def dn(args):
"""
%prog dn folder
Run Trinity-DN on a folder of reads. When paired-end (--paired) mode is on,
filenames will be scanned based on whether they contain "_1_" and "_2_".
"""
p = OptionParser(dn.__doc__)
p.add_option("--paired", default=False, action="store_true",
help="Paired-end mode [default: %default]")
p.set_home("trinity")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
folder, = args
paired = opts.paired
thome = opts.trinity_home
tfolder = folder + "_DN"
cwd = os.getcwd()
mkdir(tfolder)
os.chdir(tfolder)
flist = glob("../" + folder + "/*")
if paired:
f1 = [x for x in flist if "_1_" in x or ".1." in x]
f2 = [x for x in flist if "_2_" in x or ".2." in x]
assert len(f1) == len(f2)
r1, r2 = "left.fastq", "right.fastq"
reads = ((f1, r1), (f2, r2))
else:
r = "single.fastq"
reads = ((flist, r), )
for fl, r in reads:
fm = FileMerger(fl, r)
fm.merge(checkexists=True)
cmd = op.join(thome, "Trinity.pl")
cmd += " --seqType fq --JM 100G --CPU {0}".format(opts.cpus)
if paired:
cmd += " --left {0} --right {1}".format(reads[0][-1], reads[1][-1])
else:
cmd += " --single {0}".format(reads[0][-1])
runfile = "run.sh"
write_file(runfile, cmd, meta="run script")
os.chdir(cwd)
def prepare(args):
"""
%prog prepare [--options] folder [genome.fasta]
Run Trinity on a folder of reads. When paired-end (--paired) mode is on,
filenames will be scanned based on whether they contain the patterns
("_1_" and "_2_") or (".1." and ".2.") or ("_1." and "_2.").
By default, prepare script for DN
If genome.fasta is provided, prepare script for GG-Trinity.
If coord-sorted BAM is provided, then it will use it as starting point.
Since GG-Trinity jobs are partitioned DN-Trinity jobs run on relatively small
regions, lesser amount of CPU can be specified for each DN job using `--gg_cpu`
In such cases, the `--cpu` should be set to a larger value to help speedup
upstream steps such as GSNAP read mapping or coordinate sorting of BAM files.
Newer versions of trinity can take multiple fastq files as input.
If "--merge" is specified, the fastq files are merged together before assembling
"""
p = OptionParser(prepare.__doc__)
p.add_option("--paired", default=False, action="store_true",
help="Paired-end mode [default: %default]")
p.add_option("--merge", default=False, action="store_true",
help="Merge individual input fastq's into left/right/single" + \
" file(s) [default: %default]")
p.set_trinity_opts()
p.set_grid()
opts, args = p.parse_args(args)
if len(args) not in (1, 2):
sys.exit(not p.print_help())
inparam, = args[:1]
genome = args[1] if len(args) == 2 else None
method = "GG" if genome is not None else "DN"
paired = opts.paired
merge = opts.merge
thome = opts.trinity_home
use_bam = opts.use_bam
gg_cpu = opts.gg_cpu
pf = inparam.split(".")[0]
tfolder = "{0}_{1}".format(pf, method)
cwd = os.getcwd()
mkdir(tfolder)
os.chdir(tfolder)
flist = iglob("../" + inparam, "*.fq", "*.fastq", "*.fq.gz", "*.fastq.gz")
if paired:
f1 = [x for x in flist if "_1_" in x or ".1." in x or "_1." in x]
f2 = [x for x in flist if "_2_" in x or ".2." in x or "_2." in x]
assert len(f1) == len(f2)
if merge:
r1, r2 = "left.fastq", "right.fastq"
reads = ((f1, r1), (f2, r2))
else:
if merge:
r = "single.fastq"
reads = ((flist, r), )
if merge:
for fl, r in reads:
fm = FileMerger(fl, r)
fm.merge(checkexists=True)
cmd = op.join(thome, "Trinity")
cmd += " --seqType fq --JM {0} --CPU {1}".format(opts.JM, opts.cpus)
cmd += " --min_contig_length {0}".format(opts.min_contig_length)
if opts.bflyGCThreads:
cmd += " --bflyGCThreads {0}".format(opts.bflyGCThreads)
if method == "GG":
cmd += " --genome {0} --genome_guided_max_intron {1}".format(genome, opts.max_intron)
if use_bam:
cmd += " --genome_guided_use_bam {0}".format(use_bam)
if gg_cpu:
cmd += " --genome_guided_CPU {0}".format(gg_cpu)
if opts.grid and opts.grid_conf_file:
cmd += " --grid_conf_file={0}".format(opts.grid_conf_file)
if paired:
if merge:
cmd += " --left {0} --right {1}".format(reads[0][-1], reads[1][-1])
else:
for lf, rf in zip(f1, f2):
cmd += " --left {0}".format(lf)
cmd += " --right {0}".format(rf)
else:
if merge:
cmd += " --single {0}".format(reads[0][-1])
else:
for f in flist:
cmd += " --single {0}".format(f)
if opts.extra:
cmd += " {0}".format(opts.extra)
runfile = "run.sh"
write_file(runfile, cmd)
os.chdir(cwd)
def prepare(args):
"""
%prog prepare [--options] folder [--bam rnaseq.coordSorted.bam]
Run Trinity on a folder of reads. When paired-end (--paired) mode is on,
filenames will be scanned based on whether they contain the patterns
("_1_" and "_2_") or (".1." and ".2.") or ("_1." and "_2.").
