def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(
version=
"%prog version: $Id: cgat_script_template.py 2871 2010-03-03 10:20:44Z andreas $",
usage=globals()["__doc__"])
parser.add_option(
"-a",
"--first-gtf-file",
dest="gtf_a",
type="string",
help="supply a gtf file - will compress uncompressed files")
parser.add_option(
"-b",
"--second-gtf-file",
dest="gtf_b",
type="string",
help="supply a second gtf file - will compress uncompressed files")
parser.add_option("-s",
"--scripts-dir",
dest="scripts_dir",
type="string",
help="supply a location for accessory scripts")
parser.add_option("--no-venn",
dest="no_venn",
action="store_true",
help="set if no venn is to be drawn")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv)
gtf_files = [options.gtf_a, options.gtf_b]
merged_files = []
prefices = []
E.info("merging gtf files")
for gtf in gtf_files:
if gtf.endswith(".gtf.gz"):
outfile = IOTools.snip(gtf, ".gtf.gz") + ".merged.gtf.gz"
prefices.append(IOTools.snip(gtf, ".gtf.gz"))
merged_files.append(outfile)
statement = '''zcat %s | python %s/gtf2gtf.py --method=merge-transcripts --log=%s.log | gzip > %s''' % (
gtf, options.scripts_dir, outfile, outfile)
P.execute(statement)
elif gtf.endswith(".gtf"):
outfile = IOTools.snip(gtf, ".gtf") + ".merged.gtf.gz"
prefices.append(IOTools.snip(gtf, ".gtf"))
merged_files.append(outfile)
statement = '''cat %s | python %s/gtf2gtf.py --method=merge-transcripts --log=%s.log | gzip > %s''' % (
gtf, options.scripts_dir, outfile, outfile)
E.execute(statement)
else:
raise ValueError("cannot perform merge on %s: is not a gtf file" %
gtf)
for prefix in prefices:
if options.gtf_a.find(prefix) != -1:
gtf_a = prefix + ".merged.gtf.gz"
prefix_a = prefix
elif options.gtf_b.find(prefix) != -1:
gtf_b = prefix + ".merged.gtf.gz"
prefix_b = prefix
E.info("intersecting gtf files")
# intersect the resulting merged files
scriptsdir = options.scripts_dir
intersection_out = "_vs_".join([prefix_a, prefix_b
]) + ".intersection.gtf.gz"
statement = '''intersectBed -a %(gtf_a)s -b %(gtf_b)s -s -wa
| python %(scriptsdir)s/gtf2gtf.py --method=merge-transcripts --log=log | gzip > %(intersection_out)s'''
P.run()
if not options.no_venn:
E.info("producing venn diagram for %s vs %s..." %
(options.gtf_a, options.gtf_b))
# produce the venn diagram
intersection_file = intersection_out
gtf_a_merged = gtf_a
gtf_b_merged = gtf_b
# create dictionary key
gtf_pair = (gtf_a_merged, gtf_b_merged)
# containers for counts
count_gtf_merged_a = 0
count_gtf_merged_b = 0
count_intersection = 0
# create GTF iterator objects
gtf_iterator_a = GTF.iterator(IOTools.open_file(gtf_pair[0]))
gtf_iterator_b = GTF.iterator(IOTools.open_file(gtf_pair[1]))
gtf_iterator_intersection = GTF.iterator(
IOTools.open_file(intersection_file))
# do the counts for each file
E.info("counting entries in %s" % gtf_a)
for entry in gtf_iterator_a:
count_gtf_merged_a += 1
print("counts for gtf-a: ", count_gtf_merged_a)
E.info("counting entries in %s" % gtf_b)
for entry in gtf_iterator_b:
count_gtf_merged_b += 1
print("counts for gtf-b: ", count_gtf_merged_b)
E.info("counting entries in %s" % intersection_file)
for entry in gtf_iterator_intersection:
count_intersection += 1
print("counts for intersection: ", count_intersection)
# this is the important bit - basically take an arbitrary list of numbers to represent the list of lincrna in the refnoncoding set
# then use the intersection count to represent the overlapping section in the lincrna set and add a set of random numbers to this
# set to make up the remaining - non-overlapping set
result = {}
