GFA

class gratools.Graph.GFA(gfa_path: ~pathlib.Path, logger: ~logging.Logger = <factory>, gfa_name: str | None = None, version: float | None = None, header_gfa: list = <factory>, sample_reference: str | None = None, bam_segments_file: ~pathlib.Path | None = None, dict_link_SA_SB: ~collections.defaultdict = <factory>, dict_samples_chrom: ~collections.defaultdict = <factory>, dict_segments_size: ~collections.defaultdict = <factory>, dict_segments_samples: ~collections.defaultdict = <factory>, dict_samples_bed: ~collections.defaultdict = <factory>, works_path: ~pathlib.Path | None = None, bed_path: ~pathlib.Path | None = None, bam_path: ~pathlib.Path | None = None)[source]

Bases: object

A class to parse and process GFA files, including handling BAM files and extracting segments and links.

gfa_path

The path to the GFA file.

Type:: Path

gfa_name

The name of the GFA file.

Type:: str

version

The version of the GFA file.

Type:: float

header_gfa

The header information from the GFA file.

Type:: list

sample_reference

The reference sample from the GFA file.

Type:: str

bam_segments_file

The path to the BAM segments file.

Type:: Path

dict_link_SA_SB

A dictionary of links between segments.

Type:: defaultdict

dict_samples_chrom

A dictionary of sample chromosomes.

Type:: defaultdict

dict_segments_size

A dictionary of segment sizes.

Type:: defaultdict

dict_segments_samples

A dictionary of segment samples.

Type:: defaultdict

works_path

The path to the working directory.

Type:: Path

bed_path

The path to the BED files directory.

Type:: Path

bam_path

The path to the BAM files directory.

Type:: Path

Attributes Summary

`bam_path`
`bam_segments_file`
`bed_path`
`gfa_name`
`sample_reference`
`version`
`works_path`

Methods Summary

`parse_gfa`()	Parse the GFA file to extract specific information.
`save_header`()	Save the header information in a text file.
`save_samples_bed`()	Sauvegarde et trie les segments des échantillons dans un fichier BED.
`save_samples_chrom`()	Save the samples and their corresponding chromosomes in a text file.
`tag_bam`()	Tags the BAM file with the given dictionary of segment links and segment samples.

Attributes Documentation

bam_path: Path = None

bam_segments_file: Path = None

bed_path: Path = None

gfa_name: str = None

sample_reference: str = None

version: float = None

works_path: Path = None

Methods Documentation

parse_gfa()[source]: Parse the GFA file to extract specific information. Reads the GFA file, processes each line based on its type (Header, Segment, Link, Walk), and performs specific actions for each line type. The function updates the header information, writes to a BAM file, builds a dictionary, and processes the walk line.

save_header()[source]: Save the header information in a text file.

save_samples_bed()[source]: Sauvegarde et trie les segments des échantillons dans un fichier BED.

save_samples_chrom()[source]: Save the samples and their corresponding chromosomes in a text file.

tag_bam()[source]

Tags the BAM file with the given dictionary of segment links and segment samples.

This function takes the self.bam_segments_file and uses the Bam class to tag it with the self.dict_link_SA_SB and self.dict_segments_samples dictionaries. The resulting tagged BAM file is then assigned to self.bam_segments_file.

Parameters:: self (object) – The instance of the class.
Returns:: None