def runMISOlocal(pickledDir, bamFile, readlen, overhanglen, outdir,\
paired_end, settings_f):
""" Function to run MISO on a single bam file locally, i.e. do not copy to a node.
Args:
pickledDir (str/path): Directory pointing towards pickled MISO annotations. This database can be generated with the MISO -index flag
bamFile (str/path): Directory containing sorted indexed bam file. *Please Note* Bam files must not be trimmed. MISO is not capable of processing mixed read lengths.
readlen (int): Length of reads for bamFile
overhanglen (int): The required number of nucleotides to overlap a splice junction to be considered in subsequent
outDir (str/path): Directory where MISO results will be stored
paired_end (bool): Paired-End mode. Currently MISO cannot handle paired-end data, this flag defaults to <False>
settings_f (str/path): This file contains a list of flags to provide the cluster to allow for ease of job submission
Returns:
Nothing. Generates a directory <outDir> where pickled MISO events and PSI values are stored.
"""
if paired_end == False or paired_end == 'False':
paired_end = None
Settings.load(settings_f)
run_events_analysis.compute_all_genes_psi(
pickledDir, bamFile, int(readlen), outdir,
overhang_len=int(overhanglen),
paired_end=paired_end, settings_fname=settings_f)
def runMISOlocal(pickledDir, bamFile, readlen, overhanglen, outdir,\
paired_end, settings_f):
if paired_end == False or paired_end == 'False':
paired_end = None
Settings.load(settings_f)
#if not os.path.exists(outdir):
# print 'running', outdir
run_events_analysis.compute_all_genes_psi(\
pickledDir, bamFile, int(readlen), outdir,\
overhang_len=int(overhanglen),\
paired_end=paired_end, settings_fname=settings_f)
def main():
from optparse import OptionParser
parser = OptionParser()
##
## Main options
##
parser.add_option("--compute-gene-psi", dest="compute_gene_psi",
nargs=4, default=None,
help="Compute Psi using for a given multi-isoform gene. "
"Expects four arguments: the first is a gene ID or set "
"of comma-separated (no spaces) gene IDs, "
"the second is a GFF indexed file with the gene "
"information, the third is a sorted and "
"indexed BAM file with reads aligned to the gene, "
"and the fourth is an output directory.")
parser.add_option("--paired-end", dest="paired_end",
nargs=2, default=None,
help="Run in paired-end mode. Takes a mean and standard "
"deviation for the fragment length distribution (assumed "
"to have discretized normal form.)")
parser.add_option("--compute-genes-from-file", dest="compute_genes_from_file",
nargs=3, default=None,
help="Runs on a set of genes from a file. Takes as input: "
"(1) a two-column tab-delimited file, where column 1 is the "
"event ID (ID field from GFF) and the second column is "
"the path to the indexed GFF file for that event. "
"MISO will run on all the events described in the file, "
"(2) a sorted, indexed BAM file to run on, and (3) a "
"directory to output results to.")
##
## Psi utilities
##
parser.add_option("--compare-samples", dest="samples_to_compare",
nargs=3, default=None,
help="Compute comparison statistics between the two "
"given samples. Expects three directories: the first is "
"sample1's MISO output, the second is sample2's MISO "
"output, and the third is the directory where "
"results of the sample comparison will be outputted.")
parser.add_option("--comparison-labels", dest="comparison_labels",
nargs=2, default=None,
help="Use these labels for the sample comparison "
"made by --compare-samples. "
"Takes two arguments: the label for sample 1 "
"and the label for sample 2, where sample 1 and "
"sample 2 correspond to the order of samples given "
"to --compare-samples.")
parser.add_option("--summarize-samples", dest="summarize_samples",
nargs=2, default=None,
help="Compute summary statistics of the given set "
"of samples. Expects a directory with MISO output "
"and a directory to output summary file to.")
parser.add_option("--summary-label", dest="summary_label",
nargs=1, default=None,
help="Label for MISO summary file. If not given, "
"uses basename of MISO output directory.")
parser.add_option("--use-cluster", action="store_true",
dest="use_cluster", default=False)
parser.add_option("--chunk-jobs", dest="chunk_jobs",
default=False, type="int",
help="Size (in number of events) of each job to "
"chunk events file into. Only applies when "
"running on cluster.")
parser.add_option("--settings-filename", dest="settings_filename",
default=os.path.join(miso_settings_path,
"settings",
"miso_settings.txt"),
help="Filename specifying MISO settings.")
parser.add_option("--read-len", dest="read_len", type="int",
default=None)
parser.add_option("--overhang-len", dest="overhang_len", type="int",
default=None)
parser.add_option("--event-type", dest="event_type", default=None,
help="Event type of two-isoform "
"events (e.g. 'SE', 'RI', 'A3SS', ...)")
parser.add_option("--use-compressed", dest="use_compressed",
nargs=1, default=None,
help="Use compressed event IDs. Takes as input a "
"genes_to_filenames.shelve file produced by the "
"index_gff script.")
