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assemblatron.py
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#!/usr/bin/env python
import sys
import os
import argparse
import numpy
import math
import itertools
wd=os.path.dirname(os.path.realpath(__file__))
sys.path.insert(0, '{}/scripts'.format(wd))
import call
import stats
def assemble(args,wd):
fermi="{}/fermikit/fermi.kit/".format(wd)
bfc_path="{}/bfc".format(wd)
if not args.noec:
#run kmc
kmc_prefix="{}.kmc".format(args.prefix)
kmc="kmc -k{} -m30 {} {} {}".format(args.k,args.fastq,kmc_prefix,args.tmp)
os.system(kmc)
#apply bloom filter and build the index
ropebwt="{}/ropebwt2 -m {} -dNCr - > {}.fmd 2> {}.fmd.log".format(fermi,args.batch,args.prefix,args.prefix)
bfc="{}/bfc-kmc -k {} -T -t {} {} {} 2> {}.flt.fq.gz.log".format(bfc_path,args.k,args.cores,kmc_prefix,args.fastq,args.prefix)
os.system("{} | {}".format(bfc,ropebwt))
else:
ropebwt="{}/ropebwt2 -m {} -dNCr {} > {}.fmd".format(fermi,args.batch,args.fastq,args.prefix)
os.system(ropebwt)
#assemble
os.system( "{}/fermi2 assemble -l {} -t {} {}.fmd | gzip -1 > {}.pre.gz".format(fermi,args.l,args.cores,args.prefix,args.prefix,args.prefix) )
if args.A:
os.system("{}/fermi2 simplify -CA -R {} -d {} {}.pre.gz 2> {}.mag.gz.log > {}.mag".format(fermi,args.r,args.r,args.prefix,args.prefix, args.prefix))
else:
os.system("{}/fermi2 simplify -CS -R {} -d {} {}.pre.gz 2> {}.mag.gz.log > {}.mag".format(fermi,args.r,args.r,args.prefix,args.prefix, args.prefix))
if args.align:
os.system("bwa mem -x intractg -t {} {} {}.mag | samtools view -Sbh - | sambamba sort -m 10G -t /dev/stdin -o {}.bam".format(args.cores,args.ref,args.prefix,args.cores,args.prefix))
version = "1.0.0"
parser = argparse.ArgumentParser("""Assemblatron: a de novo assembly pipeline""".format(version),add_help=False)
parser.add_argument('--assemble' , help="Perform de novo assembly using the Fermi2 assembler", required=False, action="store_true")
parser.add_argument('--local' , help="Perform local de novo assembly using the Fermi2 assembler", required=False, action="store_true")
parser.add_argument('--sv' , help="call SV from the aligned contigs", required=False, action="store_true")
parser.add_argument('--snv' , help="call snv from the aligned contigs", required=False, action="store_true")
parser.add_argument('--stats' , help="compute assembly stats from aligned contigs", required=False, action="store_true")
parser.add_argument('--align' , help="align contigs to reference using bwa mem", required=False, action="store_true")
parser.add_argument('--fasta' , help="convert aligned contigs bam file to fasta", required=False, action="store_true")
parser.add_argument('--fastq' , help="convert bam to fastq", required=False, action="store_true")
args, unknown = parser.parse_known_args()
if args.assemble:
parser = argparse.ArgumentParser("""Assemblatron assemble - a wrapper for the fermi assembler""")
parser.add_argument('--assemble' , help="Perform de novo assembly using the Fermi2 assembler", required=False, action="store_true")
parser.add_argument('--fastq',required = True, type=str, help="input fastq")
parser.add_argument('--prefix',required = True,type=str, help="prefix of the output files")
parser.add_argument('--noec' , help="skip error correction, useful for small datasets (local assembly etc)", required=False, action="store_true")
parser.add_argument('--cores',type=int, default =16, help="number of cores (default = 16)")
parser.add_argument('--batch',type=str, default ="20g", help="batch size for multi-string indexing; 0 for single-string (default=20g)")
parser.add_argument('-l',type=int, default =81, help="min match (default = 81)")
parser.add_argument('-k',type=int, default =41, help="minimum kmer length for kmc/bfc error correction (default = 41)")
parser.add_argument('-r',type=float, default =0.9, help="minimum coverlap ratio between vertices (default=0.9)")
parser.add_argument('-A', help="Agressive bubble poping, produce more contigous assemblies, sometimes at cost of lower precisison",required=False, action="store_true")
parser.add_argument('--align', help="align contigs to reference using bwa mem", required=False, action="store_true")
parser.add_argument('--ref',type=str, help="reference fasta, required for alignment of the contigs")
parser.add_argument('--tmp',type=str,default="$TMPDIR", help="tmp directory, kmc will write tmp files here (default=$TMPDIR)")
args= parser.parse_args()
if not os.path.isdir(args.tmp) and not args.noec:
print "error: no such directory {}".format(args.tmp)
print "set the --tmp variable to an existing folder"
quit()
if not args.align or (args.align and args.ref):
assemble(args,wd)
elif args.align and not args.ref:
print ("you need a reference to align the contigs: Please supply the reference path through the --ref parameter")
elif args.local:
parser = argparse.ArgumentParser("""Assemblatron local - a wrapper for the fermi assembler""")
parser.add_argument('--local' , help="Perform local de novo assembly using the Fermi2 assembler", required=False, action="store_true")
parser.add_argument('--bam',required = True, type=str, help="input bam")
parser.add_argument('-l',type=int, default =81, help="min match (default = 81)")
parser.add_argument('--region',type=str,required=True, help="genomic region to assemble; using sthe ame format as samtools. Multiple regions are allowed",nargs='*')