E.info("assembling count lists")
result[gtf_pair] = {
"gtf-b":
list(map(str, range(count_gtf_merged_b))),
"gtf-a":
list(map(str, range(count_intersection))) + list(
map(str, [
random.random()
for i in range(count_intersection, count_gtf_merged_a)
]))
}
R_source = os.path.join(os.path.abspath(options.scripts_dir),
"venn_diagram.R")
R.source(R_source)
prefix_a = prefix_a.replace(".", "_").replace("-", "_")
prefix_b = prefix_b.replace(".", "_").replace("-", "_")
R('''prefix.a <- "%s"''' % prefix_a)
R('''prefix.b <- "%s"''' % prefix_b)
E.info("drawing venn diagram to %s" %
(prefix_a + "_vs_" + prefix_b + ".overlap.png"))
R["venn.diagram2"](R.list(A=result[gtf_pair]["gtf-a"],
B=result[gtf_pair]["gtf-b"]),
prefix_a + "_vs_" + prefix_b + ".overlap.png", **{
'cat.cex':
1.5,
'main.fontfamily':
"Arial",
'cat.pos':
FloatVector((0, 0)),
'cat.fontfamily':
"Arial",
'main.cex':
1.8,
'height':
1000,
'width':
1000,
'cex':
2,
'fontfamily':
"Arial",
'lwd':
R.c(1, 1),
'fill':
R.c(R.rgb(0, 0, 0.5, 0.5),
R.rgb(0.5, 0, 0, 0.5)),
'category.names':
R.c(prefix_a, prefix_b),
'margin':
R.c(0.1, 0.1, 0.1, 0.1)
})
# write footer and output benchmark information.
E.stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option(
"-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with Samtools indexed genome [default=%default].")
parser.add_option(
"-b",
"--bam-file",
dest="bam_file",
type="string",
help="filename of bam to add reads to [default=%default].")
parser.add_option("-i",
"--insertsize-mean",
dest="isize",
type="string",
help="Insert size [default=%default].")
parser.add_option(
"-s",
"--insertsize-std",
dest="isd",
type="string",
help="Insert size standard deviation [default=%default].")
parser.add_option("-r",
"--num-reads",
dest="nreads",
type="string",
help="Number of random reads to add [default=%default].")
parser.add_option("-l",
"--read-length",
dest="readlength",
type="string",
help="length of reads to generate [default=%default].")
parser.add_option("-o",
"--output-section",
dest="output_file",
type="string",
help="output filename [default=%default].")
parser.set_defaults(
genome_file=None,
bam_file=None,
isize=250,
isd=20,
nreads=10000,
readlength=50,
output_file=None,
)
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv)
# Generate random reads and add to bam
track = os.path.basename(options.bam_file)[:-len(".bam")]
readlen = options.readlength
isize = options.isize
isd = options.isd
nreads = options.nreads
genome = options.genome_file
bam = options.bam_file
out = options.output_file
statement = '''
java -jar -Xmx2048m /ifs/apps/bio/simseq-72ce499/SimSeq.jar
-1 %(readlen)s -2 %(readlen)s \
--error /ifs/apps/bio/simseq-72ce499/examples/hiseq_mito_default_bwa_mapping_mq10_1.txt \
--error2 /ifs/apps/bio/simseq-72ce499/examples/hiseq_mito_default_bwa_mapping_mq10_2.txt \
--insert_size %(isize)s \
--insert_stdev %(isd)s \
--read_number %(nreads)s \
--read_prefix simseq_ \
--reference %(genome)s \
--duplicate_probability 0.0 \
--out simseq.sam > simseq.log; ''' % locals()
E.execute(statement % locals())
statement = '''samtools view -bS -t %(genome)s.fai -o simseq.bam simseq.sam;
samtools sort simseq.bam simseq.srt;
samtools sort %(bam)s %(track)s.srt;
samtools merge %(out)s %(track)s.srt.bam simseq.srt.bam;
samtools index %(out)s;'''
E.execute(statement % locals())
# write footer and output benchmark information.
E.stop()
