def prepare_synteny(tourfile, lastfile, odir, p, opts):
"""
Prepare synteny plots for movie().
"""
qbedfile, sbedfile = get_bed_filenames(lastfile, p, opts)
qbedfile = op.abspath(qbedfile)
sbedfile = op.abspath(sbedfile)
qbed = Bed(qbedfile, sorted=False)
contig_to_beds = dict(qbed.sub_beds())
# Create a separate directory for the subplots and movie
mkdir(odir, overwrite=True)
os.chdir(odir)
logging.debug("Change into subdir `{}`".format(odir))
# Make anchorsfile
anchorsfile = ".".join(op.basename(lastfile).split(".",
2)[:2]) + ".anchors"
fw = open(anchorsfile, "w")
for b in Blast(lastfile):
print >> fw, "\t".join(
(gene_name(b.query), gene_name(b.subject), str(int(b.score))))
fw.close()
# Symlink sbed
symlink(sbedfile, op.basename(sbedfile))
return anchorsfile, qbedfile, contig_to_beds
def prepare_synteny(tourfile, lastfile, odir, p, opts):
"""
Prepare synteny plots for movie().
"""
qbedfile, sbedfile = get_bed_filenames(lastfile, p, opts)
qbedfile = op.abspath(qbedfile)
sbedfile = op.abspath(sbedfile)
qbed = Bed(qbedfile, sorted=False)
contig_to_beds = dict(qbed.sub_beds())
# Create a separate directory for the subplots and movie
mkdir(odir, overwrite=True)
os.chdir(odir)
logging.debug("Change into subdir `{}`".format(odir))
# Make anchorsfile
anchorsfile = ".".join(op.basename(lastfile).split(".", 2)[:2]) \
+ ".anchors"
fw = open(anchorsfile, "w")
for b in Blast(lastfile):
print >> fw, "\t".join((gene_name(b.query), gene_name(b.subject),
str(int(b.score))))
fw.close()
# Symlink sbed
symlink(sbedfile, op.basename(sbedfile))
return anchorsfile, qbedfile, contig_to_beds
def mcscanx(args):
"""
%prog mcscanx athaliana.athaliana.last athaliana.bed
Wrap around MCScanX.
"""
p = OptionParser(mcscanx.__doc__)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
blastfile = args[0]
bedfiles = args[1:]
prefix = "_".join(op.basename(x)[:2] for x in bedfiles)
symlink(blastfile, prefix + ".blast")
allbedfile = prefix + ".gff"
fw = open(allbedfile, "w")
for i, bedfile in enumerate(bedfiles):
prefix = chr(ord('A') + i)
make_gff(bedfile, prefix, fw)
fw.close()
def mcscanx(args):
"""
%prog mcscanx athaliana.athaliana.last athaliana.bed
Wrap around MCScanX.
"""
p = OptionParser(mcscanx.__doc__)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
blastfile = args[0]
bedfiles = args[1:]
prefix = "_".join(op.basename(x)[:2] for x in bedfiles)
symlink(blastfile, prefix + ".blast")
allbedfile = prefix + ".gff"
fw = open(allbedfile, "w")
for i, bedfile in enumerate(bedfiles):
prefix = chr(ord('A') + i)
make_gff(bedfile, prefix, fw)
fw.close()
def assemble(args):
"""
%prog assemble pasa_db_name genome.fasta transcripts-dn.fasta [transcript-gg.fasta]
Run the PASA alignment assembly pipeline
If two transcript fasta files (Trinity denovo and genome guided) are provided
and the `--compreh` param is enabled, the PASA Comprehensive Transcriptome DB
protocol is followed <http://pasa.sourceforge.net/#A_ComprehensiveTranscriptome>
Using the `--prepare` option creates a shell script with the run commands without
executing the pipeline
"""
p = OptionParser(assemble.__doc__)
p.set_pasa_opts()
p.add_option("--prepare", default=False, action="store_true",
help="Prepare PASA run script with commands [default: %default]")
p.set_grid()
p.set_grid_opts()
opts, args = p.parse_args(args)
if len(args) not in (3, 4):
sys.exit(not p.print_help())
pasa_db, genome, dnfasta, = args[:3]
ggfasta = args[3] if len(args) == 4 else None
PASA_HOME = opts.pasa_home
if not op.isdir(PASA_HOME):
logging.error("PASA_HOME={0} directory does not exist".format(PASA_HOME))
sys.exit()
aligners = opts.aligners.split(",")
for aligner in aligners:
if aligner not in ALLOWED_ALIGNERS:
logging.error("Error: Unknown aligner `{0}`".format(aligner))
logging.error("Can be any of {0}, ".format("|".join(ALLOWED_ALIGNERS)) + \
"combine multiple aligners in list separated by comma")
sys.exit()
clean = opts.clean
seqclean = op.join(opts.tgi_home, "seqclean")
accn_extract = which(op.join(PASA_HOME, "misc_utilities", \
"accession_extractor.pl"))
launch_pasa = which(op.join(PASA_HOME, "scripts", \
"Launch_PASA_pipeline.pl"))
build_compreh_trans = which(op.join(PASA_HOME, "scripts", \
"build_comprehensive_transcriptome.dbi"))
fl_accs = opts.fl_accs
cpus = opts.cpus
grid = opts.grid
prepare, runfile = opts.prepare, "run.sh"
