class StaphAureusN315Recipe(BaseRecipe):
def __init__(self):
super(StaphAureusN315Recipe, self).__init__()
self.source = SourceFile(self.repo, "staph_aureus_n315.fna.gz",
"https://www.ncbi.nlm.nih.gov/nuccore/NC_002745.2?report=fasta&log$=seqview&format=text")
self.bt2 = ConstructedFile(self.repo, "staph_aureus_n315.bt2")
def name(self):
return 'staph_aureus_n315'
def fileTypes(self):
return ['gz_fasta_nucl', 'bt2_index']
def resultSchema(self):
return {
'fasta': 'gz_fasta_nucl',
'bt2': ['bt2_index'] * 6
}
def makeRecipe(self):
self.source.resolve()
self.repo.saveFiles(self,
'fasta',
self.source.filepath())
self.bt2.resolve()
bt2Indices = glob(self.bt2.filepath() + '*')
self.repo.saveFiles(self,
'bt2',
*bt2Indices)
class Uniref90Recipe(BaseRecipe):
'''
Recipe for uniref90 with diamond index
'''
def __init__(self):
super(Uniref90Recipe, self).__init__()
#self.source = SourceFile(self.repo, "uniref90.faa.gz")
self.dmnd = ConstructedFile(self.repo, "uniref90_annotated.1.1.dmnd")
def name(self):
return 'uniref90'
def fileTypes(self):
return ['gz_fasta_aa', 'dmnd-db']
def resultSchema(self):
return {
'fasta': 'gz_fasta_aa',
'dmnd': 'dmnd-db'
}
def makeRecipe(self):
#self.source.resolve()
#self.repo.saveFiles(self,
#'fasta',
#self.source.filepath())
self.dmnd.resolve()
self.repo.saveFiles(self,
'dmnd',
self.dmnd.filepath())
class CARDRecipe(BaseRecipe):
'''
Recipe for the comprehensive antibiotic resistance
database
'''
def __init__(self):
super(CARDRecipe, self).__init__()
self.source = SourceFile(self.repo, "card.faa.gz")
self.sbred = ConstructedFile(self.repo, "card.shortbred_markers.faa")
self.dmnd = ConstructedFile(self.repo, "card.dmnd")
def name(self):
return 'card'
def fileTypes(self):
return ['gz_fasta_aa', 'fasta_aa', 'dmnd-db']
def resultSchema(self):
return {
'fasta': 'gz_fasta_aa',
'sbred': 'fasta_aa',
'dmnd': 'dmnd-db',
}
def makeRecipe(self):
self.source.resolve()
self.repo.saveFiles(self, 'fasta', self.source.filepath())
self.sbred.resolve()
self.repo.saveFiles(self, 'sbred', self.sbred.filepath())
self.dmnd.resolve()
self.repo.saveFiles(self, 'dmnd', self.dmnd.filepath())
class HG38UCSCGenomeRecipe(BaseRecipe):
'''
Recipe for the hg38 genome from UCSC.
