def rp_mecat_cns(argv):
'''调用mecat纠错raw reads
'''
'''
if [ -z $1 ] ; then
echo Usage: mecat_correction rawreads
exit 1
fi
rawreads=$1
threads=20
mecat2pw -j 0 -d $rawreads -o rawreads.pm.can -w wrk_dir -t $threads
mecat2cns -i 0 -t $threads rawreads.pm.can $rawreads corrected.fasta
'''
try:
rawreads = argv[0]
cnsreads = argv[1]
threads = int(argv[2]) if len(argv) >= 3 else 4
pm = "rawreads.pm.can"
cmd = "mecat2pw -j 0 -d %s -o %s -w wrk_dir -t %d" % (rawreads, pm,
threads)
tl.run_if_modified([rawreads], [pm], cmd)
cmd = "mecat2cns -i 0 -t %d %s %s %s" % (threads, pm, rawreads,
cnsreads)
tl.run_if_modified([pm], [cnsreads], cmd)
tl.run("rm -rf %s* wrk_dir" % pm)
except:
traceback.print_exc()
print("----------------")
print(rp_mecat_cns.__doc__)
def rp_racon(argv):
'''调用minimap2和racon完成polish
rp_racon contigs reads polished [threads(4)] [minimap2_options(-x map-pb)] [racon_options()]
'''
try:
contigs = argv[0]
reads = argv[1]
polished = argv[2]
threads = int(argv[3]) if len(argv) >= 4 else 4
minimap2_options = argv[4] if len(argv) >= 5 else "-x map-pb"
racon_options = argv[5] if len(argv) >= 6 else ""
rd2ctg = "__rd2ctg__.paf"
cmd = "minimap2 %s -t %d %s %s > %s" % (minimap2_options, threads,
contigs, reads, rd2ctg)
tl.run_if_modified([contigs, reads], [rd2ctg], cmd)
cmd = "racon %s -t %d %s %s %s > %s" % (racon_options, threads, reads,
rd2ctg, contigs, polished)
tl.run_if_modified([reads, contigs, rd2ctg], [polished], cmd)
#tl.run("rm -f " + rd2ctg)
except:
traceback.print_exc()
print("----------------")
print(rp_racon.__doc__)
def rp_mummerplot(argv):
parser = argparse.ArgumentParser()
parser.add_argument("reference", type=str)
parser.add_argument("contigs", type=str)
try:
args = parser.parse_args(argv)
contigs = args.contigs
refs = args.reference
cmd = f"nucmer -l 100 -c 1000 -d 10 --banded -D 5 {contigs} {refs}"
tl.run_if_modified([], [], cmd)
cmd = f"delta-filter -i 95 -o 95 out.delta > out.best.delta"
tl.run_if_modified([], [], cmd)
cmd = f"dnadiff -d out.best.delta"
tl.run_if_modified([], [], cmd)
cmd = f"mummerplot out.best.delta --fat -f -png"
tl.run_if_modified([], [], cmd)
#tl.run("rm -f ")
except:
traceback.print_exc()
print("----------------")
print(rp_racon.__doc__)
def rp_miniasm(argv):
'''调用minimap2+miniasm完成组装
'''
# minimap + miniasm
try:
reads = argv[0]
contigs = argv[1]
threads = argv[2]
minimap2_options = argv[2]
overlaps = "__overlaps.paf"
graph = "__graph.gfa"
cmd = f"minimap2 -t {threads} {minimap2_options} {reads} {reads} | gzip -1 > {overlaps}"
tl.run_if_modified([reads], [overlaps], cmd)
cmd = f"miniasm -f {reads} {overlaps} > {graph}"
tl.run_if_modified([reads, overlaps], [graph], cmd)
# awk '/^S/{print ">"$2"\n"$3}' $graph > $contigs
cmd = f"""awk '/^S/{{print ">"$2"\n"$3}}' {graph} > {contigs}"""
tl.run_if_modified([graph], [contigs], cmd)
tl.run(f"rm -f {overlaps} {graph}")
except:
traceback.print_exc()
print("----------------")
print(rp_miniasm.__doc__)
def eval_read_accuracy(argv):
'''评估reads的准确度，首先对reads采样（100M），然后使用minimap2(--eqx)比对到ref上，最后评估错误率。
'''
parser = argparse.ArgumentParser();
try:
reads = argv[0]
stub = argv[1]
ref = "./ref.fna"
workdir = "__wrkdir"
if not os.path.exists(workdir): os.mkdir(workdir)
name, _ = os.path.splitext(os.path.split(reads)[1])
sample_size = 100000000
subreads = "%s/%s-%dM.fasta" % (workdir, name, sample_size/1000000)
rd2ref = "%s/%s-rd2ref.paf" % (workdir, name)
result = "%s/%s-%s" % (workdir, name, stub)
cmd = "python3 %s/read.py rd_sample random %s %s %d" % (get_this_script_folder(), reads, subreads, sample_size)
tl.run_if_modified([reads], [subreads], cmd)
cmd = "minimap2 -x asm20 -t 40 %s %s -c --eqx > %s" % (ref, subreads, rd2ref)
tl.run_if_modified([subreads, ref], [rd2ref], cmd)
cmd = "python3 %s/paffile.py paf_accuracy %s 2>&1 | tee %s" % (get_this_script_folder(), rd2ref, result)
print(cmd)
tl.run_if_modified([rd2ref], [result], cmd)
os.system("cat %s" % result)
except:
traceback.print_exc()
print("----------------")
print(eval_read_accuracy.__doc__)
def rp_sam4igv(argv):
'''将sam文件处理成igv可显示的格式，生成xxx.sorted.bam xxx.sorted.bam.bai
rp_sam4igv xxx.sam
'''
try:
samfname = argv[0]
assert samfname.endswith(".sam")
name = samfname[:-4]
cmd = "samtools view -bS %s > %s.bam" % (samfname, name)
tl.run_if_modified(samfname, name + ".bam", cmd)
cmd = "samtools sort %s.bam -o %s.sorted.bam" % (name, name)
tl.run_if_modified(name + ".bam", name + ".sorted.bam", cmd)
cmd = "samtools index %s.sorted.bam" % name
tl.run_if_modified(name + ".sorted.bam", name + ".sorted.bam.bai", cmd)
tl.run("rm -f %s.bam" % name)
except:
traceback.print_exc()
print("----------------")
print(rp_sam4igv.__doc__)
def rp_purge_dups(argv):
parser = argparse.ArgumentParser()
parser.add_argument("reads", type=str)
parser.add_argument("contigs", type=str)
parser.add_argument("--threads", type=int, default=20)
try:
args = parser.parse_args(argv)
contigs = args.contigs
reads = args.reads
threads = args.threads
#cmd = f"minimap2 -xmap-pb {contigs} {reads} | gzip -c - > rd2ctg.paf.gz"
cmd = "minimap2 -x map-pb -t %d %s %s | gzip -c - > rd2ctg.paf.gz" % (
threads, contigs, reads)
tl.run_if_modified([contigs, reads], ["rd2ctg.paf.gz"], cmd)
cmd = "pbcstat rd2ctg.paf.gz"
tl.run_if_modified(["rd2ctg.paf.gz"], ["PB.base.cov", "PB.stat"], cmd)
cmd = "calcuts PB.stat > cutoffs 2>calcults.log"
tl.run_if_modified(["PB.stat"], ["cutoffs"], cmd)
_, name = os.path.split(contigs)
split_contigs = name + ".split"
#cmd = f"split_fa {contigs} > {split_contigs}"
cmd = "split_fa %s > %s" % (contigs, split_contigs)
tl.run_if_modified([contigs], [split_contigs], cmd)
#cmd = f"minimap2 -xasm5 -DP {split_contigs} {split_contigs} | gzip -c - > ctg2ctg.paf.gz"
cmd = "minimap2 -x asm20 -DP -t %d %s %s | gzip -c - > ctg2ctg.paf.gz" % (
threads, split_contigs, split_contigs)
tl.run_if_modified([split_contigs], ["ctg2ctg.paf.gz"], cmd)
cmd = "purge_dups -2 -T cutoffs -c PB.base.cov ctg2ctg.paf.gz > dups.bed 2> purge_dups.log"
tl.run_if_modified(["PB.base.cov", "ctg2ctg.paf.gz", "cutoffs"],
["dups.bed"], cmd)
#cmd = f"get_seqs dups.bed {contigs}"
cmd = "get_seqs dups.bed %s" % contigs
tl.run_if_modified(["dups.bed", contigs], ["purged.fa"], cmd)
#tl.run("rm -f ")
except:
pass