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 build(args):
"""
%prog build input.bed scaffolds.fasta
Build associated genome FASTA file and CHAIN file that can be used to lift
old coordinates to new coordinates. The CHAIN file will be used to lift the
original marker positions to new positions in the reconstructed genome. The
new positions of the markers will be reported in *.lifted.bed.
"""
p = OptionParser(build.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
inputbed, scaffolds = args
pf = inputbed.rsplit(".", 1)[0]
mapbed = pf + ".bed"
chr_agp = pf + ".chr.agp"
chr_fasta = pf + ".chr.fasta"
if need_update((chr_agp, scaffolds), chr_fasta):
agp_build([chr_agp, scaffolds, chr_fasta])
unplaced_agp = pf + ".unplaced.agp"
if need_update((chr_agp, scaffolds), unplaced_agp):
write_unplaced_agp(chr_agp, scaffolds, unplaced_agp)
unplaced_fasta = pf + ".unplaced.fasta"
if need_update((unplaced_agp, scaffolds), unplaced_fasta):
agp_build([unplaced_agp, scaffolds, unplaced_fasta])
combined_agp = pf + ".agp"
if need_update((chr_agp, unplaced_agp), combined_agp):
FileMerger((chr_agp, unplaced_agp), combined_agp).merge()
combined_fasta = pf + ".fasta"
if need_update((chr_fasta, unplaced_fasta), combined_fasta):
FileMerger((chr_fasta, unplaced_fasta), combined_fasta).merge()
chainfile = pf + ".chain"
if need_update((combined_agp, scaffolds, combined_fasta), chainfile):
fromagp([combined_agp, scaffolds, combined_fasta])
liftedbed = mapbed.rsplit(".", 1)[0] + ".lifted.bed"
if need_update((mapbed, chainfile), liftedbed):
cmd = "liftOver -minMatch=1 {0} {1} {2} unmapped".\
format(mapbed, chainfile, liftedbed)
sh(cmd)
sort([liftedbed, "-i"]) # Sort bed in place
def merge(args):
"""
%prog merge folder1 ...
Consolidate split contents in the folders. The folders can be generated by
the split() process and several samples may be in separate fastq files. This
program merges them.
"""
p = OptionParser(merge.__doc__)
p.add_option("--outdir",
default="outdir",
help="Output final reads in [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
folders = args
outdir = opts.outdir
mkdir(outdir)
files = flatten(glob("{0}/*.*.fastq".format(x)) for x in folders)
files = list(files)
key = lambda x: op.basename(x).split(".")[0]
files.sort(key=key)
for id, fns in groupby(files, key=key):
fns = list(fns)
outfile = op.join(outdir, "{0}.fastq".format(id))
FileMerger(fns, outfile=outfile).merge(checkexists=True)
def refine(args):
"""
%prog refine breakpoints.bed gaps.bed
Find gaps within or near breakpoint region.
"""
p = OptionParser(refine.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
breakpointsbed, gapsbed = args
ncols = len(open(breakpointsbed).next().split())
logging.debug("File {0} contains {1} columns.".format(
breakpointsbed, ncols))
cmd = "intersectBed -wao -a {0} -b {1}".format(breakpointsbed, gapsbed)
pf = "{0}.{1}".format(breakpointsbed.split(".")[0], gapsbed.split(".")[0])
ingapsbed = pf + ".bed"
sh(cmd, outfile=ingapsbed)
fp = open(ingapsbed)
data = [x.split() for x in fp]
nogapsbed = pf + ".nogaps.bed"
largestgapsbed = pf + ".largestgaps.bed"
nogapsfw = open(nogapsbed, "w")
largestgapsfw = open(largestgapsbed, "w")
for b, gaps in groupby(data, key=lambda x: x[:ncols]):
gaps = list(gaps)
gap = gaps[0]
if len(gaps) == 1 and gap[-1] == "0":
assert gap[-2] == "."