This genome is used in the CAP because:
- hg38 is the most recent as of December 2017
- it includes alt contigs. Bad for variant calling, good for filtering
- it uses human readable chromosome names
- it uses the rCRS mitochondrial sequence
'''
def __init__(self):
super(HG38UCSCGenomeRecipe, self).__init__()
self.source = SourceFile(self.repo, "hg38_ucsc.fna.gz",
"http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz")
self.bt2 = ConstructedFile(self.repo, "hg38_ucsc.bt2")
def name(self):
return 'hg38_ucsc'
def fileTypes(self):
return ['gz_fasta_nucl', 'bt2_index']
def resultSchema(self):
return {
'fasta': 'gz_fasta_nucl',
'bt2': ['bt2_index'] * 6
}
def makeRecipe(self):
self.source.resolve()
self.repo.saveFiles(self,
'fasta',
self.source.filepath())
self.bt2.resolve()
bt2Indices = glob(self.bt2.filepath() + '*')
self.repo.saveFiles(self,
'bt2',
*bt2Indices)
class MeganRecipe(BaseRecipe):
'''
Recipe for uniref90 with diamond index
'''
def __init__(self):
super(MeganRecipe, self).__init__()
self.acc2taxa = SourceFile(self.repo, "prot_acc2tax-May2017.abin")
self.blast2lca = ConstructedFile(self.repo, "blast2lca")
def name(self):
return 'megan'
def fileTypes(self):
return ['megan_table']
def resultSchema(self):
return {'acc2taxa': 'megan_table', 'blast2lca': 'megan_table'}
def makeRecipe(self):
self.acc2taxa.resolve()
self.repo.saveFiles(self, 'acc2taxa', self.acc2taxa.filepath())
self.blast2lca.resolve()
self.repo.saveFiles(self, 'blast2lca', self.blast2lca.filepath())
class NRProteinRecipe(BaseRecipe):
'''
Recipe for uniref90 with diamond index
'''
def __init__(self):
super(NRProteinRecipe, self).__init__()
self.fasta = SourceFile(self.repo, "nr.faa.gz")
self.dmnd = ConstructedFile(self.repo, "nr.dmnd")
def name(self):
return 'nr_protein'
def fileTypes(self):
return ['gz_fasta_aa', 'dmnd-db']
def resultSchema(self):
return {'fasta': 'gz_fasta_aa', 'dmnd': 'dmnd-db'}
def makeRecipe(self):
self.fasta.resolve()
self.repo.saveFiles(self, 'fasta', self.fasta.filepath())
self.dmnd.resolve()
self.repo.saveFiles(self, 'dmnd', self.dmnd.filepath())
class MethyltransferaseRecipe(BaseRecipe):
'''
Recipe for the comprehensive antibiotic resistance
database
'''
def __init__(self):
super(MethyltransferaseRecipe, self).__init__()
self.fasta = SourceFile(self.repo, "methyls.faa")
self.dmnd = ConstructedFile(self.repo, "methyls.dmnd")
def name(self):
return 'methyl'
def fileTypes(self):
return ['gz_fasta_aa', 'dmnd-db']
def resultSchema(self):
return {'fasta': 'gz_fasta_aa', 'dmnd': 'dmnd-db'}
def makeRecipe(self):
self.fasta.resolve()
self.repo.saveFiles(self, 'fasta', self.fasta.filepath())
self.dmnd.resolve()
self.repo.saveFiles(self, 'dmnd', self.dmnd.filepath())
class CommonMacrobialRecipe(BaseRecipe):
'''
Recipe for database of common macrobial genomes
'''
def __init__(self):
super(CommonMacrobialRecipe, self).__init__()
self.source = SourceFile(self.repo, "macrobes.fna.gz")
self.bt2 = ConstructedFile(self.repo, "common_macrobial.bt2")
def name(self):
return 'common_macrobial'
def fileTypes(self):
return ['gz_fasta_nucl', 'bt2_index']
def resultSchema(self):
return {'fasta': 'gz_fasta_nucl', 'bt2': ['bt2_index'] * 6}
def makeRecipe(self):
self.source.resolve()
self.repo.saveFiles(self, 'fasta', self.source.filepath())
self.bt2.resolve()
bt2Indices = glob(self.bt2.filepath() + '*')
self.repo.saveFiles(self, 'bt2', *bt2Indices)
class MegaresRecipe(BaseRecipe):
def __init__(self):
super(MegaresRecipe, self).__init__()
self.fasta = SourceFile(self.repo, "megares.fa")
self.bt2 = ConstructedFile(self.repo, "megares.bt2")
self.csv = SourceFile(self.repo, "megares.csv")
def name(self):
return 'megares'
def fileTypes(self):
return ['fasta_nucl', 'bt2_index', 'csv']
def resultSchema(self):
return {'fasta': 'fasta_nucl', 'bt2': ['bt2_index'] * 6, 'csv': 'csv'}
def makeRecipe(self):
self.fasta.resolve()
self.repo.saveFiles(self, 'fasta', self.fasta.filepath())
self.csv.resolve()
self.repo.saveFiles(self, 'csv', self.csv.filepath())
self.bt2.resolve()
bt2Indices = glob(self.bt2.filepath() + '*')
self.repo.saveFiles(self, 'bt2', *bt2Indices)