parser.add_argument('-r',type=float, default =0.9, help="minimum coverlap ratio between vertices (default=0.9)")
parser.add_argument('--ref',type=str, help="reference fasta, required for alignment of the contigs")
args= parser.parse_args()
fermi="{}/fermikit/fermi.kit/".format(wd)
samtools="samtools view -bh {} {} | samtools fastq - ".format(args.bam," ".join(args.region))
ropebwt="{}/ropebwt2 -dNCr - ".format(fermi)
fermi_assemble="{}/fermi2 assemble -l {} - ".format(fermi,args.l)
fermi_simplify="{}/fermi2 simplify -C -R {} -d {} - ".format(fermi,args.r,args.r,args.l)
os.system("{} | {} | {} | {}".format(samtools,ropebwt,fermi_assemble,fermi_simplify))
elif args.sv:
parser = argparse.ArgumentParser("""Assemblatron sv - a variant caller using aligned contigs""")
parser.add_argument('--sv' , help="call SV from the aligned contigs", required=False, action="store_true")
parser.add_argument('--bam',required = True,type=str, help="input bam (contigs)")
parser.add_argument('--q',type=int, default =10 ,help="minimum allowed mapping quality(default = 10)", required=False)
parser.add_argument('--len_ctg' ,type=int, default = 40, help="minimum uniquelly mapped contig length(default = 40)", required=False)
parser.add_argument('--max_size' ,type=int, help="filter variants exceeding the following value (bp) (default=infinity)", required=False)
parser.add_argument('--max_contigs' ,type=int, default = 8, help="filter breakpoint regions containing too many contings (default=8 contigs)", required=False)
parser.add_argument('--max_coverage' ,type=int, default = 3, help="filter breakpoint regions located in high coverage regions (default=3*avg_chromosomal_coverage)", required=False)
parser.add_argument('--min_size' ,type=int, default = 50, help="minimum variant size)", required=False)
parser.add_argument('--sample' ,type=str, help="sample id, as shown in the format column", required=False)
args= parser.parse_args()
call.main(args)
elif args.stats:
parser = argparse.ArgumentParser("""Assemblatron stats - compute assembly stats""")
parser.add_argument('--stats' , help="compute assembly stats from aligned contigs", required=False, action="store_true")
parser.add_argument('--bam',required = True,type=str, help="input bam (contigs)")
args= parser.parse_args()
stats.assembly_stats(args)
elif args.align:
parser = argparse.ArgumentParser("""Assemblatron align - align contigs to the reference using bwa mem""")
parser.add_argument('--align' , help="align contigs to reference using bwa mem", required=False, action="store_true")
parser.add_argument('--ref',required = True,type=str, help="reference fasta")
parser.add_argument('--mem' , help="maximum memory (gigabytes)", type=int, default=10)
parser.add_argument('--cores' ,type=int, default = 8, help="number of cores (default = 8)", required=False)
parser.add_argument('--contigs',required = True,type=str, help="input contigs")
parser.add_argument('--prefix',required = True,type=str, help="output prefix")
args= parser.parse_args()
os.system("bwa mem -x intractg -t {} {} {} | samtools view -Sbh - | sambamba sort -m {}G /dev/stdin -o {}.bam".format(args.cores,args.ref,args.contigs,args.mem,args.prefix))
os.system( "samtools index {}.bam".format(args.prefix) )
elif args.fasta:
parser = argparse.ArgumentParser("""Assemblatron fasta - converts bam to fasta using samtools""")
parser.add_argument('--fasta' , help="convert bam to fasta", required=False, action="store_true")
parser.add_argument('--bam',required = True,type=str, help="input bam (contigs)")
args= parser.parse_args()
os.system("samtools fasta {} ".format(args.bam))
elif args.fastq:
parser = argparse.ArgumentParser("""Assemblatron fastq - converts bam to fastq using samtools""")
parser.add_argument('--fastq' , help="convert bam to fastq", required=False, action="store_true")
parser.add_argument('--bam',required = True,type=str, help="input bam (aligned reads)")
parser.add_argument('--cores' ,type=int, default = 8, help="number of cores (default = 2)", required=False)
parser.add_argument('--sort' , help="sort the output fastq based on the read names(required for later aligning paired-reads)", required=False, action="store_true")
parser.add_argument('--mem' , help="maximum memory (gigabytes)", type=int, default=20)
args= parser.parse_args()
if args.sort:
os.system("sambamba sort -n -m {}G -t {} {} -o /dev/stdout | samtools fastq -".format(args.mem,args.cores,args.bam))
else:
os.system("samtools fastq {}".format(args.bam))
elif args.snv:
parser = argparse.ArgumentParser("""Assemblatron snv - call snvs and indels usisng htsbox pileup""")
parser.add_argument('--snv' , help="call snv from the aligned contigs", required=False, action="store_true")
parser.add_argument('--bam',required = True,type=str, help="input bam (contigs)")
parser.add_argument('--ref',required = True,type=str, help="reference fasta")
parser.add_argument('-q' ,type=int,default=10, help="minimum mapping quality of contigs (default=10)")
parser.add_argument('-r' ,type=int,default=4, help="minimum number of reads supporting the SNV (default=4)")
args= parser.parse_args()
os.system("{}/fermikit/htsbox/htsbox pileup -d -c -V.05 -S 50 -q{} -s{} -f {} {} ".format(wd,args.q,args.r,args.ref,args.bam))
else:
parser.print_help()