Annotation module

class Annotation.Annotator

Bases: object

This class parse all information about Illumina probes.

USAGE:

annotations = Annotation.Annotator()

get_all_probe_ids()

Get all probe ids.

Returns

a list of probe ids.

get_all_probes()

Get a list of all probes.

Returns

A list of all probes in the Annotation object.

get_coord(probe)

Get genomic coordinate of a probe.

Parameters

probe – A probe object

Returns

An integer indicator of probe numbers

get_keys(dic_keys)

Get Probe id from probe dictionaries

Parameters

dic_keys – Probe dict.

Returns

returns a list of probe id.

get_number()

Get numbers of probes

Returns

An integer representing the number of probes.

get_probe(probe_id)

This function returns the info associated with an id.

Parameters

probe_id – ILLUMINA ID

Returns

all info

get_probes(list_of_ids)

This function returns a list of probe object from a list of ids.

Parameters

list_of_ids –

Returns

A list of probe objects.

get_probes_from_chr_loc(chr_loc)

Get a list of probes that are within a genomic region

Parameters

chr_loc – Genomic location interval

Returns

A list of probes.

get_probes_from_cpg(cpg_loc)

Get a list probe objects from cpg location.

Parameters

cpg_loc – from CpG object

Returns

probes.

get_probes_from_gene(gene_name)

Get a list probe objects from an associated gene name.

Parameters

gene_name – Gene name in string format

Returns

A probe.

get_probes_from_loc(loc)

Get a list probe objects from genomic location.

Parameters

loc – from Location object.

Returns

probes.

get_probes_id_from_chr_loc(chr_loc)

Get a list of probe ids that are witihn a genomic region

Parameters

chr_loc – Genomic location interval

Returns

A list of probe ids.

get_probes_id_from_cpg(cpg_loc)

Get all probes ids associated with CpG sites.

Parameters

cpg_loc –

Returns

a list of probe ids.

get_probes_id_from_gene(gene_name)

Get all probes ids associated with a gene.

Parameters

gene_name –

Returns

a lst of probe ids.

get_probes_id_from_loc(probe_loc)

Get all probes ids associated with genomic locations.

Parameters

probe_loc –

Returns

a list of probe ids.

get_probes_id_from_probe(probe_list)

Get all probes ids from a list of probe objects.

Parameters

probe_list – A list of probe ids.

Returns

a list of probe ids.

remove_snp_probes()

This function will removes all SNPs associated with probes.

Returns

returns a new probe listing.

sort_coord_probe(probes)

This function sorts probes based on the probe genomic location. Best used in combination with plotting module.

Parameters

probes – Input probe list.

Returns

A sorted probe list.

class Annotation.ChrLoc(chromosome, start, end)

Bases: object

defines a chromosomal interval.

USAGE:

my_probe = Annotation.ChrLoc("X", 122333232, 123334444)

class Annotation.CpG_location

Bases: object

CpG location is defined here.

ISLAND = 'Island'

NSHELF = 'N_Shelf'

NSHORE = 'N_Shore'

SSHELF = 'S_Shelf'

SSHORE = 'S_Shore'

class Annotation.Feature(feature)

Bases: object

This class parse features associated with probes.

class Annotation.Location

Bases: object

Probe location is defined here.

BODY = 'Body'

EXON = 'Exon'

TSS1500 = 'TSS1500'

TSS200 = 'TSS200'

UTR3 = "3'UTR"

UTR5 = "5'UTR"

class Annotation.Probe

Bases: object

This class holds probe info.

USAGE:

my_probe = Annotation.Probe()

class Annotation.SNP

Bases: object

This class defines the SNPs in probes. Can be used to filter probes.

Annotation.get_probes(annotations, probes_ids)

Get a list of probes from probe ids

Parameters

• annotations – Annotation object that has been initiated properly.

• probes_ids – A list of probe ids.

Returns

A list of probes.

Annotation.get_probes_from_feature(probes_ids, filter_val)

This function returns filters probes based on a feature.

Parameters

• probes_ids – The probe ids that you would like to filter.

• filter_val – Feature to be filtered.

Returns

Returns a list of probes.