ragoo: RaGOO/ragoo.py comparison

comparison RaGOO/ragoo.py @ 13:b9a3aeb162ab draft default tip

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author	dereeper
date	Mon, 26 Jul 2021 18:22:37 +0000
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-:68a9ec9ce51e
+:b9a3aeb162ab
+#!/usr/bin/env python
+from collections import defaultdict
+from collections import OrderedDict
+import copy
+from intervaltree import IntervalTree
+from ragoo_utilities.PAFReader import PAFReader
+from ragoo_utilities.SeqReader import SeqReader
+from ragoo_utilities.ReadCoverage import ReadCoverage
+from ragoo_utilities.ContigAlignment import ContigAlignment
+from ragoo_utilities.ContigAlignment import UniqueContigAlignment
+from ragoo_utilities.ContigAlignment import LongestContigAlignment
+from ragoo_utilities.GFFReader import GFFReader
+from ragoo_utilities.utilities import run, log, reverse_complement, read_contigs, read_gz_contigs
+from ragoo_utilities.break_chimera import get_ref_parts, cluster_contig_alns, avoid_gff_intervals, update_gff, break_contig, get_intra_contigs
+def update_misasm_features(features, breaks, contig, ctg_len):
+# Get ctg len from ReadCoverage object
+break_list = [0] + sorted(breaks) + [ctg_len]
+borders = []
+for i in range(len(break_list) - 1):
+borders.append((break_list[i], break_list[i+1]))
+# Pop the features to be updated
+contig_feats = features.pop(contig)
+# Initialize lists for new broken contig headers
+for i in range(len(borders)):
+features[contig + '_misasm_break:' + str(borders[i][0]) + '-' + str(borders[i][1])] = []
+t = IntervalTree()
+for i in borders:
+t[i[0]:i[1]] = i
+for i in contig_feats:
+query = t[i.start]
+assert len(query) == 1
+break_start = list(query)[0].begin
+break_end = list(query)[0].end
+query_border = (break_start, break_end)
+break_number = borders.index(query_border)
+i.seqname = contig + '_misasm_break:' + str(borders[break_number][0]) + '-' + str(borders[break_number][1])
+i.start = i.start - break_start
+i.end = i.end - break_start
+features[
+contig + '_misasm_break:' + str(borders[break_number][0]) + '-' + str(borders[break_number][1])].append(i)
+return features
+def remove_gff_breaks(gff_ins, breaks):
+"""
+Given a list of candidate breakpoints proposed by misassembly correction, remove any such break points that
+fall within the interval of a gff feature. This should be called once per contig.
+:param gff_ins: List of GFFLines
+:param breaks: candidate break points
+:return:
+"""
+# Make an interval tree from the intervals of the gff lines
+t = IntervalTree()
+for line in gff_ins:
+# If the interval is one bp long, skip
+if line.start == line.end:
+continue
+t[line.start:line.end] = (line.start, line.end)
+return [i for i in breaks if not t[i]]
+def write_misasm_broken_ctgs(contigs_file, breaks, out_prefix, in_gff=None, in_gff_name=None):
+current_path = os.getcwd()
+os.chdir('ctg_alignments')
+if in_gff and in_gff_name:
+with open(in_gff_name, 'w') as f:
+for i in in_gff.keys():
+for j in in_gff[i]:
+f.write(str(j) + '\n')
+x = SeqReader("../../" + contigs_file)
+f = open(out_prefix + ".misasm.break.fa", 'w')
+for header, seq in x.parse_fasta():
