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evaluate.py
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import re
import os
import pickle
import subprocess
import torch
import dgl
from Bio import SeqIO
from Bio import Seq
chr_lens = {
'chr1' : 248387328,
'chr2' : 242696752,
'chr3' : 201105948,
'chr4' : 193574945,
'chr5' : 182045439,
'chr6' : 172126628,
'chr7' : 160567428,
'chr8' : 146259331,
'chr9' : 150617247,
'chr10': 134758134,
'chr11': 135127769,
'chr12': 133324548,
'chr13': 113566686,
'chr14': 101161492,
'chr15': 99753195,
'chr16': 96330374,
'chr17': 84276897,
'chr18': 80542538,
'chr19': 61707364,
'chr20': 66210255,
'chr21': 45090682,
'chr22': 51324926,
'chrX' : 154259566,
}
def walk_to_sequence(walks, graph, reads, edges):
contigs = []
for i, walk in enumerate(walks):
prefixes = [(src, graph.edata['prefix_length'][edges[src,dst]]) for src, dst in zip(walk[:-1], walk[1:])]
sequences = [reads[src][:prefix] for (src, prefix) in prefixes]
contig = Seq.Seq(''.join(sequences) + reads[walk[-1]]) # TODO: why is this map here? Maybe I can remove it if I work with strings
contig = SeqIO.SeqRecord(contig)
contig.id = f'contig_{i+1}'
contig.description = f'length={len(contig)}'
contigs.append(contig)
return contigs
def save_assembly(contigs, save_dir, idx, suffix=''):
assembly_path = os.path.join(save_dir, f'{idx}_assembly{suffix}.fasta')
SeqIO.write(contigs, assembly_path, 'fasta')
def calculate_N50(contigs):
"""Calculate N50 for contigs.
Args:
list_of_lengths (list): List of SeqRecord objects.
Returns:
float: N50 value.
"""
lengths_list = [len(c.seq) for c in contigs]
lengths_list.sort(reverse=True)
total_length = sum(lengths_list)
total_bps = 0
for length in lengths_list:
total_bps += length
if total_bps >= total_length / 2:
return length
return -1
def calculate_NG50(contigs, ref_length):
"""Calculate NG50 for contigs.
Args:
list_of_lengths (list): List of SeqRecord objects.
Returns:
int: NG50 value.
"""
if ref_length <= 0:
return -1
lengths_list = [len(c.seq) for c in contigs]
lengths_list.sort(reverse=True)
total_bps = 0
for length in lengths_list:
total_bps += length
if total_bps >= ref_length / 2:
return length
return -1
def quick_evaluation(contigs, chrN):
# contigs = walk_to_sequence(walks, graph, reads, edges)
lengths_list = [len(c.seq) for c in contigs]
num_contigs = len(contigs)
longest_contig = max(lengths_list)
n50 = calculate_N50(contigs)
if chrN:
chr_len = chr_lens[chrN]
reconstructed = sum(lengths_list) / chr_len
ng50 = calculate_NG50(contigs, chr_len)
else:
reconstructed = ng50 = -1
return num_contigs, longest_contig, reconstructed, n50, ng50
def txt_output(f, txt):
print(f'{txt}')
f.write(f'{txt}\n')
def print_summary_old(data_path, idx, chrN, num_contigs, longest_contig, reconstructed, n50, ng50):
reports_dir = os.path.join(data_path, 'reports')
if not os.path.isdir(reports_dir ):
os.mkdir(reports_dir)
with open(f'{reports_dir}/{idx}_report.txt', 'w') as f:
txt_output(f, f'-'*80)
txt_output(f, f'Report for graph {idx} in {data_path}')
txt_output(f, f'Graph created from {chrN}')
txt_output(f, f'Num contigs:\t{num_contigs}')
txt_output(f, f'Longest contig:\t{longest_contig}')
txt_output(f, f'Reconstructed:\t{reconstructed * 100:2f}%')
txt_output(f, f'N50:\t{n50}')
txt_output(f, f'NG50:\t{ng50}')
def print_summary(data_path, idx, chrN, num_contigs, longest_contig, reconstructed, n50, ng50):
print(f'-'*80)
print(f'Report for graph {idx} in {data_path}')
# print(f'Graph created from {chrN}')
print(f'Num contigs:\t{num_contigs}')
print(f'Longest contig:\t{longest_contig}')
# print(f'Reconstructed:\t{reconstructed * 100:2f}%')
print(f'N50:\t{n50}')
# print(f'NG50:\t{ng50}')
def run_minigraph(ref, asm, paf):
minigraph = f'/home/vrcekl/minigraph/minigraph'
# paftools = f'/home/vrcekl/minimap2-2.24_x64-linux/paftools.js'
# paf = os.path.join(save_path, f'asm.paf')
# cmdaa = f'{minigraph} -xasm -g10k -r10k --show-unmap=yes {ref} {asm} > {paf} && k8 {paftools} asmstat {idx} {paf} > {report}'
cmd = f'{minigraph} -t32 -xasm -g10k -r10k --show-unmap=yes {ref} {asm}'.split(' ')
with open(paf, 'w') as f:
p = subprocess.Popen(cmd, stdout=f)
return p
def parse_pafs(idx, report, paf):
paftools = f'/home/vrcekl/minimap2/paftools.js'
# paf = os.path.join(save_path, f'asm.paf')
cmd = f'k8 {paftools} asmstat {idx} {paf}'.split()
with open(report, 'w') as f:
p = subprocess.Popen(cmd, stdout=f)
return p
def parse_minigraph_for_chrs(save_path):
ng50, nga50 = {}, {}
for i in range(1, 24):
if i == 23:
i = 'X'
stat_path = f'{save_path}/chr{i}/reports/0_minigraph.txt'
try:
with open(stat_path) as f:
for line in f.readlines():
if line.startswith('NG50'):
try:
ng50_l = int(re.findall(r'NG50\s*(\d+)', line)[0])
except IndexError:
ng50_l = 0
ng50[f'chr{i}'] = ng50_l
if line.startswith('NGA50'):
try:
nga50_l = int(re.findall(r'NGA50\s*(\d+)', line)[0])
except IndexError:
nga50_l = 0
nga50[f'chr{i}'] = nga50_l
except FileNotFoundError:
print(f'Report for chr{i} at {stat_path} does not exist!')
print('NG50')
print(*ng50.values(), sep='\n')
print()
print('NGA50')
print(*nga50.values(), sep='\n')
print()
def parse_minigraph_for_full(report, save_path=None, directory=None, filename='0_minigraph.txt'):
# stat_path = f'{save_path}/{directory}/reports/{filename}'
stat_path = report
with open(stat_path) as f:
report = f.read()
print(report)