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from __future__ import absolute_import
from pkg_resources import Requirement, resource_filename
DATA_FILES = {'aligned_reads_1.cmp.h5':
['m110818_075520_42141_c100129202555500000315043109121112_s1_p0.bas.h5',
'm110818_075520_42141_c100129202555500000315043109121112_s2_p0.bas.h5']}
MOVIE_NAME_14 = "m110818_075520_42141_c100129202555500000315043109121112_s1_p0"
MOVIE_NAME_20 = "m130522_092457_42208_c100497142550000001823078008081323_s1_p0"
MOVIE_NAME_21 = "m130731_192718_42129_c100564662550000001823085912221321_s1_p0"
MOVIE_NAME_23 = "m140912_020930_00114_c100702482550000001823141103261590_s1_p0"
MOVIE_NAME_CCS = "m130727_114215_42211_c100569412550000001823090301191423_s1_p0"
MOVIE_NAME_BC = "m140307_221913_42203_c100626172550000001823119008061414_s1_p0"
def _getAbsPath(fname):
return resource_filename(Requirement.parse('pbcore'),'pbcore/data/%s' % fname)
def getBasH5_v20():
return _getAbsPath(MOVIE_NAME_20 + '.bas.h5')
def getBaxH5_v20():
return [_getAbsPath('.'.join((MOVIE_NAME_20, str(k), 'bax.h5')))
for k in range(1,4)]
def getBasH5_v21():
return _getAbsPath(MOVIE_NAME_21 + '.bas.h5')
def getBaxH5_v21():
return [_getAbsPath('.'.join((MOVIE_NAME_21, str(k), 'bax.h5')))
for k in range(1,4)]
def getBasH5_v23():
return _getAbsPath(MOVIE_NAME_23 + '.bas.h5')
def getBaxH5_v23():
return [_getAbsPath('.'.join((MOVIE_NAME_23, str(k), 'bax.h5')))
for k in range(1,4)]
def getCCSH5():
return _getAbsPath(MOVIE_NAME_CCS + '.1.ccs.h5')
def getCCSBAM():
return _getAbsPath(MOVIE_NAME_CCS + '.ccs.bam')
def getBcH5s():
return [_getAbsPath('.'.join((MOVIE_NAME_BC, str(k), 'bc.h5')))
for k in range(1,4)]
def getCmpH5s():
'''
Returns a list of dictionaries containing 2 keys: cmph5 and
bash5s. The latter are the bash5s that were used to generate the
cmp.h5 file.
'''
return [{'cmph5' : _getAbsPath(cmph5),
'bash5s': map(_getAbsPath, bash5s)}
for cmph5, bash5s in DATA_FILES.items()]
def getCmpH5AndBas():
'''
The returned value is a dictionary containing 2 keys: cmph5
and bash5s. The latter are the bash5s that were used to generate
the cmp.h5 file.
'''
return getCmpH5s()[0]
def getCmpH5():
return getCmpH5AndBas()["cmph5"]
def getBasH5s():
return getCmpH5AndBas()["bash5s"]
def getGff3():
'''
Returns the filename of an example GFFv3 file
'''
return _getAbsPath("variants.gff")
def getFasta():
'''
Returns the filename of an example FASTA file.
'''
return _getAbsPath('Fluidigm_human_amplicons.fasta')
def getTinyFasta():
"""
Returns the filename of an example FASTA file.
"""
return _getAbsPath('Fluidigm_human_amplicons_tiny.fasta')
def getLambdaFasta():
"""
Returns the filename of the FASTA of the lambda phage reference.
"""
return _getAbsPath('lambdaNEB.fa')
def getDosFormattedFasta():
"""
Returns the filename of an example FASTA file with DOS line endings
"""
return _getAbsPath('barcodes-ed65-450.fasta')
def getBlasrM4():
return _getAbsPath('blasr-output.m4')
def getBlasrM5():
return _getAbsPath('blasr-output.m5')
def getFofns():
"""
Returns a list of FOFN files
"""
return map(_getAbsPath,
["1.4_bas_files.fofn",
"2.0_bax_files.fofn",
"2.1_bax_files.fofn",
"2.1_ccs_files.fofn"])
def getBcFofn():
return _getAbsPath("bc_files.fofn")
def getBamAndCmpH5():
"""
Get a "matched" (aligned) BAM and cmp.h5 file
"""
return (_getAbsPath("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam"),
_getAbsPath("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.cmp.h5"))
def getBaxForBam():
"""
Get the bax file that was mapped to produce the bam
"""
return _getAbsPath("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5")
def getUnalignedBam():
"""
Get the unaligned BAM file, corresponding to the same bax above
"""
return _getAbsPath("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam")
def getEmptyBam():
return _getAbsPath("empty.ccs.bam")
def getEmptyAlignedBam():
return _getAbsPath("empty.aligned_subreads.bam")
def getMappingXml():
return _getAbsPath("chemistry.xml")
def getWeird():
return _getAbsPath("weird.fa")
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