By default, prepare script for DN-Trinity.
If coord-sorted BAM is provided, prepare script for GG-Trinity, using BAM
as starting point.
Newer versions of trinity can take multiple fastq files as input.
If "--merge" is specified, the fastq files are merged together before assembling
"""
p = OptionParser(prepare.__doc__)
p.add_option("--paired", default=False, action="store_true",
help="Paired-end mode [default: %default]")
p.add_option("--merge", default=False, action="store_true",
help="Merge individual input fastq's into left/right/single" + \
" file(s) [default: %default]")
p.set_trinity_opts()
p.set_fastq_names()
p.set_grid()
opts, args = p.parse_args(args)
if len(args) not in (1, 2):
sys.exit(not p.print_help())
inparam, = args[:1]
paired = opts.paired
merge = opts.merge
trinity_home = opts.trinity_home
hpc_grid_runner_home = opts.hpcgridrunner_home
method = "DN"
bam = opts.bam
if bam and op.exists(bam):
bam = op.abspath(bam)
method = "GG"
pf = inparam.split(".")[0]
tfolder = "{0}_{1}".format(pf, method)
cwd = os.getcwd()
mkdir(tfolder)
os.chdir(tfolder)
cmds = []
# set TRINITY_HOME env variable when preparing shell script
env_cmd = 'export TRINITY_HOME="{0}"'.format(trinity_home)
cmds.append(env_cmd)
if method == "DN":
assert op.exists("../" + inparam)
flist = iglob("../" + inparam, opts.names)
if paired:
f1 = [x for x in flist if "_1_" in x or ".1." in x or "_1." in x or "_R1" in x]
f2 = [x for x in flist if "_2_" in x or ".2." in x or "_2." in x or "_R2" in x]
assert len(f1) == len(f2)
if merge:
r1, r2 = "left.fastq", "right.fastq"
reads = ((f1, r1), (f2, r2))
else:
if merge:
r = "single.fastq"
reads = ((flist, r), )
if merge:
for fl, r in reads:
fm = FileMerger(fl, r)
fm.merge(checkexists=True)
cmd = op.join(trinity_home, "Trinity")
cmd += " --seqType fq --max_memory {0} --CPU {1}".format(opts.max_memory, opts.cpus)
cmd += " --min_contig_length {0}".format(opts.min_contig_length)
if opts.bflyGCThreads:
cmd += " --bflyGCThreads {0}".format(opts.bflyGCThreads)
if method == "GG":
cmd += " --genome_guided_bam {0}".format(bam)
cmd += " --genome_guided_max_intron {0}".format(opts.max_intron)
else:
if paired:
if merge:
cmd += " --left {0} --right {1}".format(reads[0][-1], reads[1][-1])
else:
cmd += " --left {0}".format(",".join(f1))
cmd += " --right {0}".format(",".join(f2))
else:
if merge:
cmd += " --single {0}".format(reads[0][-1])
else:
for f in flist:
cmd += " --single {0}".format(f)
if opts.grid and opts.grid_conf_file:
hpc_grid_runner = op.join(hpc_grid_runner_home, "hpc_cmds_GridRunner.pl")
hpc_grid_conf_file = op.join(hpc_grid_runner_home, "hpc_conf", opts.grid_conf_file)
assert op.exists(hpc_grid_conf_file), "HpcGridRunner conf file does not exist: {0}".format(hpc_grid_conf_file)
cmd += ' --grid_exec "{0} --grid_conf {1} -c"'.format(hpc_grid_runner, hpc_grid_conf_file)
if opts.extra:
cmd += " {0}".format(opts.extra)
cmds.append(cmd)
if opts.cleanup:
cleanup_cmd = 'rm -rf !("Trinity.fasta"|"Trinity.gene_trans_map"|"Trinity.timing")' \
if method == "DN" else \
'rm -rf !("Trinity-GG.fasta"|"Trinity-GG.gene_trans_map"|"Trinity.timing")'
cmd.append(cleanup_cmd)
runfile = "run.sh"
write_file(runfile, "\n".join(cmds))
os.chdir(cwd)
def prepare(args):
"""
%prog prepare [--options] folder [genome.fasta]
Run Trinity on a folder of reads. When paired-end (--paired) mode is on,
filenames will be scanned based on whether they contain the patterns
("_1_" and "_2_") or (".1." and ".2.") or ("_1." and "_2.").
