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List of all members.
Detailed Description
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See COPYING file distributed along with the MGTAXA package for the copyright and license terms.
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App-derived class for CRISPR array processing in "Moore genomes" dataset
Member Function Documentation
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::annotMicCrisprGb |
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self ) |
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Add CRISPR arrays as annotation to Genbank format files
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::loadClosedSql |
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self ) |
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Load meta-info about Genbank non-Moore closed marine genomes into SQL tables
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::loadMic |
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self ) |
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Load data from Mic genomes necessary to run our CRISPR pipeline on them
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::loadMicProtAnnotCrisprSql |
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self ) |
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Create SQL table with the most definitive name for CAS genes and their coordinates
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::loadMicProtHitsSql |
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self ) |
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Load reliable protein HMM hits for Moore and other closed genomes into SQL tables
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::loadMooreSql |
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self ) |
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Load meta-info about Moore genomes into SQL tables
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::makeMicNucFasta |
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self ) |
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Export microbial GB nucl sequence into FASTA, store seq IDs into SQL table along the way, and split files for Piler run
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::mergeMicPathsSql |
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self ) |
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Merge tables *_path with files paths for different sources of data, such as Moore and other Genbank marine genomes.
@post Results are in mic_path table
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::plotCrispr |
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self ) |
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Use Bio.Graphics.GenomeDiagram to generate pictures of CRISPR genes and arrays from pre-processed Genbank files
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::plotCrisprOneBioGd |
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self, |
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seqRec, |
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outGraphFileRoot |
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Use Bio.Graphics.GenomeDiagram to generate pictures of CRISPR genes and arrays from one SeqRecord from a pre-processed Genbank file
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::plotCrisprOneBioGff |
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self, |
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seqRec, |
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outGraphFileRoot |
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Generate GFF files of CRISPR genes and arrays from one SeqRecord from a pre-processed Genbank file, using Bio sandbox module
| def MGT::Proj::CrisprMooreApp::CrisprMooreApp::plotCrisprOneGff |
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self, |
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seqRec, |
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outGraphFileRoot |
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Generate GFF files and graphics for CRISPR genes and arrays from one SeqRecord from a pre-processed Genbank file
The documentation for this class was generated from the following file:
- mgtaxa/MGT/Proj/CrisprMooreApp.py
