Annotation module

class Annotation.Annotator

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)

defines a chromosomal interval.

USAGE:

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

class Annotation.CpG_location

CpG location is defined here.

ISLAND = 'Island'

NSHELF = 'N_Shelf'

NSHORE = 'N_Shore'

SSHELF = 'S_Shelf'

SSHORE = 'S_Shore'

class Annotation.Feature(feature)

This class parse features associated with probes.

class Annotation.Location

Probe location is defined here.

BODY = 'Body'

EXON = 'Exon'

TSS1500 = 'TSS1500'

TSS200 = 'TSS200'

UTR3 = "3'UTR"

UTR5 = "5'UTR"

class Annotation.Probe

This class holds probe info.

USAGE:

my_probe = Annotation.Probe()

class Annotation.SNP

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.