mgkit.io.snpdat module¶

SNPDat reader

class mgkit.io.snpdat.SNPDatRow(line=None, rev_comp=None)[source]¶

Bases: object

Class containing information ouputted by SNPDat in its result file. One instance contains information about a row in the file.

chr_name¶

the queried SNPs chromosome ID

Type:	str

chr_pos¶

queried SNPs genomic location

Type:	int

in_feat¶

Whether or not the queried SNP was within a feature

Type:	bool

region¶

Region containing the SNP; either exonic, intronic or intergenic

Type:	str

feat_dist¶

Distance to nearest feature

Type:	int

feature¶

Either the closest feature to the SNP or the feature containing the SNP

Type:	str

num_features¶

number of different features that the SNP is annotated to

Type:	int

feat_num¶

number of annotations of the current feature

Type:	int

feat_start¶

Start of feature (bp)

Type:	int

feat_end¶

End of feature (bp)

Type:	int

gene_id¶

gene ID for the current feature

Type:	str

gene_name¶

gene name for the current feature

Type:	str

transcript_id¶

transcript ID for the current feature

Type:	str

transcript_name¶

transcript name for the current feature

Type:	str

exon¶

exon that contains the current feature and the total number of annotated exons for the gene containing the feature

Type:	tuple

strand¶

strand sense of the feature

Type:	str

ann_frame¶

annotated reading frame (when contained in the GTF)

Type:	str

frame¶

reading frame estimated by SNPdat

Type:	str

num_stops¶

estimated number of stop codons in the estimated reading frame

Type:	int

codon¶

codon containing the SNP, position in the codon and reference base and mutation

Type:	tuple

nuc_change¶

amino acid for the reference codon and new amino acid with the mutation in place

Type:	tuple

nuc_ref¶

reference nucleotide

Type:	str, None

aa_change¶

amino acid for the reference codon and new amino acid with the mutation in place

Type:	str

synonymous¶

Whether or not the mutation is synonymous

Type:	bool

protein_id¶

protein ID for the current feature

Type:	str

messages¶

messages in the SNPDat line

Type:	str

aa_change

ann_frame

chr_name

chr_pos

codon

exon

feat_dist

feat_end

feat_num

feat_start

feature

frame

gene_id

gene_name

in_feat

messages

nuc_change

nuc_ref

num_features

num_stops

protein_id

region

strand

synonymous

transcript_id

transcript_name

mgkit.io.snpdat.snpdat_reader(f_handle)[source]¶

Simple SNPDat reader.

f_handle: file handle or string for the SNPDat result file

Returns:	generator of SNPDatRow instances