By default, prepare script for DN
If genome.fasta is provided, prepare script for GG-Trinity.
If coord-sorted BAM is provided, then it will use it as starting point.
Since GG-Trinity jobs are partitioned DN-Trinity jobs run on relatively small
regions, lesser amount of CPU can be specified for each DN job using `--gg_cpu`
In such cases, the `--cpu` should be set to a larger value to help speedup
upstream steps such as GSNAP read mapping or coordinate sorting of BAM files.
Newer versions of trinity can take multiple fastq files as input.
If "--merge" is specified, the fastq files are merged together before assembling
"""
p = OptionParser(prepare.__doc__)
p.add_option("--paired",
default=False,
action="store_true",
help="Paired-end mode [default: %default]")
p.add_option("--merge", default=False, action="store_true",
help="Merge individual input fastq's into left/right/single" + \
" file(s) [default: %default]")
p.set_trinity_opts()
p.set_grid()
opts, args = p.parse_args(args)
if len(args) not in (1, 2):
sys.exit(not p.print_help())
inparam, = args[:1]
assert op.exists(inparam)
genome = args[1] if len(args) == 2 else None
method = "GG" if genome is not None else "DN"
paired = opts.paired
merge = opts.merge
thome = opts.trinity_home
use_bam = opts.use_bam
gg_cpu = opts.gg_cpu
pf = inparam.split(".")[0]
tfolder = "{0}_{1}".format(pf, method)
cwd = os.getcwd()
mkdir(tfolder)
os.chdir(tfolder)
flist = iglob("../" + inparam, opts.names)
if paired:
f1 = [x for x in flist if "_1_" in x or ".1." in x or "_1." in x]
f2 = [x for x in flist if "_2_" in x or ".2." in x or "_2." in x]
assert len(f1) == len(f2)
if merge:
r1, r2 = "left.fastq", "right.fastq"
reads = ((f1, r1), (f2, r2))
else:
if merge:
r = "single.fastq"
reads = ((flist, r), )
if merge:
for fl, r in reads:
fm = FileMerger(fl, r)
fm.merge(checkexists=True)
cmd = op.join(thome, "Trinity")
cmd += " --seqType fq --max_memory {0} --CPU {1}".format(
opts.max_memory, opts.cpus)
cmd += " --min_contig_length {0}".format(opts.min_contig_length)
if opts.bflyGCThreads:
cmd += " --bflyGCThreads {0}".format(opts.bflyGCThreads)
if method == "GG":
cmd += " --genome {0} --genome_guided_max_intron {1}".format(
genome, opts.max_intron)
if use_bam:
cmd += " --genome_guided_use_bam {0}".format(use_bam)
if gg_cpu:
cmd += " --genome_guided_CPU {0}".format(gg_cpu)
if opts.grid and opts.grid_conf_file:
cmd += " --grid_conf_file={0}".format(opts.grid_conf_file)
if paired:
if merge:
cmd += " --left {0} --right {1}".format(reads[0][-1], reads[1][-1])
else:
for lf, rf in zip(f1, f2):
cmd += " --left {0}".format(lf)
cmd += " --right {0}".format(rf)
else:
if merge:
cmd += " --single {0}".format(reads[0][-1])
else:
for f in flist:
cmd += " --single {0}".format(f)
if opts.extra:
cmd += " {0}".format(opts.extra)
cmd += " --bypass_java_version_check"
runfile = "run.sh"
write_file(runfile, cmd)
os.chdir(cwd)