##
## Gene utilities
##
parser.add_option("--view-gene", dest="view_gene",
nargs=1, default=None,
help="View the contents of a gene/event that has "
"been indexed. Takes as input an "
"indexed (.pickle) filename.")
(options, args) = parser.parse_args()
if options.compute_gene_psi is None:
greeting()
##
## Load the settings file
##
Settings.load(os.path.expanduser(options.settings_filename))
use_compressed = None
if options.use_compressed is not None:
use_compressed = \
os.path.abspath(os.path.expanduser(options.use_compressed))
if not os.path.exists(use_compressed):
print "Error: mapping filename from event IDs to compressed IDs %s " \
"is not found." %(use_compressed)
sys.exit(1)
else:
print "Compression being used."
if options.samples_to_compare is not None:
sample1_dirname = os.path.abspath(options.samples_to_compare[0])
sample2_dirname = os.path.abspath(options.samples_to_compare[1])
output_dirname = os.path.abspath(options.samples_to_compare[2])
if not os.path.isdir(output_dirname):
print "Making comparisons directory: %s" %(output_dirname)
misc_utils.make_dir(output_dirname)
ht.output_samples_comparison(sample1_dirname,
sample2_dirname,
output_dirname,
sample_labels=options.comparison_labels,
use_compressed=use_compressed)
##
## Main interface based on SAM files
##
if options.compute_genes_from_file != None:
# Run on events given by file
run_compute_genes_from_file(options)
if options.compute_gene_psi != None:
run_compute_gene_psi(options)
##
## Summarizing samples
##
if options.summarize_samples:
samples_dir = \
os.path.abspath(os.path.expanduser(options.summarize_samples[0]))
if options.summary_label != None:
samples_label = options.summary_label
print "Using summary label: %s" %(samples_label)
else:
samples_label = \
os.path.basename(os.path.expanduser(samples_dir))
assert(len(samples_label) >= 1)
summary_output_dir = \
os.path.abspath(os.path.join(os.path.expanduser(options.summarize_samples[1]),
'summary'))
if not os.path.isdir(summary_output_dir):
os.makedirs(summary_output_dir)
summary_filename = os.path.join(summary_output_dir,
'%s.miso_summary' %(samples_label))
summarize_sampler_results(samples_dir, summary_filename,
use_compressed=use_compressed)
if options.view_gene != None:
indexed_gene_filename = \
os.path.abspath(os.path.expanduser(options.view_gene))
print "Viewing genes in %s" %(indexed_gene_filename)
gff_genes = gff_utils.load_indexed_gff_file(indexed_gene_filename)
if gff_genes == None:
print "No genes."
sys.exit(1)
for gene_id, gene_info in gff_genes.iteritems():
print "Gene %s" %(gene_id)
gene_obj = gene_info['gene_object']
print " - Gene object: ", gene_obj
print "=="
print "Isoforms: "
for isoform in gene_obj.isoforms:
print " - ", isoform
print "=="
print "mRNA IDs: "
for mRNA_id in gene_info['hierarchy'][gene_id]['mRNAs']:
print "%s" %(mRNA_id)
print "=="
print "Exons: "
for exon in gene_obj.parts:
print " - ", exon
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--run", dest="compute_genes_psi",
nargs=2, default=None,
help="Compute Psi values for a given GFF annotation "
"of either whole mRNA isoforms or isoforms produced by "
"single alternative splicing events. Expects two "
"arguments: an indexed GFF directory with genes to "
"process, and a sorted, indexed BAM file (with "
"headers) to run on.")
parser.add_option("--event-type", dest="event_type", nargs=1,
help="[OPTIONAL] Type of event (e.g. SE, RI, A3SS, ...)",
default=None)
parser.add_option("--use-cluster", dest="use_cluster",
action="store_true", default=False,
help="Run events on cluster.")
parser.add_option("--chunk-jobs", dest="chunk_jobs",
default=False, type="int",
help="Size (in number of events) of each job to chunk "
"events file into. Only applies when running on cluster.")
parser.add_option("--no-filter-events", dest="no_filter_events",
action="store_true", default=False,
help="Do not filter events for computing Psi. "
"By default, MISO computes Psi only for events that "
"have a sufficient number of junction reads. "
"The default filter varies by event type.")