pctcov, pctid = opts.pctcov, opts.pctid
compreh_pctid = opts.compreh_pctid
compreh_pctcov, bpsplice = opts.compreh_pctcov, opts.bpsplice
cmds = []
# set PASAHOME env variable if preparing shell script
if prepare:
env_cmd = 'export PASAHOME="{0}"'.format(PASA_HOME)
cmds.append(env_cmd)
if ggfasta:
transcripts = FileMerger([dnfasta, ggfasta], tfasta).merge()
accn_extract_cmd = "cat {0} | {1} > {2}".format(dnfasta, accn_extract, tdn)
cmds.append(accn_extract_cmd)
if not prepare:
sh(accn_extract_cmd)
else:
symlink(dnfasta, tfasta)
transcripts = tfasta
if opts.grid and not opts.threaded:
opts.threaded = opts.cpus
prjobid = None
if clean:
ccpus = 16 if cpus >= 16 else cpus
cleancmd = "{0} {1} -c {2} -l 60".format(seqclean, transcripts, ccpus)
if prepare:
cmds.append(cleancmd)
else:
prjobid = sh(cleancmd, grid=grid, grid_opts=opts)
aafw = must_open(aaconf, "w")
print(alignAssembly_conf.format("{0}_pasa".format(pasa_db), \
pctcov, pctid, bpsplice), file=aafw)
aafw.close()
symlink(genome, gfasta)
aacmd = "{0} -c {1} -C -R -g {2}".format(launch_pasa, aaconf, gfasta)
aacmd += " -t {0}.clean -T -u {0}".format(transcripts) if clean else \
" -t {0}".format(transcripts)
if fl_accs:
symlink(fl_accs, flaccs)
aacmd += " -f {0}".format(flaccs)
if ggfasta:
aacmd += " --TDN {0}".format(tdn)
aacmd += " --ALIGNERS {0} -I {1} --CPU {2}".format(",".join(aligners), \
opts.intron, cpus)
if prepare:
cmds.append(aacmd)
else:
opts.hold_jid = prjobid
prjobid = sh(aacmd, grid=grid, grid_opts=opts)
if opts.compreh and ggfasta:
comprehcmd = "{0} -c {1} -t {2}".format(build_compreh_trans, aaconf, transcripts)
comprehcmd += " --min_per_ID {0} --min_per_aligned {1}".format(compreh_pctid, compreh_pctcov)
if prepare:
cmds.append(comprehcmd)
else:
opts.hold_jid = prjobid
prjobid = sh(comprehcmd, grid=grid, grid_opts=opts)
if prepare:
write_file(runfile, "\n".join(cmds)) # initialize run script
def compare(args):
"""
%prog compare pasa_db_name [--annots_gff3=annotation.gff3]
Run the PASA annotation comparison pipeline
This assumes that PASA alignment assembly has alredy been completed and
run directory contains `genome.fasta` and `transcript.fasta` files.
If `--annots_gff3` is specified, the PASA database is loaded with the annotations
first before starting annotation comparison. Otherwise, it uses previously
loaded annotation data.
Using the `--prepare` option creates a shell script with the run commands without
executing the pipeline
"""
p = OptionParser(compare.__doc__)
p.set_pasa_opts(action="compare")
p.add_option("--prepare", default=False, action="store_true",
help="Prepare PASA run script with commands [default: %default]")
p.set_grid()
p.set_grid_opts()
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
pasa_db, = args
PASA_HOME = opts.pasa_home
if not op.isdir(PASA_HOME):
logging.error("PASA_HOME={0} directory does not exist".format(PASA_HOME))
sys.exit()
launch_pasa = which(op.join(PASA_HOME, "scripts", \
"Launch_PASA_pipeline.pl"))
annots_gff3 = opts.annots_gff3
grid = opts.grid
prepare, runfile = opts.prepare, "run.sh"
os.chdir(pasa_db)
if prepare:
write_file(runfile, "", append=True, skipcheck=True) # initialize run script
acfw = must_open(acconf, "w")
print(annotCompare_conf.format("{0}_pasa".format(pasa_db), \
opts.pctovl, opts.pct_coding, opts.pctid_prot, opts.pctlen_FL, \
opts.pctlen_nonFL, opts.orf_size, opts.pct_aln, opts.pctovl_gene, \
opts.stompovl, opts.trust_FL, opts.utr_exons), file=acfw)
acfw.close()
if not op.exists(gfasta):
sys.exit("Genome fasta file `{0}` does not exist".format(gfasta))
transcripts = tfasta
if not op.exists(transcripts):
sys.exit("Transcript fasta file `{0}` does not exist".format(transcripts))
if op.exists("{0}.clean".format(transcripts)):
transcripts = "{0}.clean".format(transcripts)
accmd = "{0} -c {1} -A -g {2} -t {3} --GENETIC_CODE {4}".format(launch_pasa, \
acconf, gfasta, transcripts, opts.genetic_code)
if annots_gff3:
if not op.exists(annots_gff3):
sys.exit("Annotation gff3 file `{0}` does not exist".format(annots_gff3))
symlink(annots_gff3, annotation)
accmd += " -L --annots_gff3 {0}".format(annotation)
if prepare:
write_file(runfile, accmd, append=True)
else:
sh(accmd, grid=grid, grid_opts=opts)
def movie(args):
"""
%prog movie test.tour test.clm ref.contigs.last
Plot optimization history.