+header = header[1:]
+if header not in breaks:
+f.write(">" + header + "\n")
+f.write(seq + "\n")
+else:
+# Break the contig
+ctg_len = len(seq)
+break_list = [0] + sorted(breaks[header]) + [ctg_len]
+for i in range(len(break_list) - 1):
+f.write(">" + header + "_misasm_break:" + str(break_list[i]) + "-" + str(break_list[i+1]) + "\n")
+f.write(seq[break_list[i]:break_list[i+1]] + "\n")
+os.chdir(current_path)
+def align_misasm_broken(out_prefix):
+current_path = os.getcwd()
+os.chdir('ctg_alignments')
+ctgs_file = out_prefix + ".misasm.break.fa"
+cmd = '{} -k19 -w19 -t{} ../../{}  {} ' \
+'> contigs_brk_against_ref.paf 2> contigs_brk_against_ref.paf.log'.format(minimap_path, t, reference_file,
+ctgs_file)
+if not os.path.isfile('contigs_brk_against_ref.paf'):
+run(cmd)
+os.chdir(current_path)
+def write_contig_clusters(unique_dict, thresh, skip_list):
+# Get a list of all chromosomes
+all_chroms = set([unique_dict[i].ref_chrom for i in unique_dict.keys()])
+current_path = os.getcwd()
+output_path = current_path + '/groupings'
+if not os.path.exists(output_path):
+os.makedirs(output_path)
+os.chdir('groupings')
+for i in all_chroms:
+open(i + '_contigs.txt', 'w').close()
+for i in unique_dict.keys():
+this_chr = unique_dict[i].ref_chrom
+this_confidence = unique_dict[i].confidence
+if this_confidence > thresh:
+if not i in skip_list:
+file_name = str(this_chr) + '_contigs.txt'
+with open(file_name, 'a') as f:
+f.write(i + '\t' + str(this_confidence) + '\n')
+os.chdir(current_path)
+def clean_alignments(in_alns, l=10000, in_exclude_file='', uniq_anchor_filter=False, merge=False):
+# Exclude alignments to undesired reference headers and filter alignment lengths.
+exclude_list = []
+if in_exclude_file:
+with open('../' + in_exclude_file) as f:
+for line in f:
+exclude_list.append(line.rstrip().replace('>', '').split()[0])
+empty_headers = []
+for header in in_alns.keys():
+in_alns[header].exclude_ref_chroms(exclude_list)
+in_alns[header].filter_lengths(l)
+if uniq_anchor_filter:
+in_alns[header].unique_anchor_filter()
+if merge:
+in_alns[header].merge_alns()
+# Check if our filtering has removed all alignments for a contig
+if len(in_alns[header].ref_headers) == 0:
+empty_headers.append(header)
+for header in empty_headers:
+in_alns.pop(header)
+return in_alns
+def read_paf_alignments(in_paf):
+# Read in PAF alignments
+# Initialize a dictionary where key is contig header, and value is ContigAlignment.
+alns = dict()
+x = PAFReader(in_paf)
+for paf_line in x.parse_paf():
+if paf_line.contig in alns:
+alns[paf_line.contig].add_alignment(paf_line)
+else:
+alns[paf_line.contig] = ContigAlignment(paf_line.contig)
+alns[paf_line.contig].add_alignment(paf_line)
+return alns
+def get_contigs_from_groupings(in_file):
+contigs = []
+with open(in_file) as f:
+for line in f:
+contigs.append(line.split('\t')[0])
+return contigs
+def get_location_confidence(in_ctg_alns):
+# Use interval tree to get all alignments with the reference span
+# Go through each of them and if any start is less than the min_pos or any end is greater than
+# the max_pos, change the borders to those values. Then use the algorithm that Mike gave me.
