List of all members.
Detailed Description
Accumulator for feature locations
Member Function Documentation
| def MGT::BioUtil::FeatureLocIndex::extract |
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self, |
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feat |
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Extract location of a single feature.
This is supposed to be called repeatedly, and the results are
accumulated inside this instance.
| def MGT::BioUtil::FeatureLocIndex::toFasta |
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self, |
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rec, |
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outFeat = None, |
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outNonFeat = None |
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) |
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Output feature sequences and/or non-feature (e.g. non-coding regions) sequences as FASTA.
This should be called after feature locations have been accumulated with calls to extract().
@param rec SeqRecord on which the accumulated features are defined.
@param idPrefix IDs in FASTA deflines will be constructed as "idPrefix_i_j" where i is feature
index starting from 0 in the list of accumulated features, and j is location range starting from
0 within a single feature
@param outFeat Output stream for feature sequences
@param outNonFeat Output stream for non-feature sequences.
@note Features will be written with strand taken into account, but inter-feature regions will
be writen always on the positive strand.
@note The current implementation will merge overlapping features, with strand of the
overlapping region picked from one of the features in undefined order
The documentation for this class was generated from the following file:
