def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('neostore', is_binary=True)
self.add_composite_file('neostore.id', is_binary=True)
self.add_composite_file('neostore.counts.db.a', is_binary=True)
self.add_composite_file('neostore.counts.db.b', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db.id', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db.names', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db.names.id', is_binary=True)
self.add_composite_file('neostore.nodestore.db', is_binary=True)
self.add_composite_file('neostore.nodestore.db.id', is_binary=True)
self.add_composite_file('neostore.nodestore.db.labels', is_binary=True)
self.add_composite_file('neostore.nodestore.db.labels.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db', is_binary=True)
self.add_composite_file('neostore.propertystore.db.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.arrays', is_binary=True)
self.add_composite_file('neostore.propertystore.db.arrays.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index.keys', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index.keys.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.strings', is_binary=True)
self.add_composite_file('neostore.propertystore.db.strings.id', is_binary=True)
self.add_composite_file('neostore.relationshipgroupstore.db', is_binary=True)
self.add_composite_file('neostore.relationshipgroupstore.db.id', is_binary=True)
self.add_composite_file('neostore.relationshipstore.db', is_binary=True)
self.add_composite_file('neostore.relationshipstore.db.id', is_binary=True)
self.add_composite_file('neostore.relationshiptypestore.db.names', is_binary=True)
self.add_composite_file('neostore.relationshiptypestore.db.names.id', is_binary=True)
self.add_composite_file('neostore.schemastore.db', is_binary=True)
self.add_composite_file('neostore.schemastore.db.id', is_binary=True)
self.add_composite_file('neostore.transaction.db.0', is_binary=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('neostore', is_binary=True)
self.add_composite_file('neostore.id', is_binary=True)
self.add_composite_file('neostore.counts.db.a', is_binary=True)
self.add_composite_file('neostore.counts.db.b', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db.id', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db.names', is_binary=True)
self.add_composite_file('neostore.labeltokenstore.db.names.id', is_binary=True)
self.add_composite_file('neostore.nodestore.db', is_binary=True)
self.add_composite_file('neostore.nodestore.db.id', is_binary=True)
self.add_composite_file('neostore.nodestore.db.labels', is_binary=True)
self.add_composite_file('neostore.nodestore.db.labels.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db', is_binary=True)
self.add_composite_file('neostore.propertystore.db.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.arrays', is_binary=True)
self.add_composite_file('neostore.propertystore.db.arrays.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index.keys', is_binary=True)
self.add_composite_file('neostore.propertystore.db.index.keys.id', is_binary=True)
self.add_composite_file('neostore.propertystore.db.strings', is_binary=True)
self.add_composite_file('neostore.propertystore.db.strings.id', is_binary=True)
self.add_composite_file('neostore.relationshipgroupstore.db', is_binary=True)
self.add_composite_file('neostore.relationshipgroupstore.db.id', is_binary=True)
self.add_composite_file('neostore.relationshipstore.db', is_binary=True)
self.add_composite_file('neostore.relationshipstore.db.id', is_binary=True)
self.add_composite_file('neostore.relationshiptypestore.db.names', is_binary=True)
self.add_composite_file('neostore.relationshiptypestore.db.names.id', is_binary=True)
self.add_composite_file('neostore.schemastore.db', is_binary=True)
self.add_composite_file('neostore.schemastore.db.id', is_binary=True)
self.add_composite_file('neostore.transaction.db.0', is_binary=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('blastdb.nhr', is_binary=True) # sequence headers
self.add_composite_file('blastdb.nin', is_binary=True) # index file
self.add_composite_file('blastdb.nsq', is_binary=True) # nucleotide sequences
# alias ( -gi_mask option of makeblastdb)
self.add_composite_file('blastdb.nal', is_binary=False, optional=True)
# sorted sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file('blastdb.nhd', is_binary=True, optional=True)
# index of sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file('blastdb.nhi', is_binary=True, optional=True)
# sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file('blastdb.nnd', is_binary=True, optional=True)
# index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file('blastdb.nni', is_binary=True, optional=True)
# OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nog', is_binary=True, optional=True)
# sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nsd', is_binary=True, optional=True)
# index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nsi', is_binary=True, optional=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('blastdb.nhr',
is_binary=True) # sequence headers
self.add_composite_file('blastdb.nin', is_binary=True) # index file
self.add_composite_file('blastdb.nsq',
is_binary=True) # nucleotide sequences
# alias ( -gi_mask option of makeblastdb)
self.add_composite_file('blastdb.nal', is_binary=False, optional=True)
# sorted sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file('blastdb.nhd', is_binary=True, optional=True)
# index of sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file('blastdb.nhi', is_binary=True, optional=True)
# sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file('blastdb.nnd', is_binary=True, optional=True)
# index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file('blastdb.nni', is_binary=True, optional=True)
# OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nog', is_binary=True, optional=True)
# sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nsd', is_binary=True, optional=True)
# index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nsi', is_binary=True, optional=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('blastdb.phr', is_binary=True)
self.add_composite_file('blastdb.pin', is_binary=True)
self.add_composite_file('blastdb.psq', is_binary=True)
self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
self.add_composite_file('blastdb.aux', is_binary=True, optional=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('blastdb.phr', is_binary=True)
self.add_composite_file('blastdb.pin', is_binary=True)
self.add_composite_file('blastdb.psq', is_binary=True)
self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
self.add_composite_file('blastdb.aux', is_binary=True, optional=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
# Component file comments are as in BlastNucDb except where noted
self.add_composite_file('blastdb.phr', is_binary=True)
self.add_composite_file('blastdb.pin', is_binary=True)
self.add_composite_file('blastdb.psq', is_binary=True) # protein sequences
self.add_composite_file('blastdb.phd', is_binary=True, optional=True)
self.add_composite_file('blastdb.phi', is_binary=True, optional=True)
self.add_composite_file('blastdb.pnd', is_binary=True, optional=True)
self.add_composite_file('blastdb.pni', is_binary=True, optional=True)
self.add_composite_file('blastdb.pog', is_binary=True, optional=True)
self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
def __init__(self, **kwd):
"""Construct object from input files."""
Data.__init__(self, **kwd)
self.add_composite_file(
'se.rds',
is_binary=True,
description="Summarized experiment RDS object",
)
self.add_composite_file(
'assays.h5',
is_binary=True,
description="Summarized experiment data array",
)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
# Component file comments are as in BlastNucDb except where noted
self.add_composite_file('blastdb.phr', is_binary=True)
self.add_composite_file('blastdb.pin', is_binary=True)
self.add_composite_file('blastdb.psq',
is_binary=True) # protein sequences
self.add_composite_file('blastdb.phd', is_binary=True, optional=True)
self.add_composite_file('blastdb.phi', is_binary=True, optional=True)
self.add_composite_file('blastdb.pnd', is_binary=True, optional=True)
self.add_composite_file('blastdb.pni', is_binary=True, optional=True)
self.add_composite_file('blastdb.pog', is_binary=True, optional=True)
self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('blastdb.nhr', is_binary=True) # sequence headers
self.add_composite_file('blastdb.nin', is_binary=True) # index file
self.add_composite_file('blastdb.nsq', is_binary=True) # nucleotide sequences
self.add_composite_file('blastdb.nal', is_binary=False, optional=True) # alias ( -gi_mask option of makeblastdb)
self.add_composite_file('blastdb.nhd', is_binary=True, optional=True) # sorted sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file('blastdb.nhi', is_binary=True, optional=True) # index of sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file('blastdb.nnd', is_binary=True, optional=True) # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file('blastdb.nni', is_binary=True, optional=True) # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file('blastdb.nog', is_binary=True, optional=True) # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nsd', is_binary=True, optional=True) # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file('blastdb.nsi', is_binary=True, optional=True) # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
# self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True) # first volume of the MegaBLAST index generated by makembindex
# The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
self.add_composite_file('blastdb.shd', is_binary=True, optional=True) # MegaBLAST index superheader (-old_style_index false option of makembindex)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('lastdb.ssp', is_binary=True)
self.add_composite_file('lastdb.tis', is_binary=True)
self.add_composite_file('lastdb.sds', is_binary=True)
self.add_composite_file('lastdb.suf', is_binary=True)
self.add_composite_file('lastdb.des', is_binary=True)
self.add_composite_file('lastdb.bck', is_binary=True)
self.add_composite_file('lastdb.prj', is_binary=False)
## These next two are my own concotions
# a map from id or accession to taxid
self.add_composite_file('lastdb.tax', is_binary=False, optional=True)
# a map form id or accession to description
self.add_composite_file('lastdb.ids', is_binary=False, optional=True)
