def compare(settings, logs_outdir, delay=5, dry_run=False):
"""
Run a MISO samples comparison between all pairs of samples.
"""
settings_filename = utils.pathify(settings)
misowrap_obj = mw.MISOWrap(settings_filename, logs_outdir, logger_label="compare")
bam_files = misowrap_obj.bam_files
sample_labels = misowrap_obj.sample_labels
read_len = misowrap_obj.read_len
overhang_len = misowrap_obj.overhang_len
miso_bin_dir = misowrap_obj.miso_bin_dir
miso_output_dir = misowrap_obj.miso_outdir
comparison_groups = misowrap_obj.comparison_groups
comparisons_dir = misowrap_obj.comparisons_dir
utils.make_dir(comparisons_dir)
misowrap_obj.logger.info("Running MISO comparisons...")
##
## Compute comparisons between all pairs
## in a sample group
##
for comp_group in comparison_groups:
sample_pairs = utils.get_pairwise_comparisons(comp_group)
print " - Total of %d comparisons" % (len(sample_pairs))
for sample1, sample2 in sample_pairs:
# For each pair of samples, compare their output
# along each event type
misowrap_obj.logger.info("Comparing %s %s" % (sample1, sample2))
# Directories for each sample
sample1_dir = os.path.join(miso_output_dir, sample1)
sample2_dir = os.path.join(miso_output_dir, sample2)
for event_type in misowrap_obj.event_types:
sample1_event_dir = os.path.join(sample1_dir, event_type)
sample2_event_dir = os.path.join(sample2_dir, event_type)
job_name = "compare_%s_%s_%s" % (sample1, sample2, event_type)
event_comparisons_dir = os.path.join(comparisons_dir, event_type)
compare_cmd = "%s --compare-samples %s %s %s " "--comparison-labels %s %s" % (
misowrap_obj.compare_miso_cmd,
sample1_event_dir,
sample2_event_dir,
event_comparisons_dir,
sample1,
sample2,
)
misowrap_obj.logger.info("Executing: %s" % (compare_cmd))
if misowrap_obj.use_cluster:
if not dry_run:
misowrap_obj.my_cluster.launch_job(compare_cmd, job_name, ppn=1)
time.sleep(delay)
else:
if not dry_run:
os.system(compare_cmd)
def compare(settings,
logs_outdir,
delay=5,
dry_run=False):
"""
Run a MISO samples comparison between all pairs of samples.
"""
settings_filename = utils.pathify(settings)
misowrap_obj = mw.MISOWrap(settings_filename,
logs_outdir,
logger_label="compare")
bam_files = misowrap_obj.bam_files
sample_labels = misowrap_obj.sample_labels
read_len = misowrap_obj.read_len
overhang_len = misowrap_obj.overhang_len
miso_bin_dir = misowrap_obj.miso_bin_dir
miso_output_dir = misowrap_obj.miso_outdir
comparison_groups = misowrap_obj.comparison_groups
comparisons_dir = misowrap_obj.comparisons_dir
utils.make_dir(comparisons_dir)
misowrap_obj.logger.info("Running MISO comparisons...")
##
## Compute comparisons between all pairs
## in a sample group
##
for comp_group in comparison_groups:
sample_pairs = utils.get_pairwise_comparisons(comp_group)
print " - Total of %d comparisons" %(len(sample_pairs))
for sample1, sample2 in sample_pairs:
# For each pair of samples, compare their output
# along each event type
misowrap_obj.logger.info("Comparing %s %s" %(sample1,
sample2))
# Directories for each sample
sample1_dir = os.path.join(miso_output_dir,
sample1)
sample2_dir = os.path.join(miso_output_dir,
sample2)
for event_type in misowrap_obj.event_types:
sample1_event_dir = os.path.join(sample1_dir,
event_type)
sample2_event_dir = os.path.join(sample2_dir,
event_type)
job_name = "compare_%s_%s_%s" %(sample1,
sample2,
event_type)
event_comparisons_dir = \
os.path.join(comparisons_dir,
event_type)
compare_cmd = "%s --compare-samples %s %s %s " \
"--comparison-labels %s %s" \
%(misowrap_obj.compare_miso_cmd,
sample1_event_dir,
sample2_event_dir,
event_comparisons_dir,
sample1,
sample2)
misowrap_obj.logger.info("Executing: %s" %(compare_cmd))
if misowrap_obj.use_cluster:
if not dry_run:
misowrap_obj.my_cluster.launch_job(compare_cmd,
job_name,
ppn=1)
time.sleep(delay)
else:
if not dry_run:
os.system(compare_cmd)
def combine_comparisons(
settings,
logs_outdir,
common_cols=["isoforms", "chrom", "strand", "mRNA_starts", "mRNA_ends", "gene_id", "gene_symbol"],
delay=5,
dry_run=False,
NA_VAL="NA",
):
"""
Output combined MISO comparisons. For each event type,
combine the MISO comparisons for the relevant groups
based on the 'comparison_groups' in the misowrap
settings file.