parser.add_option("--settings-filename", dest="settings_filename",
default=os.path.join(miso_settings_path,
"settings",
"miso_settings.txt"),
help="Filename specifying MISO settings.")
parser.add_option("--read-len", dest="read_len", default=None, type="int",
help="Length of sequenced reads.")
parser.add_option("--paired-end", dest="paired_end", nargs=2, default=None,
help="Run in paired-end mode. Takes mean and "
"standard deviation of insert length distribution.")
parser.add_option("--overhang-len", dest="overhang_len",
default=None, type="int",
help="Length of overhang constraints "
"imposed on junctions.")
parser.add_option("--output-dir", dest="output_dir", default=None,
help="Directory for MISO output.")
parser.add_option("--job-name", dest="job_name", nargs=1,
help="Name for jobs submitted to queue for SGE jobs. " \
"Default is misojob", default="misojob")
parser.add_option("--SGEarray", dest="SGEarray",
action="store_true", default=False,
help="Use MISO on cluster with Sun Grid Engine. "
"To be used in conjunction with --use-cluster option.")
parser.add_option("--prefilter", dest="prefilter", default=False,
action="store_true",
help="Prefilter events based on coverage. If given as "
"argument, run will begin by mapping BAM reads to event "
"regions (using bedtools), and omit events that do not "
"meet coverage criteria from the run. By default, turned "
"off. Note that events that do not meet the coverage criteria "
"will not be processed regardless, but --prefilter simply "
"does this filtering step at the start of the run, potentially "
"saving computation time so that low coverage events will not "
"be processed or distributed to jobs if MISO is run on a "
"cluster. This options requires bedtools to be installed and "
"available on path.")
parser.add_option("-p", dest="num_proc", default=None, nargs=1,
help="Number of processors to use. Only applies when running " \
"MISO on a single machine with multiple cores; does not apply " \
"to runs submitted to cluster with --use-cluster.")
parser.add_option("--version", dest="version", default=False,
action="store_true",
help="Print MISO version.")
parser.add_option("--no-wait", dest="no_wait", default=False,
action="store_true",
help="If passed in, do not wait on cluster jobs after " \
"they are submitted. By default, wait.")
##
## Gene utilities
##
parser.add_option("--view-gene", dest="view_gene",
nargs=1, default=None,
help="View the contents of a gene/event that has "
"been indexed. Takes as input an "
"indexed (.pickle) filename.")
(options, args) = parser.parse_args()
greeting()
if options.version:
print "MISO version %s\n" %(misopy.__version__)
##
## Load the settings file
##
if not os.path.isdir(miso_settings_path):
print "Error: %s is not a directory containing a default MISO " \
"settings filename. Please specify a settings filename " \
"using --settings-filename."
return
settings_filename = \
os.path.abspath(os.path.expanduser(options.settings_filename))
Settings.load(settings_filename)
if (not options.use_cluster) and options.chunk_jobs:
print "Error: Chunking jobs only applies when using " \
"the --use-cluster option to run MISO on cluster."
sys.exit(1)
if (not options.use_cluster) and options.SGEarray:
print "Error: SGEarray implies that you are using an SGE cluster," \
"please run again with --use-cluster option enabled."
sys.exit(1)
##
## Quantitation using BAM for all genes
##
if options.compute_genes_psi != None:
# GFF filename with genes to process
gff_filename = \
os.path.abspath(os.path.expanduser(options.compute_genes_psi[0]))
# BAM filename with reads
bam_filename = \
os.path.abspath(os.path.expanduser(options.compute_genes_psi[1]))
if options.output_dir == None:
print "Error: need --output-dir to compute Psi values."
sys.exit(1)
# Output directory to use
output_dir = os.path.abspath(os.path.expanduser(options.output_dir))
##
## Load the main logging object
##
logs_output_dir = os.path.join(output_dir, "logs")
main_logger = get_main_logger(logs_output_dir)
if options.read_len == None:
main_logger.error("need --read-len to compute Psi values.")
sys.exit(1)
overhang_len = 1
if options.paired_end != None and options.overhang_len != None:
main_logger.warning("cannot use --overhang-len in paired-end mode.\n" \
"Using overhang = 1")
if options.overhang_len != None:
overhang_len = options.overhang_len
# Whether to wait on cluster jobs or not
wait_on_jobs = not options.no_wait
compute_all_genes_psi(gff_filename, bam_filename,
options.read_len, output_dir,
main_logger,
overhang_len=overhang_len,
use_cluster=options.use_cluster,
SGEarray=options.SGEarray,
job_name=options.job_name,
chunk_jobs=options.chunk_jobs,
paired_end=options.paired_end,
settings_fname=settings_filename,
prefilter=options.prefilter,
num_proc=options.num_proc,
wait_on_jobs=wait_on_jobs)
if options.view_gene != None:
indexed_gene_filename = \
os.path.abspath(os.path.expanduser(options.view_gene))
print "Viewing genes in %s" %(indexed_gene_filename)
gff_genes = gff_utils.load_indexed_gff_file(indexed_gene_filename)
if gff_genes == None:
print "No genes."
