biofx.annotator package

Submodules

biofx.annotator.GSCannotation module

Module to retrieve annotations from GSC resources. @cchng

Created in January 2015.

class biofx.annotator.GSCannotation.Ensembl(resource='/projects/yshen_prj/db/Ensembl_69_transcripts.txt')

Bases: object

Legacy resource. Avoid if possible.

get_ensembl_gene_id(enst)

get_ensembl_transcript_id(ensg)

class biofx.annotator.GSCannotation.Hugo(resource='/projects/yshen_prj/db/hugo_genenames_08Mar2012.txt')

Bases: object

Legacy resource. Avoid if possible.

get_gene_name(symbol)

class biofx.annotator.GSCannotation.WTSSGeneExon(ensg2genesymbol, resource='/projects/wtsspipeline/resources/Homo_sapiens/bfa_NCBI-37-TCGA/transcript_coverage/ens69_mito_as_MT_no_LRG_genes/gene_exon.txt')

Bases: object

Information from WTSS gene_exon.txt file

get_map()

Returns:map of gene symbol to exon coordinates Return type:dict

class biofx.annotator.GSCannotation.WTSSGeneInfo(resource='/projects/wtsspipeline/resources/Homo_sapiens/bfa_NCBI-37-TCGA/transcript_coverage/ens69_mito_as_MT_no_LRG_genes/gene_info.txt')

Bases: object

Parse and retrieve information from WTSS gene_info.txt file

Parameters:resource (string) – path to gene_info.txt file in WTSS formatting Raises:IOError – resource file provided does not exist

get_ensg2symbol()

Returns:a mapping with ensembl gene ID as keys and gene symbol as values Return type:dict Raises:RuntimeError – Something went wrong with populating mappings

get_ensg_from_enst(enst)

Get Ensembl gene ID from Ensembl transcript ID.

Parameters:enst (string) – Ensembl transcript ID Returns:Ensembl gene ID. NA if Ensembl transcript ID not found Return type:string

get_ensg_from_symbol(symbol)

Get Ensembl gene ID from gene symbol. One to many mapping.

Parameters:symbol (string) – Gene symbol Returns:Ensembl gene ID. comma-delimited if multiple. “NA” symbol not found. Return type:string

get_enst2ensg()

Returns:a mapping with ensembl transcript ID as keys and ensembl gene ID as values Return type:dict Raises:RuntimeError – Something went wrong with populating mappings

get_gene_symbol(ensg)

Get gene symbol from Ensembl gene ID

Parameters:ensg (string) – Ensembl gene ID Returns:gene symbol. NA if gene symbol not found Return type:(string)

get_strand_from_gene_symbol(gene_symbol)

Parameters:gene_symbol (string) – gene symbol Returns:strand. NA if gene symbol not found Return type:string

get_symbol2ensg()

Returns:a mapping with gene symbol as keys and ensembl gene ID as values Return type:dict Raises:RuntimeError – Something went wrong with populating mappings

biofx.annotator.VariantAnnotation module

@cchng

class biofx.annotator.VariantAnnotation.SnpEff(java_mem='Xmx4g', version=None)

Bases: object

A wrapper for snpeff/snpsift 4.1 excecution.

annotate_with_snpeff(input_file, output_file, genome, snpeff=None)

Annotation input with snpeff. Runs classic and hgvs annotations concurrently.

Parameters:

• input_file (string) – input vcf file path
• output_file (string) – output vcf file path. hgvs output has an hgvs suffix appended
• genome (string) – genome used for snpeff
• snpeff (string) – snpeff executable

Returns:

list of return values

Return type:

revals (list)

annotate_with_snpsift(input_file, output_file, annotate, snpsift=None)

Annotate input with snpsift.

Parameters:

• input_file (string) – input vcf file path
• output_file (string) – output vcf file path
• annotate (string) – vcf file used for snpsift annotation
• snpsift (string) – snpsift executable

Returns:

return value

Return type:

reval (int)

Module contents