def __init__(self):
self.filename = "" # name of file that contains the genome sequence
self.genomeType = "unknown" # typically, "chromosome", "plasmid", "virus", "segmented", "satellite"
self.name = "unknown" # common name (e.g., Drosophila)
self.genomeName = "unkknown" # more specific name (e.g., 'Yp phage YP123')
self.species = "unknown" # Latin name (e.g., Drosophila melanogaster)
self.annotationList = [] # using phate_annotation.py classes
self.contigSet = phate_fastaSequence.multiFasta()
self.geneSet = phate_fastaSequence.multiFasta()
self.proteinSet = phate_fastaSequence.multiFasta()
self.contigSet.moleculeType = 'contig'
self.contigSet.sequenceType = 'nt'
self.geneSet.moleculeType = 'gene'
self.geneSet.sequenceType = 'nt'
self.proteinSet.moleculeType = 'peptide'
self.proteinSet.sequenceType = 'aa'
self.codeBaseDir = "" # needs to be set
self.outputDir = "" # needs to be set
def __init__(self):
self.filename = "" # name of file that contains the genome sequence
self.genomeType = "unknown" # typically, "chromosome", "plasmid", "virus", "segmented", "satellite"
self.name = "unknown" # common name (e.g., Drosophila)
self.genomeName = "unkknown" # more specific name (e.g., 'Yp phage YP123')
self.species = "unknown" # Latin name (e.g., Drosophila melanogaster)
self.annotationList = [] # using phate_annotation.py classes
self.contigSet = phate_fastaSequence.multiFasta()
self.geneSet = phate_fastaSequence.multiFasta()
self.proteinSet = phate_fastaSequence.multiFasta()
self.contigSet.moleculeType = 'contig'
self.contigSet.sequenceType = 'nt'
self.geneSet.moleculeType = 'gene'
self.geneSet.sequenceType = 'nt'
self.proteinSet.moleculeType = 'peptide'
self.proteinSet.sequenceType = 'aa'
self.psat = { # Parameters for handling PSAT annotation for proteins; this dict reflected in each protein's annot obj
"jobID": "", # PSAT job ID
"jobName": "", # PSAT job name
"fileName": "", # PSAT output file path/name
}
self.codeBaseDir = "" # needs to be set
self.outputDir = "" # needs to be set