print >> nogapsfw, "\t".join(b)
continue
gaps = [(int(x[-1]), x) for x in gaps]
maxgap = max(gaps)[1]
print >> largestgapsfw, "\t".join(maxgap)
nogapsfw.close()
largestgapsfw.close()
closestgapsbed = pf + ".closestgaps.bed"
closestgapsfw = open(closestgapsbed, "w")
cmd = "closestBed -a {0} -b {1} -d".format(nogapsbed, gapsbed)
sh(cmd, outfile=closestgapsbed)
refinedbed = pf + ".refined.bed"
FileMerger([largestgapsbed, closestgapsbed], outfile=refinedbed).merge()
# Clean-up
toclean = [nogapsbed, largestgapsbed, closestgapsbed]
FileShredder(toclean)
return refinedbed
def augustus(args):
"""
%prog augustus fastafile
Run parallel AUGUSTUS. Final results can be reformatted using
annotation.reformat.augustus().
"""
p = OptionParser(augustus.__doc__)
p.add_option("--species",
default="maize",
help="Use species model for prediction")
p.add_option("--hintsfile", help="Hint-guided AUGUSTUS")
p.add_option("--nogff3",
default=False,
action="store_true",
help="Turn --gff3=off")
p.set_home("augustus")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(fastafile, ) = args
cpus = opts.cpus
mhome = opts.augustus_home
gff3 = not opts.nogff3
suffix = ".gff3" if gff3 else ".out"
cfgfile = op.join(mhome, "config/extrinsic/extrinsic.M.RM.E.W.cfg")
outdir = mkdtemp(dir=".")
fs = split([fastafile, outdir, str(cpus)])
augustuswrap_params = partial(
augustuswrap,
species=opts.species,
gff3=gff3,
cfgfile=cfgfile,
hintsfile=opts.hintsfile,
)
g = Jobs(augustuswrap_params, fs.names)
g.run()
gff3files = [x.rsplit(".", 1)[0] + suffix for x in fs.names]
outfile = fastafile.rsplit(".", 1)[0] + suffix
FileMerger(gff3files, outfile=outfile).merge()
shutil.rmtree(outdir)
if gff3:
from jcvi.annotation.reformat import augustus as reformat_augustus
reformat_outfile = outfile.replace(".gff3", ".reformat.gff3")
reformat_augustus([outfile, "--outfile={0}".format(reformat_outfile)])
def parallel_musclewrap(clustfile, cpus, minsamp=0):
musclewrap_minsamp = partial(musclewrap, minsamp=minsamp)
if cpus == 1:
return musclewrap_minsamp(clustfile)
from jcvi.apps.grid import Jobs
outdir = mkdtemp(dir=".")
fs = split([clustfile, outdir, str(cpus), "--format=clust"])
g = Jobs(musclewrap_minsamp, fs.names)
g.run()
clustnames = [x.replace(".clust", ".clustS") for x in fs.names]
clustSfile = clustfile.replace(".clust", ".clustS")
FileMerger(clustnames, outfile=clustSfile).merge()
shutil.rmtree(outdir)
def scaffold(args):
"""
%prog scaffold ctgfasta reads1.fasta mapping1.bed
reads2.fasta mapping2.bed ...
Run BAMBUS on set of contigs, reads and read mappings.
