List of all members.
Detailed Description
From all known known phage-host associations, pick a a stratified set of pairs.
Currently, we pick one phage-host pair per microbial genus, wherever available.
This is done to have a reasonable hope that a given phage has only a single true microbial host in the resulting set.
Thus, all assignments by whatever classification algorithm to a different host can be considered as false positives.
This class has two modes of operation. First one selects host/virus sequence pairs and can save them.
Second one can load saved pairs into memory.
Constructor & Destructor Documentation
| def MGT::PhageHostDb::PhageHostSeqPicker::__init__ |
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self, |
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taxaTree |
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Constructor.
@param taxaTree - taxonomy tree
@pre sequences must be assigned by mapFastaRecordsToTaxaTree (unless load() will be called)
@pre host data must be assigned by loadHosts (unless load() will be called)
Member Function Documentation
| def MGT::PhageHostDb::PhageHostSeqPicker::groupSeqHosts |
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self ) |
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Group seqHosts by genera, each value contains dict {host:set(vir)}
| def MGT::PhageHostDb::PhageHostSeqPicker::makeIdLabsPicks |
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self, |
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div = "all" |
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Return IdLables(gi->taxid) object for microbial, viral or all sequences selected by pickPairs()
| def MGT::PhageHostDb::PhageHostSeqPicker::printGroupSeqHosts |
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self ) |
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Print dict of dicts of lists {mic genus : mic species : phages}
| def MGT::PhageHostDb::PhageHostSeqPicker::saveSeqIds |
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self, |
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out |
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Save a set of all (microbial and viral) sequence IDs (GIs) selected by pickPairs().
This is for pulling all relevant sequences into internal representation.
| def MGT::PhageHostDb::PhageHostSeqPicker::seqHostVirPairs |
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self ) |
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Return a set([(vir,seqhost),...]) for a quick lookup of a given vir,host pair
The documentation for this class was generated from the following file:
- mgtaxa/MGT/PhageHostDb.py
