def prepare_overlap(genome):
"""Converts indexing info into a dictionary"""
package_dir = "/".join(os.path.abspath(__file__).split("/")[:-3])
genome_dir = package_dir + '/annotations/' + genome
if os.path.isdir(genome_dir):
est_file = genome_dir + '/' + 'all_est.txt'
index_file = est_file + '.idx'
est_overlap = OverlapCoord(est_file, index_file)
est_overlap.extract_index()
return est_overlap
return None
def prepare_overlap(genome, annodir):
"""Converts indexing info into a dictionary"""
genome_dir = os.path.join(annodir, genome)
if os.path.isdir(genome_dir):
est_file = genome_dir + '/' + 'all_est.txt'
index_file = est_file + '.idx'
est_overlap = OverlapCoord(est_file, index_file)
est_overlap.extract_index()
return est_overlap
return None
def prepare_overlap(genome, chrom):
"""Extracts index info into dictionary"""
package_dir = "/".join(os.path.abspath(__file__).split("/")[:-3])
genome_dir = package_dir + '/annotations/' + genome
if not os.path.isdir(genome_dir):
return None
snp_file = genome_dir + '/snp/' + chrom + '-snp.txt'
index_file = snp_file + '.idx'
if not os.path.exists(snp_file) or not os.path.exists(index_file):
return None
snp_overlap = OverlapCoord(snp_file, index_file)
snp_overlap.extract_index()
return snp_overlap
def prepare_overlap(genome, chrom, annodir):
"""Extracts index info into dictionary"""
genome_dir = os.path.join(annodir, genome)
if not os.path.isdir(genome_dir):
return None
snp_file = genome_dir + "/snp/" + chrom + "-snp.txt"
index_file = snp_file + ".idx"
if not os.path.exists(snp_file) or not os.path.exists(index_file):
return None
snp_overlap = OverlapCoord(snp_file, index_file)
snp_overlap.extract_index()
return snp_overlap
def prepare_overlap(genome, annodir):
"""Extracts index info into dictionary"""
genome_dir = os.path.join(annodir, genome)
if not os.path.isdir(genome_dir):
return None
dgv_file = genome_dir + '/dgv.txt'
index_file = genome_dir + '/dgv.idx'
if not os.path.exists(dgv_file) or not os.path.exists(index_file):
return None
dgv_overlap = OverlapCoord(dgv_file, index_file)
dgv_overlap.extract_index()
return dgv_overlap
def prepare_overlap(genome):
"""Extracts index info into dictionary"""
package_dir = "/".join(os.path.abspath(__file__).split("/")[:-3])
genome_dir = package_dir + '/annotations/' + genome
if not os.path.isdir(genome_dir):
return None
dgv_file = genome_dir + '/dgv.txt'
index_file = genome_dir + '/dgv.idx'
if not os.path.exists(dgv_file) or not os.path.exists(index_file):
return None
dgv_overlap = OverlapCoord(dgv_file, index_file)
dgv_overlap.extract_index()
return dgv_overlap
def prepare_overlap(cls, genome, models):
"""Prepares transcript overlapping for given genome and models"""
overlaps = {}
config = ConfigParser.ConfigParser()
config.read(PACKAGE_DIR + "/configs/model_matcher.cfg")
for m in models.split(','):
config = ConfigParser.ConfigParser()
config.read(PACKAGE_DIR + "/configs/model_matcher.cfg")
annot_file = index = None
if genome in config.sections():
for field in config.options(genome):
if field.lower() == m.lower():
annot_file = PACKAGE_DIR + "/annotations/" + genome + "/" + config.get(genome, field)
if annot_file and os.path.exists(annot_file):
index_file = annot_file.replace('.txt', '.idx')
txt_overlap = OverlapCoord(annot_file, index_file)
txt_overlap.extract_index()
overlaps[m] = txt_overlap
return overlaps
def prepare_overlap(cls, genome, models, annodir, mmcfg):
"""Prepares transcript overlapping for given genome and models"""
overlaps = {}
config = ConfigParser.ConfigParser()
config.read(mmcfg)
for m in models.split(','):
config = ConfigParser.ConfigParser()
config.read(mmcfg)
annot_file = index = None
if genome in config.sections():
for field in config.options(genome):
if field.lower() == m.lower():
annot_file = os.path.join(annodir, genome, config.get(genome, field))
if annot_file and os.path.exists(annot_file):
index_file = annot_file.replace('.txt', '.idx')
txt_overlap = OverlapCoord(annot_file, index_file)
txt_overlap.extract_index()
overlaps[m] = txt_overlap
return overlaps