"""
from jcvi.formats.base import FileMerger
from jcvi.formats.bed import mates
from jcvi.formats.contig import frombed
from jcvi.formats.fasta import join
from jcvi.utils.iter import grouper
p = OptionParser(scaffold.__doc__)
p.add_option("--conf",
help="BAMBUS configuration file [default: %default]")
p.add_option(
"--prefix",
default=False,
action="store_true",
help="Only keep links between IDs with same prefix [default: %default]"
)
opts, args = p.parse_args(args)
nargs = len(args)
if nargs < 3 or nargs % 2 != 1:
sys.exit(not p.print_help())
ctgfasta = args[0]
duos = list(grouper(2, args[1:]))
trios = []
for fastafile, bedfile in duos:
prefix = bedfile.rsplit(".", 1)[0]
matefile = prefix + ".mates"
matebedfile = matefile + ".bed"
if need_update(bedfile, [matefile, matebedfile]):
matesopt = [bedfile, "--lib", "--nointra"]
if opts.prefix:
matesopt += ["--prefix"]
matefile, matebedfile = mates(matesopt)
trios.append((fastafile, matebedfile, matefile))
# Merge the readfasta, bedfile and matefile
bbfasta, bbbed, bbmate = "bambus.reads.fasta", "bambus.bed", "bambus.mates"
for files, outfile in zip(zip(*trios), (bbfasta, bbbed, bbmate)):
FileMerger(files, outfile=outfile).merge(checkexists=True)
ctgfile = "bambus.contig"
idsfile = "bambus.ids"
frombedInputs = [bbbed, ctgfasta, bbfasta]
if need_update(frombedInputs, ctgfile):
frombed(frombedInputs)
inputfasta = "bambus.contigs.fasta"
singletonfasta = "bambus.singletons.fasta"
cmd = "faSomeRecords {0} {1} ".format(ctgfasta, idsfile)
sh(cmd + inputfasta)
sh(cmd + singletonfasta + " -exclude")
# Run bambus
prefix = "bambus"
cmd = "goBambus -c {0} -m {1} -o {2}".format(ctgfile, bbmate, prefix)
if opts.conf:
cmd += " -C {0}".format(opts.conf)
sh(cmd)
cmd = "untangle -e {0}.evidence.xml -s {0}.out.xml -o {0}.untangle.xml".\
format(prefix)
sh(cmd)
final = "final"
cmd = "printScaff -e {0}.evidence.xml -s {0}.untangle.xml -l {0}.lib " \
"-merge -detail -oo -sum -o {1}".format(prefix, final)
sh(cmd)
oofile = final + ".oo"
join([inputfasta, "--oo={0}".format(oofile)])
def refine(args):
"""
%prog refine breakpoints.bed gaps.bed
Find gaps within or near breakpoint region.
For breakpoint regions with no gaps, there are two options:
- Break in the middle of the region
- Break at the closest gap (--closest)
"""
p = OptionParser(refine.__doc__)
p.add_option(
"--closest",
default=False,
action="store_true",
help="In case of no gaps, use closest",
)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
breakpointsbed, gapsbed = args
ncols = len(open(breakpointsbed).next().split())
logging.debug("File {0} contains {1} columns.".format(breakpointsbed, ncols))
cmd = "intersectBed -wao -a {0} -b {1}".format(breakpointsbed, gapsbed)
pf = "{0}.{1}".format(breakpointsbed.split(".")[0], gapsbed.split(".")[0])
ingapsbed = pf + ".bed"
sh(cmd, outfile=ingapsbed)
fp = open(ingapsbed)
data = [x.split() for x in fp]
nogapsbed = pf + ".nogaps.bed"
largestgapsbed = pf + ".largestgaps.bed"
nogapsfw = open(nogapsbed, "w")
largestgapsfw = open(largestgapsbed, "w")
for b, gaps in groupby(data, key=lambda x: x[:ncols]):
gaps = list(gaps)
gap = gaps[0]
if len(gaps) == 1 and gap[-1] == "0":
assert gap[-3] == "."
print("\t".join(b), file=nogapsfw)
continue
gaps = [(int(x[-1]), x) for x in gaps]
maxgap = max(gaps)[1]
print("\t".join(maxgap), file=largestgapsfw)
nogapsfw.close()
largestgapsfw.close()
beds = [largestgapsbed]
toclean = [nogapsbed, largestgapsbed]
if opts.closest:
closestgapsbed = pf + ".closestgaps.bed"
cmd = "closestBed -a {0} -b {1} -d".format(nogapsbed, gapsbed)
sh(cmd, outfile=closestgapsbed)
beds += [closestgapsbed]
toclean += [closestgapsbed]
else:
pointbed = pf + ".point.bed"
pbed = Bed()
bed = Bed(nogapsbed)
for b in bed:
pos = (b.start + b.end) / 2
b.start, b.end = pos, pos
pbed.append(b)
pbed.print_to_file(pointbed)
beds += [pointbed]
toclean += [pointbed]
refinedbed = pf + ".refined.bed"
FileMerger(beds, outfile=refinedbed).merge()
# Clean-up
FileShredder(toclean)
return refinedbed
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 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)