in call to get_alignment_file_parser() (Default: “”)
disabledlist, optional: list of parameter names that were disabled when the argparser was created in get_alignment_file_parser(). (Default: [])
printerfile-like, optional: A stream to which stderr-like info can be written (default: NullWriter)

Returns

GenomeArray, SparseGenomeArray, or BAMGenomeArray

See also

get_alignment_file_parser: Function that creates ArgumentParser whose output Namespace is processed by this function

plastid.util.scriptlib.argparsers.get_genome_hash_from_mask_args(args, prefix='mask_', printer=NullWriter())[source]¶

Return a GenomeHash of regions from command-line arguments

Parameters

argsargparse.Namespace: Namespace object from get_mask_file_parser()
prefixstr, optional: string prefix to add to default argument options. Must be same prefix that was added in call to get_mask_file_parser() (Default: “mask_”)
printerfile-like: A stream to which stderr-like info can be written (Default: NullWriter)

Returns

GenomeHash: Hashed data structure of masked genomic regions

See also

get_mask_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

plastid.util.scriptlib.argparsers.get_mask_file_parser(prefix='mask_', disabled=[])[source]¶

Create an ArgumentParser to open annotation files that describe regions of the genome to mask from analyses

Parameters

prefixstr, optional: Prefix to add to default argument options (Default: ‘mask_’)
disabledlist, optional: list of parameter names to disable from the mask file parser (Default: []. add_three is always disabled.)

Returns

argparse.ArgumentParser

See also

get_genome_hash_from_mask_args: function that parses the Namespace returned by this ArgumentParser

plastid.util.scriptlib.argparsers.get_plotting_parser(prefix='', disabled=[], title='Plotting options')[source]¶

Return an ArgumentParser to control plotting

Parameters

disabledlist, optional: list of parameter names that should be disabled from parser without preceding dashes
prefixstr, optional: string prefix to add to default argument options (Default: ‘’)
titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)

Returns

argparse.ArgumentParser

See also

get_colors_from_args: parse colors and/or colormaps from this argument parser

plastid.util.scriptlib.argparsers.get_segmentchain_file_parser(input_choices=['BED', 'BigBed', 'GTF2', 'GFF3', 'PSL'], disabled=[], prefix='', title='annotation file options (one or more annotation files required)', description='Open one or more genome annotation files')[source]¶

Create an ArgumentParser to open annotation files as SegmentChains

Parameters

input_choiceslist, optional: list of permitted alignment file type choices (Default: [“BED”,”BigBed”,”GTF2”,”GFF3”, “PSL”])
disabledlist, optional: list of parameter names that should be disabled from parser without preceding dashes
prefixstr, optional: string prefix to add to default argument options (Default: ‘’)
titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)

Returns

argparse.ArgumentParser

See also

get_segmentchains_from_args: function that parses the Namespace returned by this ArgumentParser

plastid.util.scriptlib.argparsers.get_segmentchains_from_args(args, prefix='', disabled=[], printer=NullWriter(), require_sort=False)[source]¶

Return a list of SegmentChain objects from arguments parsed by an ArgumentParser created by get_segmentchain_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_segmentchain_file_parser()
prefixstr, optional: string prefix to add to default argument options. Must be same prefix that was added in call to get_segmentchain_file_parser() (Default: “”)
disabledlist, optional: list of parameter names that were disabled when the annotation file parser was created by get_segmentchain_file_parser(). (Default: [])
printerfile-like: A stream to which stderr-like info can be written (Default: NullWriter)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: sequence of SegmentChain objects, either in order of appearance (if input was a BED or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was) GTF or GFF

See also

get_segmentchain_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function

plastid.util.scriptlib.argparsers.get_seqdict_from_args(args, index=True, prefix='', printer=NullWriter())[source]¶

Retrieve a dictionary-like object of sequences

Parameters

argsargparse.Namespace: Namespace object from get_sequence_file_parser()
prefixstr, optional: string prefix to add to default argument options. Must be same prefix that was added in call to get_sequence_file_parser() (Default: “”)
indexbool, optional: If sequence format is anything other than twobit, open with lazily-evaluating Bio.SeqIO.index() instead of Bio.SeqIO.to_dict() (Default: True)
printerfile-like: A stream to which stderr-like info can be written (Default: NullWriter)

Returns

dict-like: Dictionary-like object mapping chromosome names to Bio.SeqRecord.SeqRecord-like objects

plastid.util.scriptlib.argparsers.get_sequence_file_parser(input_choices=('fasta', 'fastq', 'twobit', 'genbank', 'embl'), disabled=(), prefix='', title='sequence options', description='')[source]¶

Return an ArgumentParser that opens annotation files from BED, BigBed, GTF2, or GFF3 formats

Parameters

input_choiceslist, optional: list of permitted sequence file type choices. (Default: ‘[“FASTA”,”twobit”,”genbank”,”embl”]’).
disabledlist, optional: list of parameter names that should be disabled from parser without preceding dashes
prefixstr, optional: string prefix to add to default argument options (Default: ‘’)
titlestr, optional: title for option group (used in command-line help screen)
descriptionstr, optional: description of parser (used in command-line help screen)

Returns

argparse.ArgumentParser

See also

get_seqdict_from_args: function that parses the Namespace returned by this ArgumentParser

plastid.util.scriptlib.argparsers.get_transcripts_from_args(args, prefix='', disabled=[], printer=NullWriter(), return_type=None, require_sort=False)[source]¶

Return a list of Transcript objects from arguments parsed by get_annotation_file_parser()

Parameters

argsargparse.Namespace: Namespace object from get_annotation_file_parser()
prefixstr, optional: string prefix to add to default argument options. Must be same prefix that was added in call to get_annotation_file_parser() (Default: ‘’)
disabledlist, optional: list of parameter names that were disabled when the annotation file parser was created by get_annotation_file_parser(). (Default: [])
printerfile-like, optional: A stream to which stderr-like info can be written (Default: NullWriter)
return_typeSegmentChain or subclass, optional: Type of object to return (Default: Transcript)
require_sortbool, optional: If True, quit if the annotation file(s) are not sorted or indexed

Returns

iterator: Transcript objects, either in order of appearance (if input was a BED, BigBed, or PSL file), or sorted lexically by chromosome, start coordinate, end coordinate, and then strand (if input was GTF2 or GFF3).

See also

get_annotation_file_parser: Function that creates argparse.ArgumentParser whose output Namespace is processed by this function