mgkit.io.snpdat module¶
SNPDat reader
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class
mgkit.io.snpdat.
SNPDatRow
(line=None, rev_comp=None)¶ Bases:
object
Class containing information ouputted by SNPDat in its result file. One instance contains information about a row in the file.
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chr_name
¶ str – the queried SNPs chromosome ID
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chr_pos
¶ int – queried SNPs genomic location
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in_feat
¶ bool – Whether or not the queried SNP was within a feature
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region
¶ str – Region containing the SNP; either exonic, intronic or intergenic
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feat_dist
¶ int – Distance to nearest feature
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feature
¶ str – Either the closest feature to the SNP or the feature containing the SNP
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num_features
¶ int – number of different features that the SNP is annotated to
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feat_num
¶ int – number of annotations of the current feature
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feat_start
¶ int – Start of feature (bp)
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feat_end
¶ int – End of feature (bp)
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gene_id
¶ str – gene ID for the current feature
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gene_name
¶ str – gene name for the current feature
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transcript_id
¶ str – transcript ID for the current feature
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transcript_name
¶ str – transcript name for the current feature
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exon
¶ tuple – exon that contains the current feature and the total number of annotated exons for the gene containing the feature
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strand
¶ str – strand sense of the feature
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ann_frame
¶ str – annotated reading frame (when contained in the GTF)
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frame
¶ str – reading frame estimated by SNPdat
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num_stops
¶ int – estimated number of stop codons in the estimated reading frame
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codon
¶ tuple – codon containing the SNP, position in the codon and reference base and mutation
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nuc_change
¶ tuple – amino acid for the reference codon and new amino acid with the mutation in place
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nuc_ref
¶ str, None – reference nucleotide
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aa_change
¶ str – amino acid for the reference codon and new amino acid with the mutation in place
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synonymous
¶ bool – Whether or not the mutation is synonymous
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protein_id
¶ str – protein ID for the current feature
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messages
¶ str – messages in the SNPDat line
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aa_change
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ann_frame
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chr_name
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chr_pos
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codon
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exon
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feat_dist
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feat_end
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feat_num
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feat_start
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feature
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frame
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gene_id
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gene_name
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in_feat
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messages
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nuc_change
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nuc_ref
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num_features
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num_stops
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protein_id
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region
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strand
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synonymous
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transcript_id
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transcript_name
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mgkit.io.snpdat.
snpdat_reader
(f_handle)¶ Simple SNPDat reader.
f_handle: file handle or string for the SNPDat result file
Returns: generator of SNPDatRow instances