+min_pos = min(in_ctg_alns.ref_starts)
+max_pos = max(in_ctg_alns.ref_ends)
+t = IntervalTree()
+# Put the reference start and end position for every alignment into the tree
+for i in range(len(in_ctg_alns.ref_headers)):
+t[in_ctg_alns.ref_starts[i]:in_ctg_alns.ref_ends[i]] = (in_ctg_alns.ref_starts[i], in_ctg_alns.ref_ends[i])
+overlaps = t[min_pos:max_pos]
+if not overlaps:
+return 0
+# If any intervals fall beyond the boundaries, replace the start/end with the boundary it exceeds
+ovlp_list = [i.data for i in overlaps]
+bounded_list = []
+for i in ovlp_list:
+if i[0] < min_pos:
+i[0] = min_pos
+if i[1] > max_pos:
+i[1] = max_pos
+bounded_list.append(i)
+# Now can just calculate the total range covered by the intervals
+ovlp_range = 0
+sorted_intervals = sorted(bounded_list, key=lambda tup: tup[0])
+max_end = -1
+for j in sorted_intervals:
+start_new_terr = max(j[0], max_end)
+ovlp_range += max(0, j[1] - start_new_terr)
+max_end = max(max_end, j[1])
+return ovlp_range / (max_pos - min_pos)
+def order_orient_contigs(in_unique_contigs, in_alns):
+current_path = os.getcwd()
+output_path = current_path + '/orderings'
+if not os.path.exists(output_path):
+os.makedirs(output_path)
+# Get longest alignments
+longest_contigs = dict()
+for i in in_alns.keys():
+# Only consider alignments to the assigned chromosome
+uniq_aln = UniqueContigAlignment(in_alns[i])
+best_header = uniq_aln.ref_chrom
+ctg_alns = copy.deepcopy(in_alns[i])
+ctg_alns.filter_ref_chroms([best_header])
+longest_contigs[i] = LongestContigAlignment(ctg_alns)
+# Save the orientations
+final_orientations = dict()
+for i in longest_contigs.keys():
+final_orientations[i] = longest_contigs[i].strand
+# Get the location and orientation confidence scores
+orientation_confidence = dict()
+location_confidence = dict()
+forward_bp = 0
+reverse_bp = 0
+for i in in_alns.keys():
+uniq_aln = UniqueContigAlignment(in_alns[i])
+best_header = uniq_aln.ref_chrom
+ctg_alns = copy.deepcopy(in_alns[i])
+ctg_alns.filter_ref_chroms([best_header])
+# Orientation confidence scores
+# Every base pair votes for the orientation of the alignment in which it belongs
+# Score is # votes for the assigned orientation over all votes
+for j in range(len(ctg_alns.ref_headers)):
+if ctg_alns.strands[j] == '+':
+forward_bp += ctg_alns.aln_lens[j]
+else:
+reverse_bp += ctg_alns.aln_lens[j]
+if final_orientations[i] == '+':
+orientation_confidence[i] = forward_bp / (forward_bp + reverse_bp)
+else:
+orientation_confidence[i] = reverse_bp / (forward_bp + reverse_bp)
+forward_bp = 0
+reverse_bp = 0
+# Location confidence
+location_confidence[i] = get_location_confidence(ctg_alns)
+all_chroms = set([in_unique_contigs[i].ref_chrom for i in in_unique_contigs.keys()])
+for this_chrom in all_chroms:
+# Intialize the list of start and end positions w.r.t the query
+ref_pos = []
+groupings_file = 'groupings/' + this_chrom + '_contigs.txt'
+contigs_list = get_contigs_from_groupings(groupings_file)
+for i in range(len(contigs_list)):
+# There is a scope issue here. Pass this (longest_contigs) to the method explicitly.
+ref_pos.append((longest_contigs[contigs_list[i]].ref_start, longest_contigs[contigs_list[i]].ref_end, i))
+final_order = [contigs_list[i[2]] for i in sorted(ref_pos)]
+# Get ordering confidence
+# To do this, get the max and min alignments to this reference chromosome
+# Then within that region, what percent of bp are covered
+with open('orderings/' + this_chrom + '_orderings.txt', 'w') as out_file:
+for i in final_order:
+# Also have a scope issue here.
+out_file.write(i + '\t' + final_orientations[i] + '\t' + str(location_confidence[i]) + '\t' + str(orientation_confidence[i]) + '\n')
+def get_orderings(in_orderings_file):
+all_orderings = []
+with open(in_orderings_file) as f:
+for line in f:
+L1 = line.split('\t')
+all_orderings.append((L1[0], L1[1].rstrip()))
+return all_orderings
+def create_pseudomolecules(in_contigs_file, in_unique_contigs, gap_size, chr0=True):
+"""
+Need to make a translation table for easy lift-over.