"""
p = OptionParser(movie.__doc__)
p.add_option("--frames",
default=500,
type="int",
help="Only plot every N frames")
p.add_option("--engine",
default="ffmpeg",
choices=("ffmpeg", "gifsicle"),
help="Movie engine, output MP4 or GIF")
p.set_beds()
opts, args, iopts = p.set_image_options(args,
figsize="16x8",
style="white",
cmap="coolwarm",
format="png",
dpi=300)
if len(args) != 3:
sys.exit(not p.print_help())
tourfile, clmfile, lastfile = args
tourfile = op.abspath(tourfile)
clmfile = op.abspath(clmfile)
lastfile = op.abspath(lastfile)
cwd = os.getcwd()
odir = op.basename(tourfile).rsplit(".", 1)[0] + "-movie"
anchorsfile, qbedfile, contig_to_beds = \
prepare_synteny(tourfile, lastfile, odir, p, opts)
args = []
for i, label, tour, tour_o in iter_tours(tourfile, frames=opts.frames):
padi = "{:06d}".format(i)
# Make sure the anchorsfile and bedfile has the serial number in,
# otherwise parallelization may fail
a, b = op.basename(anchorsfile).split(".", 1)
ianchorsfile = a + "_" + padi + "." + b
symlink(anchorsfile, ianchorsfile)
# Make BED file with new order
qb = Bed()
for contig, o in zip(tour, tour_o):
if contig not in contig_to_beds:
continue
bedlines = contig_to_beds[contig][:]
if o == '-':
bedlines.reverse()
for x in bedlines:
qb.append(x)
a, b = op.basename(qbedfile).split(".", 1)
ibedfile = a + "_" + padi + "." + b
qb.print_to_file(ibedfile)
# Plot dot plot, but do not sort contigs by name (otherwise losing
# order)
image_name = padi + "." + iopts.format
tour = ",".join(tour)
args.append([[
tour, clmfile, ianchorsfile, "--outfile", image_name, "--label",
label
]])
Jobs(movieframe, args).run()
os.chdir(cwd)
make_movie(odir, odir, engine=opts.engine, format=iopts.format)
def movie(args):
"""
%prog movie test.tour test.clm ref.contigs.last
Plot optimization history.
"""
p = OptionParser(movie.__doc__)
p.add_option("--frames", default=500, type="int",
help="Only plot every N frames")
p.add_option("--engine", default="ffmpeg", choices=("ffmpeg", "gifsicle"),
help="Movie engine, output MP4 or GIF")
p.set_beds()
opts, args, iopts = p.set_image_options(args, figsize="16x8",
style="white", cmap="coolwarm",
format="png", dpi=300)
if len(args) != 3:
sys.exit(not p.print_help())
tourfile, clmfile, lastfile = args
tourfile = op.abspath(tourfile)
clmfile = op.abspath(clmfile)
lastfile = op.abspath(lastfile)
cwd = os.getcwd()
odir = op.basename(tourfile).rsplit(".", 1)[0] + "-movie"
anchorsfile, qbedfile, contig_to_beds = \
prepare_synteny(tourfile, lastfile, odir, p, opts)
args = []
for i, label, tour, tour_o in iter_tours(tourfile, frames=opts.frames):
padi = "{:06d}".format(i)
# Make sure the anchorsfile and bedfile has the serial number in,
# otherwise parallelization may fail
a, b = op.basename(anchorsfile).split(".", 1)
ianchorsfile = a + "_" + padi + "." + b
symlink(anchorsfile, ianchorsfile)
# Make BED file with new order
qb = Bed()
for contig, o in zip(tour, tour_o):
if contig not in contig_to_beds:
continue
bedlines = contig_to_beds[contig][:]
if o == '-':
bedlines.reverse()
for x in bedlines:
qb.append(x)
a, b = op.basename(qbedfile).split(".", 1)
ibedfile = a + "_" + padi + "." + b
qb.print_to_file(ibedfile)
# Plot dot plot, but do not sort contigs by name (otherwise losing
# order)
image_name = padi + "." + iopts.format
tour = ",".join(tour)
args.append([[tour, clmfile, ianchorsfile,
"--outfile", image_name, "--label", label]])
Jobs(movieframe, args).run()
os.chdir(cwd)
make_movie(odir, odir, engine=opts.engine, format=iopts.format)
