def get_sample_bams(self):
"""
Handles ``yaml_config.cuffdiff_options.positional_args.sample_bams: from_conditions``.
"""
def join_replicate_paths(top_level_conditions, paths):
# I KNOW this has crappy big O time but the list sizes here are small
joined_rep_paths = []
for tlc in top_level_conditions:
tlc_paths = []
for path in paths:
if tlc in path:
tlc_paths.append(path)
else:
pass
joined_rep_paths.append(','.join(tlc_paths))
return joined_rep_paths
#: .. todo:: support replicate bams as: " samp1_r1.bam,samp1_r2.bam samp2_r1.bam,samp2_r2.bam "
option = self.prog_yargs.positional_args.sample_bams
if option == 'from_conditions':
paths = []
for condition in self._conditions:
bam_path = self.get_bam_path(condition)
paths.append(bam_path)
# join bam paths that are bio-replicates with commas
top_level_conditions = [
'_'.join(path.split('/')[-2].split('_')[:-1]) for path in paths
]
top_level_conditions = uniques(top_level_conditions)
joined_replicate_paths = join_replicate_paths(
top_level_conditions, paths)
return ' '.join(joined_replicate_paths)
else:
return option
def get_sample_bams(self):
"""
Handles ``yaml_config.cuffdiff_options.positional_args.sample_bams: from_conditions``.
"""
def join_replicate_paths(top_level_conditions, paths):
# I KNOW this has crappy big O time but the list sizes here are small
joined_rep_paths = []
for tlc in top_level_conditions:
tlc_paths = []
for path in paths:
if tlc in path:
tlc_paths.append(path)
else:
pass
joined_rep_paths.append(','.join(tlc_paths))
return joined_rep_paths
#: .. todo:: support replicate bams as: " samp1_r1.bam,samp1_r2.bam samp2_r1.bam,samp2_r2.bam "
option = self.prog_yargs.positional_args.sample_bams
if option == 'from_conditions':
paths = []
for condition in self._conditions:
bam_path = self.get_bam_path(condition)
paths.append(bam_path)
# join bam paths that are bio-replicates with commas
top_level_conditions = ['_'.join(path.split('/')[-2].split('_')[:-1]) for path in paths]
top_level_conditions = uniques(top_level_conditions)
joined_replicate_paths = join_replicate_paths(top_level_conditions, paths)
return ' '.join(joined_replicate_paths)
else:
return option
def get_labels(self):
"""
Handles ``yaml_config.cuffdiff_options.labels: from_conditions``.
"""
option = self.prog_yargs['labels']
if option == 'from_conditions':
labels = []
for condition in self._conditions:
labels.append(condition['name'])
labels = uniques(labels)
return ','.join(labels)
else:
return option
def get_labels(self):
"""
Handles ``yaml_config.cuffdiff_options.labels: from_conditions``.
"""
option = self.prog_yargs['labels']
if option == 'from_conditions':
labels = []
for condition in self._conditions:
labels.append(condition['name'])
labels = uniques(labels)
return ','.join(labels)
else:
return option