parser.add_argument('-o', '--outfile', help="Output file name.") parser.add_argument('-H', '--histogram_file', help="Save score histograms to FILE") parser.add_argument('-j', '--nthreads', help="Number of threads.", type=int, default=16) args = parser.parse_args() if args.top: import psutil hra = HiriseAssembly() hra.load_assembly(args.infile) hra.merge_masked_regions(debug=args.debug) print(len(hra.layout_lines)) if len(hra.layout_lines) == 0: print("#make trivial layout") hra.make_trivial_layout_lines(debug=args.debug) ces.set_exp_insert_size_dist_fit_params(hra.model_params) model = ces.model nbams = len(hra.bams) inq = JoinableQueue(maxsize=0) readers = []
parser.add_argument('-i', '--infile', default=False, help="Filename for serialised assembly input file.") parser.add_argument( '-o', '--outfile', default=False, help= "Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking." ) # -m 2 -w 1000 -M $( cat {input.threshold} ) args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) for segments_file in args.mask: asf.add_mask_regions(filename=segments_file) asf.merge_masked_regions() if args.outfile: of = open(args.outfile, "wt") else: of = sys.stdout for ocontig in asf.ocontigs_iter(): chunk = struct.unpack( "<L", hashlib.md5( ocontig.encode("utf-8")).digest()[:4])[0] % args.nchunks
from __future__ import division from __future__ import print_function from builtins import range from past.utils import old_div from hirise_assembly import HiriseAssembly if __name__=="__main__": import sys import argparse parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d','--debug',default=False ,action="store_true",help="Turn on debugging ouput") parser.add_argument('-L','--layout',default=False ,help="A file containing a layout of contigs.") parser.add_argument('-i','--infile',default=False ,help="Filename for serialised assembly input file.") parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) if args.outfile: f=open(args.outfile,"wt") for contig in asf.contigs_iter(): f.write("{}\t{}\n".format(contig,asf.contig_length(contig)))
parser.add_argument("-m", "--min_links", default=2, type=int, help="Min links to another contig to count.") parser.add_argument("-M", "--max_others", default=4, type=int, help="Max other contigs in the window.") parser.add_argument("-c", "--chunk", default=0, type=int, help="This chunk.") parser.add_argument("-q", "--mapq", default=50, type=int, help="Min map quality score.") parser.add_argument("-i", "--infile", default=False, help="Filename for serialised assembly input file.") parser.add_argument( "-o", "--outfile", default=False, help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.", ) # -m 2 -w 1000 -M $( cat {input.threshold} ) args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) for segments_file in args.mask: asf.add_mask_regions(filename=segments_file) asf.merge_masked_regions() if args.outfile: of = open(args.outfile, "wt") else: of = sys.stdout for ocontig in asf.ocontigs_iter(): chunk = struct.unpack("<L", hashlib.md5(ocontig.encode("utf-8")).digest()[:4])[0] % args.nchunks if not chunk == args.chunk: continue links = {}
if __name__=="__main__": import sys import argparse parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d','--debug',default=False ,action="store_true",help="Turn on debugging ouput") parser.add_argument('-b','--breaks',default=False ,help="File containing breaks") parser.add_argument('-i','--infile',default=False ,help="Input layout in p: lines format.") parser.add_argument('-o','--outfile',default=False,help="Filename for output.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) # asf = HiriseAssembly() # asf.load_playout(args.infile) breaks=[] scores={} for l in open(args.breaks): if l[0]=="#": continue #Scaffold102239 741 1379 5097 -5.421961663655971 scaffold,a,b,slen,score = l.strip().split() a=int(a) #start b=int(b) #end # c=int(c) #lowpoint
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d','--debug',default=False ,action="store_true",help="Turn on debugging ouput") # parser.add_argument('-L','--layout',default=False ,help="A file containing a layout of contigs.") parser.add_argument('-T','--test', default=False ,help="Compute stats for an explicitly specified region.") parser.add_argument('-B','--bin', default=False ,action="store_true",help="Bin reference sequences.") parser.add_argument('-N','--nsamples',default=10000,type=int ,help="Number of winows to sample.") parser.add_argument('-w','--window',default=1000, type=int ,help="Size of windows to examine.") parser.add_argument('-W','--binwindow',default=100000, type=int ,help="Size of windows to break reference contigs into.") parser.add_argument('-i','--infile',default=False ,help="Filename for serialised assembly input file.") # parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) n=0 asf.binsize = args.binwindow while n<args.nsamples: try: c,a,b=asf.random_window(wlen=args.window) if args.test: m=re.match("^(.*):(\d+)-(\d+)$",args.test) c=m.group(1) a=int(m.group(2)) b=int(m.group(3)) asf.window_stats(c,a,b,debug=args.debug,bins=args.bin) n+=1
parser.add_argument('-b','--breaks',default=False ,help="File containing breaks") parser.add_argument('-B','--bams',default=[],action="append" ,help="File containing breaks") parser.add_argument('-i','--infile',default=False ,help="Input layout in p: lines format.") parser.add_argument('-j','--nprocesses',default=16,type=int ,help="Number of subprocesses to use when making PDF reports.") parser.add_argument('-H','--head',default=False,type=int ,help="Maximum number of breaks to make visualizations for.") parser.add_argument('-o','--outfile',default=False,help="Filename for output.") parser.add_argument('-R','--report',default=False ,metavar="FILE", help="Generate a PDF report with visualizations of the breaks made.") parser.add_argument('-t','--threshold',default=5.0,type=float,help="Minimum acceptable LLR support.") parser.add_argument('-T','--contig_break_threshold',type=float,help="Minimum acceptable LLR support within contig sequence.") parser.add_argument('-q','--mapq',default=10.0,type=float,help="Mapping quality score cutoff.") parser.add_argument('--mask',default=False,help="File with segments to mask for dot-plot visualization.") args = parser.parse_args() if args.contig_break_threshold==None: args.contig_break_threshold = args.threshold asf = HiriseAssembly() asf.load_playout(args.infile) breaks=[] scores={} stype={} for l in open(args.breaks): if l[0]=="#": continue fields = l.strip().split() scaffold,a,b,c,score,slen = fields[:6] lowest_raw_score=args.threshold+5 clipped=False if "clippedLLR" in fields: clipped=True if not fields[6]=="False":