sys.exit(1)
for gene_id, gene_info in gff_genes.iteritems():
print "Gene %s" %(gene_id)
gene_obj = gene_info['gene_object']
print " - Gene object: ", gene_obj
print "=="
print "Isoforms: "
for isoform in gene_obj.isoforms:
print " - ", isoform
print "=="
print "mRNA IDs: "
for mRNA_id in gene_info['hierarchy'][gene_id]['mRNAs']:
print "%s" %(mRNA_id)
print "=="
print "Exons: "
for exon in gene_obj.parts:
print " - ", exon
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--run", dest="compute_genes_psi",
nargs=2, default=None,
help="Compute Psi values for a given GFF annotation "
"of either whole mRNA isoforms or isoforms produced by "
"single alternative splicing events. Expects two "
"arguments: an indexed GFF directory with genes to "
"process, and a sorted, indexed BAM file (with "
"headers) to run on.")
parser.add_option("--event-type", dest="event_type", nargs=1,
help="[OPTIONAL] Type of event (e.g. SE, RI, A3SS, ...)",
default=None)
parser.add_option("--use-cluster", dest="use_cluster",
action="store_true", default=False,
help="Run events on cluster.")
parser.add_option("--chunk-jobs", dest="chunk_jobs",
default=False, type="int",
help="Size (in number of events) of each job to chunk "
"events file into. Only applies when running on cluster.")
parser.add_option("--no-filter-events", dest="no_filter_events",
action="store_true", default=False,
help="Do not filter events for computing Psi. "
"By default, MISO computes Psi only for events that "
"have a sufficient number of junction reads. "
"The default filter varies by event type.")
parser.add_option("--settings-filename", dest="settings_filename",
default=os.path.join(miso_settings_path,
"settings",
"miso_settings.txt"),
help="Filename specifying MISO settings.")
parser.add_option("--read-len", dest="read_len", default=None, type="int",
help="Length of sequenced reads.")
parser.add_option("--paired-end", dest="paired_end", nargs=2, default=None,
help="Run in paired-end mode. Takes mean and "
"standard deviation of insert length distribution.")
parser.add_option("--overhang-len", dest="overhang_len",
default=None, type="int",
help="Length of overhang constraints "
"imposed on junctions.")
parser.add_option("--output-dir", dest="output_dir", default=None,
help="Directory for MISO output.")
parser.add_option("--job-name", dest="job_name", nargs=1,
help="Name for jobs submitted to queue for SGE jobs. " \
"Default is misojob", default="misojob")
parser.add_option("--SGEarray", dest="SGEarray",
action="store_true", default=False,
help="Use MISO on cluster with Sun Grid Engine. "
"To be used in conjunction with --use-cluster option.")
parser.add_option("--prefilter", dest="prefilter", default=False,
action="store_true",
help="Prefilter events based on coverage. If given as "
"argument, run will begin by mapping BAM reads to event "
"regions (using bedtools), and omit events that do not "
"meet coverage criteria from the run. By default, turned "
"off. Note that events that do not meet the coverage criteria "
"will not be processed regardless, but --prefilter simply "
"does this filtering step at the start of the run, potentially "
"saving computation time so that low coverage events will not "
"be processed or distributed to jobs if MISO is run on a "
"cluster. This options requires bedtools to be installed and "
"available on path.")
parser.add_option("-p", dest="num_proc", default=None, nargs=1,
help="Number of processors to use. Only applies when running " \
"MISO on a single machine with multiple cores; does not apply " \
"to runs submitted to cluster with --use-cluster.")
parser.add_option("--version", dest="version", default=False,
action="store_true",
help="Print MISO version.")
parser.add_option("--no-wait", dest="no_wait", default=False,
action="store_true",
help="If passed in, do not wait on cluster jobs after " \
"they are submitted. By default, wait.")
##
## Gene utilities
##
parser.add_option("--view-gene", dest="view_gene",
nargs=1, default=None,
help="View the contents of a gene/event that has "
"been indexed. Takes as input an "
"indexed (.pickle) filename.")