+:param in_contigs_file:
+:param in_unique_contigs:
+:param gap_size:
+:return:
+"""
+# First, read all of the contigs into memory
+remaining_contig_headers = []
+all_seqs = OrderedDict()
+x = SeqReader('../' + in_contigs_file)
+if in_contigs_file.endswith(".gz"):
+for header, seq in x.parse_gzip_fasta():
+remaining_contig_headers.append(header.split(' ')[0])
+all_seqs[header.split(' ')[0]] = seq
+else:
+for header, seq in x.parse_fasta():
+remaining_contig_headers.append(header.split(' ')[0])
+all_seqs[header.split(' ')[0]] = seq
+# Get all reference chromosomes
+all_chroms = sorted(list(set([in_unique_contigs[i].ref_chrom for i in in_unique_contigs.keys()])))
+# Iterate through each orderings file and store sequence in a dictionary
+all_pms = dict()
+pad = ''.join('N' for i in range(gap_size))
+for this_chrom in all_chroms:
+orderings_file = 'orderings/' + this_chrom + '_orderings.txt'
+orderings = get_orderings(orderings_file)
+if orderings:
+seq_list = []
+for line in orderings:
+# Mark that we have seen this contig
+remaining_contig_headers.pop(remaining_contig_headers.index('>' + line[0]))
+if line[1] == '+':
+seq_list.append(all_seqs['>' + line[0]])
+else:
+assert line[1] == '-'
+seq_list.append(reverse_complement(all_seqs['>' + line[0]]))
+all_pms[this_chrom] = pad.join(seq_list)
+all_pms[this_chrom] += '\n'
+# Get unincorporated sequences and place them in Chr0
+if remaining_contig_headers:
+if chr0:
+chr0_headers = []
+chr0_seq_list = []
+for header in remaining_contig_headers:
+chr0_headers.append(header)
+chr0_seq_list.append(all_seqs[header])
+all_pms['Chr0'] = pad.join(chr0_seq_list)
+all_pms['Chr0'] += '\n'
+# Write out the list of chr0 headers
+f_chr0_g = open('groupings/Chr0_contigs.txt', 'w')
+f_chr0_o = open('orderings/Chr0_orderings.txt', 'w')
+for i in chr0_headers:
+f_chr0_g.write(i[1:] + "\t" + "0" + '\n')
+f_chr0_o.write(i[1:] + '\t' + "+" + '\t' + "0" + '\t' + "0" + '\n')
+f_chr0_g.close()
+f_chr0_o.close()
+else:
+# Instead of making a chromosome 0, add the unplaced sequences as is.
+for header in remaining_contig_headers:
+all_pms[header[1:]] = all_seqs[header] + "\n"
+f_chr0_g = open('groupings/' + header[1:] + '_contigs.txt', 'w')
+f_chr0_o = open('orderings/' + header[1:] + '_orderings.txt', 'w')
+f_chr0_g.write(header[1:] + "\t" + "0" + '\n')
+f_chr0_o.write(header[1:] + '\t' + "+" + '\t' + "0" + '\t' + "0" + '\n')
+f_chr0_g.close()
+f_chr0_o.close()
+# Write the final sequences out to a file
+with open('ragoo.fasta', 'w') as f:
+for out_header in all_pms:
+f.write(">" + out_header + "_RaGOO\n")
+f.write(all_pms[out_header])
+def write_broken_files(in_contigs, in_contigs_name, in_gff=None, in_gff_name=None):
+current_path = os.getcwd()
+output_path = current_path + '/chimera_break'
+if not os.path.exists(output_path):
+os.makedirs(output_path)
+os.chdir('chimera_break')
+if in_gff and in_gff_name:
+with open(in_gff_name, 'w') as f:
+for i in in_gff.keys():
+for j in in_gff[i]:
+f.write(str(j) + '\n')
+with open(in_contigs_name, 'w') as f:
+for i in in_contigs.keys():
+f.write('>' + i + '\n')
+f.write(in_contigs[i] + '\n')
+os.chdir(current_path)
+def align_breaks(break_type, m_path, in_reference_file, in_contigs_file, in_num_threads):
+current_path = os.getcwd()
+os.chdir('chimera_break')
+if break_type == 'inter':
