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 genome.fasta transcripts.fasta [annotation.gff]
Run the PASA annotation comparison pipeline
If annotation.gff file is provided, 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) not in (3, 4):
sys.exit(not p.print_help())
pasa_db, genome, transcripts, = args[:3]
annotation = 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()
launch_pasa = which(op.join(PASA_HOME, "scripts", \
"Launch_PASA_pipeline.pl"))
grid = opts.grid
prepare, runfile = opts.prepare, "run.sh"
os.chdir(pasa_db)
if prepare:
write_file(runfile, "") # initialize run script
if opts.grid and not opts.threaded:
opts.threaded = opts.cpus
acfw = must_open(acconf, "w")
print >> acfw, 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)
acfw.close()
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, genome, transcripts, opts.genetic_code)
if 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 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 compare(args):
"""
%prog compare pasa_db_name genome.fasta transcripts.fasta [annotation.gff]
Run the PASA annotation comparison pipeline
If annotation.gff file is provided, 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) not in (3, 4):
sys.exit(not p.print_help())
pasa_db, genome, transcripts, = args[:3]
annotation = 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()
launch_pasa = which(op.join(PASA_HOME, "scripts", \
"Launch_PASA_pipeline.pl"))
grid = opts.grid
prepare, runfile = opts.prepare, "run.sh"
os.chdir(pasa_db)
if prepare:
write_file(runfile, "") # initialize run script
if opts.grid and not opts.threaded:
opts.threaded = opts.cpus
acfw = must_open(acconf, "w")
print >> acfw, 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)
acfw.close()
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, genome, transcripts, opts.genetic_code)
if annotation:
accmd += " -L --annots_gff3 {0}".format(annotation)
if prepare:
write_file(runfile, accmd, append=True)
else:
sh(accmd, grid=grid, grid_opts=opts)