(options, args) = parser.parse_args()
greeting()
if options.version:
print "MISO version %s\n" %(misopy.__version__)
##
## Load the settings file
##
if not os.path.isdir(miso_settings_path):
print "Error: %s is not a directory containing a default MISO " \
"settings filename. Please specify a settings filename " \
"using --settings-filename."
return
settings_filename = \
os.path.abspath(os.path.expanduser(options.settings_filename))
Settings.load(settings_filename)
if (not options.use_cluster) and options.chunk_jobs:
print "Error: Chunking jobs only applies when using " \
"the --use-cluster option to run MISO on cluster."
sys.exit(1)
if (not options.use_cluster) and options.SGEarray:
print "Error: SGEarray implies that you are using an SGE cluster," \
"please run again with --use-cluster option enabled."
sys.exit(1)
##
## Quantitation using BAM for all genes
##
if options.compute_genes_psi != None:
# GFF filename with genes to process
gff_filename = \
os.path.abspath(os.path.expanduser(options.compute_genes_psi[0]))
# BAM filename with reads
bam_filename = \
os.path.abspath(os.path.expanduser(options.compute_genes_psi[1]))
if options.output_dir == None:
print "Error: need --output-dir to compute Psi values."
sys.exit(1)
# Output directory to use
output_dir = os.path.abspath(os.path.expanduser(options.output_dir))
if options.read_len == None:
print "Error: need --read-len to compute Psi values."
sys.exit(1)
overhang_len = 1
if options.paired_end != None and options.overhang_len != None:
print "WARNING: cannot use --overhang-len in paired-end mode."
print "Using overhang = 1"
if options.overhang_len != None:
overhang_len = options.overhang_len
# Whether to wait on cluster jobs or not
wait_on_jobs = not options.no_wait
compute_all_genes_psi(gff_filename, bam_filename,
options.read_len, output_dir,
overhang_len=overhang_len,
use_cluster=options.use_cluster,
SGEarray=options.SGEarray,
job_name=options.job_name,
chunk_jobs=options.chunk_jobs,
paired_end=options.paired_end,
settings_fname=settings_filename,
prefilter=options.prefilter,
num_proc=options.num_proc,
wait_on_jobs=wait_on_jobs)
if options.view_gene != None:
indexed_gene_filename = \
os.path.abspath(os.path.expanduser(options.view_gene))
print "Viewing genes in %s" %(indexed_gene_filename)
gff_genes = gff_utils.load_indexed_gff_file(indexed_gene_filename)
if gff_genes == None:
print "No genes."
sys.exit(1)
for gene_id, gene_info in gff_genes.iteritems():
print "Gene %s" %(gene_id)
gene_obj = gene_info['gene_object']
print " - Gene object: ", gene_obj
print "=="
print "Isoforms: "
for isoform in gene_obj.isoforms:
print " - ", isoform
print "=="
print "mRNA IDs: "
for mRNA_id in gene_info['hierarchy'][gene_id]['mRNAs']:
print "%s" %(mRNA_id)
print "=="
print "Exons: "
for exon in gene_obj.parts:
print " - ", exon
def runMISOsingle(pickledDir, bamFile, readlen, overhanglen, outdir,\
paired_end, settings_f, scratchDir):
""" Function to run MISO on a single bam file.
Args:
pickledDir (str/path): Directory pointing towards pickled MISO annotations. This database can be generated with the MISO -index flag
bamFile (str/path): Directory containing sorted indexed bam file. *Please Note* Bam files must not be trimmed. MISO is not capable of processing mixed read lengths.
readlen (int): Length of reads for bamFile
overhanglen (int): The required number of nucleotides to overlap a splice junction to be considered in subsequent
outDir (str/path): Directory where MISO results will be stored
paired_end (bool): Paired-End mode. Currently MISO cannot handle paired-end data, this flag defaults to <False>
settings_f (str/path): This file contains a list of flags to provide the cluster to allow for ease of job submission
scratchDir (str/path): Directory where MISO output will be stored.
Returns:
Nothing. Generates a directory <outDir> where pickled MISO events and PSI values are stored.
"""
if paired_end == 'False':
paired_end = None
t = str(time.time()) + str(random.random())
print os.path.basename(pickledDir)
if not os.path.exists(scratchDir):
cmd = 'mkdir ' + scratchDir
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Copy pickled dir.
pickled = os.path.join(scratchDir, os.path.basename(pickledDir) + \
"." + t)
cmd = 'mkdir ' + pickled
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'cp -r ' + pickledDir + '/* ' + pickled
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Copy bam file.