## These are for multi-volumen DBs. I'm not sure they are necessary...
self.add_composite_file('lastdb0.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb0.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb0.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb0.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb0.des', is_binary=True, optional=True)
self.add_composite_file('lastdb0.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb0.prj', is_binary=False, optional=True)
self.add_composite_file('lastdb1.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb1.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb1.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb1.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb1.des', is_binary=True, optional=True)
self.add_composite_file('lastdb1.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb1.prj', is_binary=False, optional=True)
self.add_composite_file('lastdb2.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb2.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb2.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb2.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb2.des', is_binary=True, optional=True)
self.add_composite_file('lastdb2.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb2.prj', is_binary=False, optional=True)
self.add_composite_file('lastdb3.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb3.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb3.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb3.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb3.des', is_binary=True, optional=True)
self.add_composite_file('lastdb3.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb3.prj', is_binary=False, optional=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('lastdb.ssp', is_binary=True)
self.add_composite_file('lastdb.tis', is_binary=True)
self.add_composite_file('lastdb.sds', is_binary=True)
self.add_composite_file('lastdb.suf', is_binary=True)
self.add_composite_file('lastdb.des', is_binary=True)
self.add_composite_file('lastdb.bck', is_binary=True)
self.add_composite_file('lastdb.prj', is_binary=False)
self.add_composite_file('lastdb0.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb0.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb0.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb0.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb0.des', is_binary=True, optional=True)
self.add_composite_file('lastdb0.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb0.prj', is_binary=False, optional=True)
self.add_composite_file('lastdb1.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb1.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb1.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb1.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb1.des', is_binary=True, optional=True)
self.add_composite_file('lastdb1.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb1.prj', is_binary=False, optional=True)
self.add_composite_file('lastdb2.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb2.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb2.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb2.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb2.des', is_binary=True, optional=True)
self.add_composite_file('lastdb2.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb2.prj', is_binary=False, optional=True)
self.add_composite_file('lastdb3.ssp', is_binary=True, optional=True)
self.add_composite_file('lastdb3.tis', is_binary=True, optional=True)
self.add_composite_file('lastdb3.sds', is_binary=True, optional=True)
self.add_composite_file('lastdb3.suf', is_binary=True, optional=True)
self.add_composite_file('lastdb3.des', is_binary=True, optional=True)
self.add_composite_file('lastdb3.bck', is_binary=True, optional=True)
self.add_composite_file('lastdb3.prj', is_binary=False, optional=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('blastdb.nhr',
is_binary=True) # sequence headers
self.add_composite_file('blastdb.nin', is_binary=True) # index file
self.add_composite_file('blastdb.nsq',
is_binary=True) # nucleotide sequences
self.add_composite_file(
'blastdb.nal', is_binary=False,
optional=True) # alias ( -gi_mask option of makeblastdb)
self.add_composite_file(
'blastdb.nhd', is_binary=True, optional=True
) # sorted sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file(
'blastdb.nhi', is_binary=True, optional=True
) # index of sequence hash values ( -hash_index option of makeblastdb)
self.add_composite_file(
'blastdb.nnd', is_binary=True, optional=True
) # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file(
'blastdb.nni', is_binary=True, optional=True
) # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines)
self.add_composite_file(
'blastdb.nog', is_binary=True, optional=True
) # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file(
'blastdb.nsd', is_binary=True, optional=True
) # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
self.add_composite_file(
'blastdb.nsi', is_binary=True, optional=True
) # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb)
# self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True) # first volume of the MegaBLAST index generated by makembindex
# The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc.
self.add_composite_file(
'blastdb.shd', is_binary=True, optional=True
) # MegaBLAST index superheader (-old_style_index false option of makembindex)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('%s.zip',
description='neostore zip',
substitute_name_with_metadata='reference_name',
is_binary=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('%s.zip', description='neostore zip', substitute_name_with_metadata='reference_name',
is_binary=True)
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('neo4j/', is_binary=True)
self.add_composite_file('jbrowser/', is_binary=True)