"""
settings_filename = utils.pathify(settings)
logs_outdir = utils.pathify(logs_outdir)
utils.make_dir(logs_outdir)
misowrap_obj = mw.MISOWrap(settings_filename, logs_outdir, logger_label="combine_comparisons")
comparisons_dir = misowrap_obj.comparisons_dir
if not os.path.isdir(comparisons_dir):
misowrap_obj.logger.critical("Comparisons directory %s not found. " % (comparisons_dir))
sys.exit(1)
# Comparison types to combine: unfiltered comparisons and filtered comparisons
# (if available)
unfiltered_comp_dir = os.path.join(comparisons_dir, "combined_comparisons")
filtered_comp_dir = os.path.join(comparisons_dir, "filtered_events")
dirs_to_process = [unfiltered_comp_dir, filtered_comp_dir]
comparison_groups = misowrap_obj.comparison_groups
for curr_comp_dir in dirs_to_process:
if not os.path.isdir(curr_comp_dir):
print "Comparisons directory %s not found, skipping" % (curr_comp_dir)
continue
# For each event type, output the sample comparisons
for event_type in misowrap_obj.event_types:
# Collection of MISO comparison dataframes (to be merged later)
# for the current event type
comparison_dfs = []
comparison_labels = []
event_dir = os.path.join(curr_comp_dir, event_type)
if not os.path.isdir(event_dir):
misowrap_obj.logger.info("Cannot find event type %s dir, " "skipping..." % (event_type))
continue
# Look only at sample comparisons within each sample group
for comp_group in comparison_groups:
sample_pairs = utils.get_pairwise_comparisons(comp_group)
misowrap_obj.logger.info(" - Total of %d comparisons" % (len(sample_pairs)))
for sample1, sample2 in sample_pairs:
# Load miso_bf file for the current comparison
# and join it to the combined df
comparison_name = "%s_vs_%s" % (sample1, sample2)
bf_data = miso_utils.load_miso_bf_file(event_dir, comparison_name, substitute_labels=True)
if bf_data is None:
misowrap_obj.logger.warning("Could not find comparison %s" % (comparison_name))
continue
comparison_dfs.append(bf_data)
comparison_labels.append(comparison_name)
# Merge the comparison dfs together
print "Merging comparisons for %s" % (event_type)
combined_df = pandas_utils.combine_dfs(comparison_dfs)
output_filename = os.path.join(output_dir, "%s.miso_bf" % (event_type))
misowrap_obj.logger.info("Outputting %s results to: %s" % (event_type, output_filename))
if not dry_run:
combined_df.to_csv(output_filename, float_format="%.4f", sep="\t", na_rep=NA_VAL, index=True)
def combine_comparisons(settings,
logs_outdir,
common_cols=["isoforms",
"chrom",
"strand",
"mRNA_starts",
"mRNA_ends",
"gene_id",
"gene_symbol"],
delay=5,
dry_run=False,
NA_VAL="NA"):
"""
Output combined MISO comparisons. For each event type,
combine the MISO comparisons for the relevant groups
based on the 'comparison_groups' in the misowrap
settings file.
"""
settings_filename = utils.pathify(settings)
logs_outdir = utils.pathify(logs_outdir)
utils.make_dir(logs_outdir)
misowrap_obj = mw.MISOWrap(settings_filename,
logs_outdir,
logger_label="combine_comparisons")
comparisons_dir = misowrap_obj.comparisons_dir
if not os.path.isdir(comparisons_dir):
misowrap_obj.logger.critical("Comparisons directory %s not found. " \
%(comparisons_dir))
sys.exit(1)
# Comparison types to combine: unfiltered comparisons and filtered comparisons
# (if available)
unfiltered_comp_dir = os.path.join(comparisons_dir,
"combined_comparisons")
filtered_comp_dir = os.path.join(comparisons_dir,
"filtered_events")
dirs_to_process = [unfiltered_comp_dir, filtered_comp_dir]
comparison_groups = misowrap_obj.comparison_groups
for curr_comp_dir in dirs_to_process:
if not os.path.isdir(curr_comp_dir):
print "Comparisons directory %s not found, skipping" %(curr_comp_dir)
continue
# For each event type, output the sample comparisons
for event_type in misowrap_obj.event_types:
# Collection of MISO comparison dataframes (to be merged later)
# for the current event type
comparison_dfs = []
comparison_labels = []
event_dir = os.path.join(curr_comp_dir, event_type)
if not os.path.isdir(event_dir):
misowrap_obj.logger.info("Cannot find event type %s dir, " \
"skipping..." %(event_type))
continue
# Look only at sample comparisons within each sample group
for comp_group in comparison_groups:
sample_pairs = utils.get_pairwise_comparisons(comp_group)
misowrap_obj.logger.info(" - Total of %d comparisons" \
%(len(sample_pairs)))
for sample1, sample2 in sample_pairs:
# Load miso_bf file for the current comparison
# and join it to the combined df
comparison_name = "%s_vs_%s" %(sample1, sample2)
bf_data = miso_utils.load_miso_bf_file(event_dir,
comparison_name,
substitute_labels=True)
if bf_data is None:
misowrap_obj.logger.warning("Could not find comparison %s" \
%(comparison_name))
continue
comparison_dfs.append(bf_data)
comparison_labels.append(comparison_name)
# Merge the comparison dfs together
print "Merging comparisons for %s" %(event_type)
combined_df = pandas_utils.combine_dfs(comparison_dfs)
output_filename = os.path.join(output_dir,
"%s.miso_bf" %(event_type))
misowrap_obj.logger.info("Outputting %s results to: %s" \
%(event_type, output_filename))
if not dry_run:
combined_df.to_csv(output_filename,
float_format="%.4f",
sep="\t",
na_rep=NA_VAL,
index=True)