+cmd = '{} -k19 -w19 -t{} ../../{} {} ' \
+'> inter_contigs_against_ref.paf 2> inter_contigs_against_ref.paf.log'.format(m_path, in_num_threads, in_reference_file, in_contigs_file)
+if not os.path.isfile('inter_contigs_against_ref.paf'):
+run(cmd)
+else:
+cmd = '{} -k19 -w19 -t{} ../../{} {} ' \
+'> intra_contigs_against_ref.paf 2> intra_contigs_against_ref.paf.log'.format(m_path, in_num_threads, in_reference_file, in_contigs_file)
+if not os.path.isfile('intra_contigs_against_ref.paf'):
+run(cmd)
+os.chdir(current_path)
+def align_pms(m_path, num_threads, in_reference_file):
+current_path = os.getcwd()
+output_path = current_path + '/pm_alignments'
+if not os.path.exists(output_path):
+os.makedirs(output_path)
+os.chdir('pm_alignments')
+cmd = '{} -ax asm5 --cs -t{} ../../{} {} ' \
+'> pm_against_ref.sam 2> pm_contigs_against_ref.sam.log'.format(m_path, num_threads,
+in_reference_file, '../ragoo.fasta')
+if not os.path.isfile('pm_against_ref.sam'):
+run(cmd)
+os.chdir(current_path)
+def get_SVs(sv_min, sv_max, in_ref_file):
+current_path = os.getcwd()
+os.chdir('pm_alignments')
+# Change this when setup.py is ready. Just call script directly
+cmd = 'sam2delta.py pm_against_ref.sam'
+if not os.path.isfile('pm_against_ref.sam.delta'):
+run(cmd)
+cmd_2 = 'Assemblytics_uniq_anchor.py --delta pm_against_ref.sam.delta --unique-length 10000 --out assemblytics_out --keep-small-uniques'
+if not os.path.isfile('assemblytics_out.Assemblytics.unique_length_filtered_l10000.delta'):
+run(cmd_2)
+cmd_3 = 'Assemblytics_between_alignments.pl assemblytics_out.coords.tab %r %r all-chromosomes exclude-longrange bed > assemblytics_out.variants_between_alignments.bed' %(sv_min, sv_max)
+if not os.path.isfile('assemblytics_out.variants_between_alignments.bed'):
+run(cmd_3)
+cmd_4 = 'Assemblytics_within_alignment.py --delta assemblytics_out.Assemblytics.unique_length_filtered_l10000.delta --min %r > assemblytics_out.variants_within_alignments.bed' %(sv_min)
+if not os.path.isfile('assemblytics_out.variants_within_alignments.bed'):
+run(cmd_4)
+header = "reference\tref_start\tref_stop\tID\tsize\tstrand\ttype\tref_gap_size\tquery_gap_size\tquery_coordinates\tmethod\n"
+with open('assemblytics_out.variants_between_alignments.bed', 'r')as f1:
+b1 = f1.read()
+with open('assemblytics_out.variants_within_alignments.bed', 'r') as f2:
+b2 = f2.read()
+with open('assemblytics_out.Assemblytics_structural_variants.bed', 'w') as f:
+f.write(header)
+# Might need to add newlines here
+f.write(b1)
+f.write(b2)
+# Filter out SVs caused by gaps
+cmd_5 = 'filter_gap_SVs.py ../../%s' %(in_ref_file)
+run(cmd_5)
+os.chdir(current_path)
+def align_reads(m_path, num_threads, in_ctg_file, reads, tech='ont'):
+current_path = os.getcwd()
+output_path = current_path + '/ctg_alignments'
+if not os.path.exists(output_path):
+os.makedirs(output_path)
+os.chdir('ctg_alignments')
+if tech == 'sr':
+cmd = '{} -x sr -t{} ../../{} ../../{} ' \
+'> reads_against_ctg.paf 2> reads_against_ctg.paf.log'.format(m_path, num_threads, in_ctg_file, reads)
+elif tech == 'corr':
+cmd = '{} -x asm10 -t{} ../../{} ../../{} ' \
+'> reads_against_ctg.paf 2> reads_against_ctg.paf.log'.format(m_path, num_threads, in_ctg_file, reads)
+else:
+raise ValueError("Only 'sr' or 'corr' are accepted for read type.")