cmd = 'cp -fL ' + bamFile + ' ' + scratchDir
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'cp -fL ' + bamFile + '.bai ' + scratchDir
process = subprocess.Popen(cmd, shell=True)
process.wait()
bam = os.path.join(scratchDir, os.path.basename(bamFile))
# Give output directory in scratch a timestamp
out = os.path.join(scratchDir, os.path.basename(outdir + "." + t))
# LOAD SETTINGS FOR MISO
Settings.load(settings_f)
run_events_analysis.compute_all_genes_psi(\
pickled, bam, int(readlen), out, overhang_len=int(overhanglen),\
paired_end=paired_end, settings_fname=settings_f, prefilter=False)
# Summarize sample
#summary_fname = os.path.join(out, os.path.basename(outdir) + '.miso_summary')
#samples_utils.summarize_sampler_results(out, summary_fname)
if not os.path.exists(outdir):
cmd = 'mkdir -p ' + outdir
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Copy output back.
cmd = 'cp -r ' + out + '/* ' + outdir
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Remove bam, output, and pickled dir.
cmd = 'rm ' + bam
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'rm ' + bam + '.bai'
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'rm -fr ' + out
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'rm -fr ' + pickled
process = subprocess.Popen(cmd, shell=True)
process.wait()
def main():
from optparse import OptionParser
parser = OptionParser()
##
## Main options
##
parser.add_option("--compute-gene-psi", dest="compute_gene_psi",
nargs=4, default=None,
help="Compute Psi using for a given multi-isoform gene. "
"Expects four arguments: the first is a gene ID or set "
"of comma-separated (no spaces) gene IDs, "
"the second is a GFF indexed file with the gene "
"information, the third is a sorted and "
"indexed BAM file with reads aligned to the gene, "
"and the fourth is an output directory.")
parser.add_option("--paired-end", dest="paired_end",
nargs=2, default=None,
help="Run in paired-end mode. Takes a mean and standard "
"deviation for the fragment length distribution (assumed "
"to have discretized normal form.)")
parser.add_option("--compute-genes-from-file", dest="compute_genes_from_file",
nargs=3, default=None,
help="Runs on a set of genes from a file. Takes as input: "
"(1) a two-column tab-delimited file, where column 1 is the "
"event ID (ID field from GFF) and the second column is "
"the path to the indexed GFF file for that event. "
"MISO will run on all the events described in the file, "
"(2) a sorted, indexed BAM file to run on, and (3) a "
"directory to output results to.")
##
## Psi utilities
##
parser.add_option("--compare-samples", dest="samples_to_compare",
nargs=3, default=None,
help="Compute comparison statistics between the two "
"given samples. Expects three directories: the first is "
"sample1's MISO output, the second is sample2's MISO "
"output, and the third is the directory where "
"results of the sample comparison will be outputted.")
parser.add_option("--comparison-labels", dest="comparison_labels",
nargs=2, default=None,
help="Use these labels for the sample comparison "
"made by --compare-samples. "
"Takes two arguments: the label for sample 1 "
"and the label for sample 2, where sample 1 and "
"sample 2 correspond to the order of samples given "
"to --compare-samples.")
parser.add_option("--summarize-samples", dest="summarize_samples",
nargs=2, default=None,
help="Compute summary statistics of the given set "
"of samples. Expects a directory with MISO output "
"and a directory to output summary file to.")
parser.add_option("--summary-label", dest="summary_label",
nargs=1, default=None,
help="Label for MISO summary file. If not given, "
"uses basename of MISO output directory.")
parser.add_option("--use-cluster", action="store_true",
dest="use_cluster", default=False)
parser.add_option("--chunk-jobs", dest="chunk_jobs",
default=False, type="int",
help="Size (in number of events) of each job to "
"chunk events file into. Only applies when "
"running on cluster.")
parser.add_option("--settings-filename", dest="settings_filename",
default=os.path.join(miso_settings_path,
"settings",
"miso_settings.txt"),
help="Filename specifying MISO settings.")
parser.add_option("--read-len", dest="read_len", type="int",
default=None)
parser.add_option("--overhang-len", dest="overhang_len", type="int",
default=None)
parser.add_option("--event-type", dest="event_type", default=None,
help="Event type of two-isoform "
"events (e.g. 'SE', 'RI', 'A3SS', ...)")
parser.add_option("--use-compressed", dest="use_compressed",
nargs=1, default=None,
help="Use compressed event IDs. Takes as input a "
"genes_to_filenames.shelve file produced by the "
"index_gff script.")
##
## Gene utilities
##
parser.add_option("--view-gene", dest="view_gene",
nargs=1, default=None,
help="View the contents of a gene/event that has "
"been indexed. Takes as input an "
"indexed (.pickle) filename.")
