mgkit.io.snpdat module¶
SNPDat reader
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class
mgkit.io.snpdat.
SNPDatRow
(line=None, rev_comp=None)¶ Bases:
future.types.newobject.newobject
Class containing information ouputted by SNPDat in its result file. One instance contains information about a row in the file.
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exon
¶ exon that contains the current feature and the total number of annotated exons for the gene containing the feature
Type: tuple
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nuc_change
¶ amino acid for the reference codon and new amino acid with the mutation in place
Type: tuple
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aa_change
¶ amino acid for the reference codon and new amino acid with the mutation in place
Type: str
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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