+if not os.path.isfile('reads_against_ctg.paf'):
+run(cmd)
+os.chdir(current_path)
+if __name__ == "__main__":
+import os
+import argparse
+parser = argparse.ArgumentParser(description='order and orient contigs according to minimap2 alignments to a reference (v1.1)')
+parser.add_argument("contigs", metavar="<contigs.fasta>", type=str, help="fasta file with contigs to be ordered and oriented (gzipped allowed)")
+parser.add_argument("reference", metavar="<reference.fasta>", type=str, help="reference fasta file (gzipped allowed)")
+#parser.add_argument("-o", metavar="PATH", type=str, default="ragoo_output", help="output directory name")
+parser.add_argument("-e", metavar="<exclude.txt>", type=str, default="", help="single column text file of reference headers to ignore")
+parser.add_argument("-gff", metavar="<annotations.gff>", type=str, default='', help="lift-over gff features to chimera-broken contigs")
+parser.add_argument("-m", metavar="PATH", type=str, default="minimap2", help='path to minimap2 executable')
+parser.add_argument("-b", action='store_true', default=False, help="Break chimeric contigs")
+parser.add_argument("-R", metavar="<reads.fasta>", type=str, default="", help="Turns on misassembly correction. Align provided reads to the contigs to aid misassembly correction. fastq or fasta allowed. Gzipped files allowed. Turns off '-b'.")
+parser.add_argument("-T", metavar="sr", type=str, default="", help="Type of reads provided by '-R'. 'sr' and 'corr' accepted for short reads and error corrected long reads respectively.")
+parser.add_argument("-p", metavar="5", type=int, default=5, help=argparse.SUPPRESS)
+parser.add_argument("-l", metavar="10000", type=int, default=10000, help=argparse.SUPPRESS)
+parser.add_argument("-r", metavar="100000", type=int, default=100000, help="(with -b) this many bp of >1 reference sequence must be covered for a contig to be considered an interchromosomal chimera.")
+parser.add_argument("-c", metavar="1000000", type=int, default=1000000, help="(with -b) distance threshold between consecutive alignments with respect to the contig.")
+parser.add_argument("-d", metavar="2000000", type=int, default=2000000, help="(with -b) distance threshold between consecutive alignments with respect to the reference.")
+parser.add_argument("-t", metavar="3", type=int, default=3, help="Number of threads when running minimap.")
+parser.add_argument("-g", metavar="100", type=int, default=100, help="Gap size for padding in pseudomolecules.")
+parser.add_argument("-s", action='store_true', default=False, help="Call structural variants")
+parser.add_argument("-a", metavar="50", type=int, default=50, help=argparse.SUPPRESS)
+parser.add_argument("-f", metavar="10000", type=int, default=10000, help=argparse.SUPPRESS)
+parser.add_argument("-i", metavar="0.2", type=float, default=0.2, help="Minimum grouping confidence score needed to be localized.")
+parser.add_argument("-j", metavar="<skip.txt>", type=str, default="", help="List of contigs to automatically put in chr0.")
+parser.add_argument("-C", action='store_true', default=False, help="Write unplaced contigs individually instead of making a chr0")
+# Get the command line arguments
+args = parser.parse_args()
+contigs_file = args.contigs
+reference_file = args.reference
+#output_path = args.o
+exclude_file = args.e
+minimap_path = args.m
+break_chimeras = args.b
+gff_file = args.gff
+min_break_pct = args.p
+min_len = args.l
+min_range = args.r
+intra_wrt_ref_min = args.d
+intra_wrt_ctg_min = args.c
+t = args.t
+g = args.g
+call_svs = args.s
+min_assemblytics = args.a
+max_assemblytics = args.f
+group_score_thresh = args.i
+skip_file = args.j
+corr_reads = args.R
+corr_reads_tech = args.T
+make_chr0 = not args.C
+if corr_reads:
+log("Misassembly correction has been turned on. This automatically inactivates chimeric contig correction.")
+break_chimeras = False
+# Make sure that if -R, -T has been specified
+if corr_reads and not corr_reads_tech:
+raise ValueError("'-T' must be provided when using -R.")