(options, args) = parser.parse_args()
if options.compute_gene_psi is None:
greeting()
##
## Load the settings file
##
Settings.load(os.path.expanduser(options.settings_filename))
use_compressed = None
if options.use_compressed is not None:
use_compressed = \
os.path.abspath(os.path.expanduser(options.use_compressed))
if not os.path.exists(use_compressed):
print "Error: mapping filename from event IDs to compressed IDs %s " \
"is not found." %(use_compressed)
sys.exit(1)
else:
print "Compression being used."
if options.samples_to_compare is not None:
sample1_dirname = os.path.abspath(options.samples_to_compare[0])
sample2_dirname = os.path.abspath(options.samples_to_compare[1])
output_dirname = os.path.abspath(options.samples_to_compare[2])
if not os.path.isdir(output_dirname):
print "Making comparisons directory: %s" %(output_dirname)
misc_utils.make_dir(output_dirname)
ht.output_samples_comparison(sample1_dirname,
sample2_dirname,
output_dirname,
sample_labels=options.comparison_labels,
use_compressed=use_compressed)
##
## Main interface based on SAM files
##
if options.compute_genes_from_file != None:
# Run on events given by file
run_compute_genes_from_file(options)
if options.compute_gene_psi != None:
run_compute_gene_psi(options)
##
## Summarizing samples
##
if options.summarize_samples:
samples_dir = \
os.path.abspath(os.path.expanduser(options.summarize_samples[0]))
if options.summary_label != None:
samples_label = options.summary_label
print "Using summary label: %s" %(samples_label)
else:
samples_label = \
os.path.basename(os.path.expanduser(samples_dir))
assert(len(samples_label) >= 1)
summary_output_dir = \
os.path.abspath(os.path.join(os.path.expanduser(options.summarize_samples[1]),
'summary'))
if not os.path.isdir(summary_output_dir):
os.makedirs(summary_output_dir)
summary_filename = os.path.join(summary_output_dir,
'%s.miso_summary' %(samples_label))
summarize_sampler_results(samples_dir, summary_filename,
use_compressed=use_compressed)
if options.view_gene != None:
indexed_gene_filename = \
os.path.abspath(os.path.expanduser(options.view_gene))
print "Viewing genes in %s" %(indexed_gene_filename)
gff_genes = gff_utils.load_indexed_gff_file(indexed_gene_filename)
if gff_genes == None:
print "No genes."
sys.exit(1)
for gene_id, gene_info in gff_genes.iteritems():
print "Gene %s" %(gene_id)
gene_obj = gene_info['gene_object']
print " - Gene object: ", gene_obj
print "=="
print "Isoforms: "
for isoform in gene_obj.isoforms:
print " - ", isoform
print "=="
print "mRNA IDs: "
for mRNA_id in gene_info['hierarchy'][gene_id]['mRNAs']:
print "%s" %(mRNA_id)
print "=="
print "Exons: "
for exon in gene_obj.parts:
print " - ", exon
def runMISOsingle(pickledDir, bamFile, readlen, overhanglen, outdir,\
paired_end, settings_f, scratchDir):
if paired_end == 'False':
paired_end = None
t = str(time.time()) + str(random.random())
print os.path.basename(pickledDir)
if not os.path.exists(scratchDir):
cmd = 'mkdir ' + scratchDir
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Copy pickled dir.
pickled = os.path.join(scratchDir, os.path.basename(pickledDir) + \
"." + t)
cmd = 'mkdir ' + pickled
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'cp -r ' + pickledDir + '/* ' + pickled
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Copy bam file.
cmd = 'cp -fL ' + bamFile + ' ' + scratchDir
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'cp -fL ' + bamFile + '.bai ' + scratchDir
process = subprocess.Popen(cmd, shell=True)
process.wait()
bam = os.path.join(scratchDir, os.path.basename(bamFile))
# Give output directory in scratch a timestamp
out = os.path.join(scratchDir, os.path.basename(outdir + "." + t))
# LOAD SETTINGS FOR MISO
Settings.load(settings_f)
run_events_analysis.compute_all_genes_psi(\
pickled, bam, int(readlen), out, overhang_len=int(overhanglen),\
paired_end=paired_end, settings_fname=settings_f, prefilter=True)
# Summarize sample
#summary_fname = os.path.join(out, os.path.basename(outdir) + '.miso_summary')
#samples_utils.summarize_sampler_results(out, summary_fname)
if not os.path.exists(outdir):
cmd = 'mkdir -p ' + outdir
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Copy output back.
cmd = 'cp -r ' + out + '/* ' + outdir
process = subprocess.Popen(cmd, shell=True)
process.wait()
# Remove bam, output, and pickled dir.
cmd = 'rm ' + bam
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'rm ' + bam + '.bai'
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'rm -fr ' + out
process = subprocess.Popen(cmd, shell=True)
process.wait()
cmd = 'rm -fr ' + pickled
process = subprocess.Popen(cmd, shell=True)
process.wait()
def run(self, delay_constant=0.9):
"""
Run batches either locally on multi-cores
or using cluster.
