Bed

genie_registry.bed

GENIE bed class and functions

Attributes

LOGGER = logging.getLogger(__name__) module-attribute

Classes

bed

Bases: FileTypeFormat

GENIE bed format

Functions

create_gene_panel(beddf, seq_assay_id, gene_panel_path, parentid)

Create bed file and gene panel files from the bed file

PARAMETER	DESCRIPTION
beddf	bed dataframe
seq_assay_id	GENIE SEQ_ASSAY_ID
gene_panel_path	Gene panel folder path
parentid	Synapse id of gene panel folder

RETURNS	DESCRIPTION
	pd.DataFrame: configured bed dataframe

preprocess(newpath)

Standardize and grab seq assay id from the bed file path

PARAMETER	DESCRIPTION
newpath	bed file path

RETURNS	DESCRIPTION
dict	GENIE seq assay id

process_steps(beddf, newPath, parentId, databaseSynId, seq_assay_id)

Process bed file, update bed database, write bed file to path

PARAMETER	DESCRIPTION
beddf	input bed data TYPE: DataFrame
newPath	Path to new bed file TYPE: str
parentId	Synapse id to store gene panel file TYPE: str
databaseSynId	Synapse id of bed database TYPE: str
seq_assay_id	GENIE seq assay id TYPE: str

RETURNS	DESCRIPTION
str	Path to new bed file TYPE: str

Functions

create_gtf(dirname)

Create exon.gtf and gene.gtf from GRCh37 gtf

PARAMETER	DESCRIPTION
dirname	Directory where these files should live

RETURNS	DESCRIPTION
exon_gtf_path	exon GTF
gene_gtf_path	gene GTF

_add_feature_type_tobeddf(filepath, featuretype)

Add Feature_Type to dataframe

PARAMETER	DESCRIPTION
filepath	path to bed
featuretype	exon, intron, or intergenic

RETURNS	DESCRIPTION
df	empty dataframe or dataframe with appended feature type

add_feature_type(temp_bed_path, exon_gtf_path, gene_gtf_path)

Add Feature_Type to bed file (exon, intron, intergenic)

PARAMETER	DESCRIPTION
temp_bed_path	BED file without feature type
exon_gtf_path	exon gtf
gene_gtf_path	gene gtf

RETURNS	DESCRIPTION
genie_combined_path	Path to final bed file

_check_region_overlap(row, gene_positiondf)

Check if the submitted bed symbol + region overlaps with the actual gene's positions

PARAMETER	DESCRIPTION
row	row in bed file (genomic region)
gene_positiondf	Reference gene position dataframe

Return

True if the region does overlap.

_get_max_overlap_index(overlap, bed_length, boundary)

Calculate the ratio of overlap between the submitted bed region and gene position dataframe and return the index of the max overlapping region

PARAMETER	DESCRIPTION
overlap	Possible overlapping region
bed_length	Length of submitted region
boundary	specified ratio overlap

RETURNS	DESCRIPTION
	Index of regions with maximum overlap or None

_map_position_within_boundary(row, positiondf, boundary=0.9)

Map positions and checks if posision is contained within the specified percentage boundary

PARAMETER	DESCRIPTION
row	Row in bed file (genomic region)
positiondf	Reference bed position dataframe
boundary	Percent boundary defined DEFAULT: 0.9

Return

pd.Series: mapped position

remap_symbols(row, gene_positiondf)

Remap hugo symbols if there is no overlap between submitted bed region and gene positions.

PARAMETER	DESCRIPTION
row	start and end position
gene_positiondf	Actual gene position dataframe

Return

bool or Series: if the gene passed in need to be remapped or the remapped gene