from builtins import range from past.utils import old_div from hirise_assembly import HiriseAssembly # import struct # import hashlib import re if __name__ == "__main__": import sys import argparse parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument("-d", "--debug", default=False, action="store_true", help="Turn on debugging ouput") parser.add_argument("-q", "--mapq", default=55, type=float, help="Minimum map quality threshold.") parser.add_argument("-i", "--infile", default=False, help="Filename for serialised assembly input file.") parser.add_argument("-o", "--outfile", default=False, help="Filename for bedfile output.") args = parser.parse_args() if args.infile: hra = HiriseAssembly() hra.load_assembly(args.infile) if args.outfile: of = open(args.outfile, "wt") else: of = sys.stdout hra.read_deserts(mapq=55, outfile=of, min_len=1000)
# from __future__ import division from __future__ import print_function from builtins import range from past.utils import old_div from hirise_assembly import HiriseAssembly if __name__=="__main__": import sys import argparse parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d','--debug',default=False ,action="store_true",help="Turn on debugging ouput") parser.add_argument('-L','--layout',default=False ,help="A file containing a layout of contigs.") parser.add_argument('-i','--infile',default=False ,help="Filename for serialised assembly input file.") parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) if args.layout: asf.load_playout(args.layout) if args.outfile: asf.save_assembly( args.outfile )
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d','--debug',default=False,action="store_true",help="Turn on debugging ouput") parser.add_argument('-C','--nchunks' ,default=1,type=int,help="Number of chunks.") parser.add_argument('-m','--mask' ,default=[], action="append",help="Name of a file containing regions of the input assembly to mask out") parser.add_argument('-c','--chunk',default=0, type=int,help="This chunk.") parser.add_argument('-K','--contig',default=False,help="Just this contig.") parser.add_argument('-q','--mapq',default=10, type=float,help="Minimum map quality threshold.") parser.add_argument('-i','--infile',default=False,help="Filename for serialised assembly input file.") parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") # -m 2 -w 1000 -M $( cat {input.threshold} ) args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) for segments_file in args.mask: asf.add_mask_regions(filename=segments_file) asf.merge_masked_regions() if args.contig: contig_iter=iter([args.contig]) else: contig_iter = asf.ocontigs_iter() if args.outfile: of=open(args.outfile,"wt") else:
default=False, help="Filename for serialised assembly input file.") parser.add_argument('-f', '--fasta', default=False, help="Filename for original contigs fasta.") parser.add_argument( '-o', '--outfile', default=False, help= "Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking." ) args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) asf.ocontig_fasta = args.fasta if args.outfile: outfasta = fastaWriter(args.outfile) for contig in asf.contigs_iter(): outfasta.next(contig) outfasta.write(asf.get_seq(contig)) outfasta.flush() outfasta.close()
parser.add_argument( '-W', '--binwindow', default=100000, type=int, help="Size of windows to break reference contigs into.") parser.add_argument('-i', '--infile', default=False, help="Filename for serialised assembly input file.") # parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) n = 0 asf.binsize = args.binwindow while n < args.nsamples: try: c, a, b = asf.random_window(wlen=args.window) if args.test: m = re.match("^(.*):(\d+)-(\d+)$", args.test) c = m.group(1) a = int(m.group(2)) b = int(m.group(3)) asf.window_stats(c, a, b, debug=args.debug, bins=args.bin) n += 1
parser.add_argument('-q','--mapq',type=int,default=55) parser.add_argument('-S','--slice',default=False) parser.add_argument('-i','--infile',help="File containing .hra formatted hirise assembly.") parser.add_argument('-o','--outfile',help="Output file name.") parser.add_argument('-H','--histogram_file',help="Save score histograms to FILE") parser.add_argument('-j','--nthreads',help="Number of threads.",type=int,default=16) args = parser.parse_args() if args.top: import psutil hra = HiriseAssembly() hra.load_assembly(args.infile) hra.merge_masked_regions(debug=args.debug) print(len(hra.layout_lines)) if len(hra.layout_lines)==0: print("#make trivial layout") hra.make_trivial_layout_lines(debug=args.debug) ces.set_exp_insert_size_dist_fit_params(hra.model_params) model=ces.model nbams = len(hra.bams) inq = JoinableQueue(maxsize=0) readers=[]
from __future__ import print_function from builtins import range from past.utils import old_div from hirise_assembly import HiriseAssembly #import struct #import hashlib import re if __name__=="__main__": import sys import argparse parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d','--debug',default=False,action="store_true",help="Turn on debugging ouput") parser.add_argument('-q','--mapq',default=55, type=float,help="Minimum map quality threshold.") parser.add_argument('-i','--infile',default=False,help="Filename for serialised assembly input file.") parser.add_argument('-o','--outfile',default=False,help="Filename for bedfile output.") args = parser.parse_args() if args.infile: hra = HiriseAssembly() hra.load_assembly(args.infile) if args.outfile: of=open(args.outfile,"wt") else: of=sys.stdout hra.read_deserts(mapq=55,outfile=of,min_len=1000)