+skip_ctg = []
+if skip_file:
+with open(skip_file) as f:
+for line in f:
+skip_ctg.append(line.rstrip())
+current_path = os.getcwd()
+output_path = current_path + '/ragoo_output'
+if not os.path.exists(output_path):
+os.makedirs(output_path)
+os.chdir(output_path)
+# Run minimap2
+cmd = '{} -k19 -w19 -t{} ../{} ../{} ' \
+'> contigs_against_ref.paf 2> contigs_against_ref.paf.log'.format(minimap_path, t, reference_file, contigs_file)
+if not os.path.isfile('contigs_against_ref.paf'):
+run(cmd)
+# Read in the minimap2 alignments just generated
+log('Reading alignments')
+alns = read_paf_alignments('contigs_against_ref.paf')
+alns = clean_alignments(alns, l=1000, in_exclude_file=exclude_file)
+# Process the gff file
+if gff_file:
+log('Getting gff features')
+features = defaultdict(list)
+z = GFFReader('../' + gff_file)
+for i in z.parse_gff():
+features[i.seqname].append(i)
+# Break chimeras if desired
+if break_chimeras:
+# Record how many contigs are broken
+total_inter_broken = 0
+total_intra_broken = 0
+alns = clean_alignments(alns, l=10000, in_exclude_file=exclude_file, uniq_anchor_filter=True)
+# Process contigs
+log('Getting contigs')
+if contigs_file.endswith(".gz"):
+contigs_dict = read_gz_contigs('../' + contigs_file)
+else:
+contigs_dict = read_contigs('../' + contigs_file)
+log('Finding interchromosomally chimeric contigs')
+all_chimeras = dict()
+for i in alns.keys():
+ref_parts = get_ref_parts(alns[i], min_len, min_break_pct, min_range)
+if len(ref_parts) > 1:
+all_chimeras[i] = ref_parts
+log('Finding break points and breaking interchromosomally chimeric contigs')
+break_intervals = dict()
+for i in all_chimeras.keys():
+break_intervals[i] = cluster_contig_alns(i, alns, all_chimeras[i], min_len)
+# If its just going to break it into the same thing, skip it.
+if len(break_intervals[i]) <= 1:
+continue
+if gff_file:
+# If desired, ensure that breakpoints don't disrupt any gff intervals
+break_intervals[i] = avoid_gff_intervals(break_intervals[i], features[i])
+features = update_gff(features, break_intervals[i], i)
+# Break contigs according to the final break points
+contigs_dict = break_contig(contigs_dict, i, break_intervals[i])
+total_inter_broken += 1
+# Next, need to re-align before finding intrachromosomal chimeras
+# First, write out the interchromosomal chimera broken fasta
+out_inter_fasta = contigs_file[:contigs_file.rfind('.')] + '.inter.chimera.broken.fa'
+if gff_file:
+out_gff = gff_file[:gff_file.rfind('.')] + '.inter.chimera_broken.gff'
+write_broken_files(contigs_dict, out_inter_fasta, features, out_gff)
+else:
+write_broken_files(contigs_dict, out_inter_fasta)
+# Next, realign the chimera broken contigs
+align_breaks('inter', minimap_path, reference_file, out_inter_fasta, t)
+# Now, use those new alignments for intrachromosomal chimeras
+log('Reading interchromosomal chimera broken alignments')
+inter_alns = read_paf_alignments('chimera_break/inter_contigs_against_ref.paf')
+inter_alns = clean_alignments(inter_alns, l=1000, in_exclude_file=exclude_file)
+log('Finding intrachromosomally chimeric contigs')
+# Find intrachromosomally chimeric contigs
+for i in inter_alns.keys():
+intra = get_intra_contigs(inter_alns[i], 15000, intra_wrt_ref_min, intra_wrt_ctg_min)
+if intra:
+if gff_file:
+intra_break_intervals = avoid_gff_intervals(intra[1], features[intra[0]])
+else:
+intra_break_intervals = intra[1]
+# Check if the avoidance of gff intervals pushed the break point to the end of the contig.
