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