"""
batch_filenames = self.output_batch_files()
# All MISO commands, each correspond to a batch,
# and the number of jobs in each batch
all_miso_cmds = []
num_batches = len(batch_filenames)
##
## Prepare all the files necessary to run each batch
##
print "Preparing to run %d batches of jobs..." % (num_batches)
miso_run = os.path.join(miso_path, "run_miso.py")
for batch_num, batch in enumerate(batch_filenames):
batch_filename, batch_size = batch
miso_cmd = \
"python %s --compute-genes-from-file \"%s\" %s %s --read-len %d " \
%(miso_run,
batch_filename,
self.bam_filename,
self.output_dir,
self.read_len)
# Add paired-end parameters and read len/overhang len
if self.paired_end != None:
# Run in paired-end mode
frag_mean = float(self.paired_end[0])
frag_sd = float(self.paired_end[1])
miso_cmd += " --paired-end %.1f %.1f" % (frag_mean, frag_sd)
else:
# Overhang len only used in single-end mode
miso_cmd += " --overhang-len %d" % (self.overhang_len)
# Add settings filename if given
if self.settings_fname != None:
miso_cmd += " --settings-filename %s" \
%(self.settings_fname)
all_miso_cmds.append((miso_cmd, batch_size))
##
## Run all MISO commands for the batches
## either locally using multi-cores or on cluster
##
# First handle special case of SGE cluster submission
if self.use_cluster and self.SGEarray:
print "Using SGEarray..."
# Call SGE
batch_argfile = os.path.join(self.cluster_scripts_dir,
"run_args.txt")
cluster_utils.run_SGEarray_cluster(all_miso_cmds,
batch_argfile,
self.output_dir,
settings=self.settings_fname,
job_name=self.sge_job_name,
chunk=self.chunk_jobs)
# End SGE case
return
# All cluster jobs
cluster_jobs = []
for batch_num, cmd_info in enumerate(all_miso_cmds):
miso_cmd, batch_size = cmd_info
print "Running batch of %d genes.." % (batch_size)
print " - Executing: %s" % (miso_cmd)
# Make a log file for the batch, where all the output
# will be redirected
time_str = time.strftime("%m-%d-%y_%H:%M:%S")
batch_logfile = os.path.join(
self.batch_logs_dir, "batch-%d-%s.log" % (batch_num, time_str))
cmd_to_run = "%s >> \"%s\";" % (miso_cmd, batch_logfile)
if not self.use_cluster:
# Run locally
p = subprocess.Popen(cmd_to_run, shell=True)
thread_id = "batch-%d" % (batch_num)
print " - Submitted thread %s" % (thread_id)
self.threads[thread_id] = p
else:
# Setup cluster engine
Settings.load(self.settings_fname)
clustercmd = Settings.get_cluster_command()
self.cluster_engine = getClusterEngine(clustercmd,
self.settings_fname)
# Run on cluster
if batch_size >= self.long_thresh:
queue_type = "long"
else:
queue_type = "short"
# Run on cluster
job_name = "gene_psi_batch_%d" % (batch_num)
print "Submitting to cluster: %s" % (cmd_to_run)
job_id = \
self.cluster_engine.run_on_cluster(cmd_to_run,
job_name,
self.output_dir,
queue_type=queue_type)
if job_id is not None:
cluster_jobs.append(job_id)
time.sleep(delay_constant)
# Extra delay constant
time.sleep(delay_constant)
# If ran jobs on cluster, wait for them if there are any
# to wait on.
if self.wait_on_jobs:
if self.use_cluster and (len(cluster_jobs) == 0):
# If we're asked to use the cluster but the list
# of cluster jobs is empty, it means we could not
# find the IDs of the job from the submission
# system. Report this to the user.
self.main_logger.warning("Asked to wait on cluster jobs but cannot " \
"parse their job IDs from the cluster submission " \
"system.")
# Try to wait on jobs no matter what; though if 'cluster_jobs'
# is empty here, it will not wait
self.cluster_engine.wait_on_jobs(cluster_jobs, self.cluster_cmd)
else:
if self.use_cluster:
# If we're running in cluster mode and asked not
# to wait for jobs, let user know
self.main_logger.info("Not waiting on cluster jobs.")
# If ran jobs locally, wait on them to finish
# (this will do nothing if we submitted jobs to
# cluster)
self.wait_on_threads()