+if intra_break_intervals[-1][0] == intra_break_intervals[-1][1]:
+continue
+# break the contigs and update features if desired
+contigs_dict = break_contig(contigs_dict, intra[0], intra_break_intervals)
+total_intra_broken += 1
+if gff_file:
+features = update_gff(features, intra_break_intervals, intra[0])
+# Write out the intrachromosomal information
+out_intra_fasta = contigs_file[:contigs_file.rfind('.')] + '.intra.chimera.broken.fa'
+if gff_file:
+out_intra_gff = gff_file[:gff_file.rfind('.')] + '.intra.chimera_broken.gff'
+write_broken_files(contigs_dict, out_intra_fasta, features, out_intra_gff)
+else:
+write_broken_files(contigs_dict, out_intra_fasta)
+# Re align the contigs
+# Next, realign the chimera broken contigs
+align_breaks('intra', minimap_path, reference_file, out_intra_fasta, t)
+# Read in alignments of intrachromosomal chimeras and proceed with ordering and orientation
+log('Reading intrachromosomal chimera broken alignments')
+alns = read_paf_alignments('chimera_break/intra_contigs_against_ref.paf')
+alns = clean_alignments(alns, l=1000, in_exclude_file=exclude_file)
+contigs_file = '/ragoo_output/chimera_break/' + out_intra_fasta
+log('The total number of interchromasomally chimeric contigs broken is %r' % total_inter_broken)
+log('The total number of intrachromasomally chimeric contigs broken is %r' % total_intra_broken)
+# Check if misassembly correction is turned on. This is mutually exclusive with chimeric contig correction
+if corr_reads:
+# Align the raw reads to the assembly.
+log('Aligning raw reads to contigs')
+align_reads(minimap_path, t, contigs_file, corr_reads, corr_reads_tech)
+log('Computing contig coverage')
+cov_map = ReadCoverage('ctg_alignments/reads_against_ctg.paf')
+alns = clean_alignments(alns, l=10000, in_exclude_file=exclude_file, uniq_anchor_filter=True, merge=True)
+# Get the initial candidate break points.
+candidate_breaks = dict()
+for i in alns:
+candidates = alns[i].get_break_candidates()
+if candidates:
+candidate_breaks[i] = candidates
+# Validate each breakpoint by checking for excessively high or low coverage
+# Also, if a gff is provided, check to ensure that we don't break within a gff feature interval
+val_candidate_breaks = dict()
+for i in candidate_breaks:
+candidates = cov_map.check_break_cov(i, candidate_breaks[i])
+if gff_file:
+candidates = remove_gff_breaks(features[i], candidates)
+if candidates:
+val_candidate_breaks[i] = list(set(candidates))
+if gff_file:
+features = update_misasm_features(features, val_candidate_breaks[i], i, cov_map.ctg_lens[i])
+# Break the contigs
+if gff_file:
+out_misasm_gff = gff_file[:gff_file.rfind('.')] + '.misasm.broken.gff'
+write_misasm_broken_ctgs(contigs_file, val_candidate_breaks, contigs_file[:contigs_file.rfind('.')], in_gff=features, in_gff_name=out_misasm_gff)
+else:
+write_misasm_broken_ctgs(contigs_file, val_candidate_breaks, contigs_file[:contigs_file.rfind('.')])
+# Align the broken contigs back to the reference
+align_misasm_broken(contigs_file[:contigs_file.rfind('.')])
+alns = read_paf_alignments('ctg_alignments/contigs_brk_against_ref.paf')
+alns = clean_alignments(alns, l=1000, in_exclude_file=exclude_file)
+contigs_file = '/ragoo_output/ctg_alignments/' + contigs_file[:contigs_file.rfind('.')] + ".misasm.break.fa"
+# Assign each contig to a corresponding reference chromosome.
+log('Assigning contigs')
+all_unique_contigs = dict()
+for i in alns.keys():
+all_unique_contigs[i] = UniqueContigAlignment(alns[i])
+# Add to this the list of headers that did not make it
+write_contig_clusters(all_unique_contigs, group_score_thresh, skip_ctg)
+log('Ordering and orienting contigs')
+order_orient_contigs(all_unique_contigs, alns)
+log('Creating pseudomolecules')
+create_pseudomolecules(contigs_file, all_unique_contigs, g, make_chr0)
+if call_svs:
+log('Aligning pseudomolecules to reference')
+align_pms(minimap_path, t, reference_file)
+log('Getting structural variants')
+get_SVs(min_assemblytics, max_assemblytics, reference_file)
+log('goodbye')

Mercurial > repos > dereeper > ragoo

comparison RaGOO/ragoo.py @ 13:b9a3aeb162ab draft default tip