使用Python解决序列重叠问题
tblastn比对出来候选HSP区段,我们需要根据一定的基因长度范围来进行区域延伸去重叠,然后进行下一步操作。对HSP区域的延伸要考虑基因的长度以及目标基因组scafflod or chromosome长度,不是一件容易的事情。
这里采用了dataclass以及改写slots存储数据方式,减少内存占用以及加快读取速度,attrgetter对列表字典结构排序,biopython里的SeqIO.parse感觉挺慢的,不过懒得重写了,用了据说更快的SimpleFastaParser来解析,实际测试下来速度确实更快,主要是用来存储scaffold或chromosome长度,以防延伸超出边界。
去重叠的原理在于先排序,然后判断前一区间的末尾是否小于后一区间开始,若为假则重叠,根据长度/得分来判断删除前一区间还是后一区间。
以下运行得到的结果仍然是blast的tabular格式(之后可以经过一些简单的shell命令处理,可转成bed格式,结合bedtools批量提取序列)。
注:如果你需要去重的格式不为blast tabular,简单的利用一些工具如awk/sed/perl/python/shell各种改变格式就好,只需要第二列的id,第九列的序列起始,第十列的序列结束,第十二列的得分有意义,作为排序用到的字段,其余字段都可缺省
from dataclasses import dataclass, replace from operator import attrgetter from Bio.SeqIO.FastaIO import SimpleFastaParser import getopt import sys """ 用法: #根据基因组文件,延伸上下游区域 example 1. region_tools.py -u <int> -d <int> -i <blast_tabular> -o extend.txt [-g <genome_file>] #去除重叠区域,保留最长,并用-t指定筛去小于某长度的结果 example 2. region_tools.py -f -i extend.txt -t <region_length> -o filter.txt #延伸+去重+根据得分保留 example 3. region_tools.py -u <int> -d <int> -f -s -i <blast_tabular> [-g <genome_file>] -o output.txt """ @dataclass class Rec: __slots__ = ("q_id", "s_id", "identity", "alignment_length", "mismatches", "gap_openings", "q_start", "q_end", "s_start", "s_end", "e_value", "bit_score") q_id: str s_id: str identity: str alignment_length: str mismatches: str gap_openings: str q_start: str q_end: str s_start: int s_end: int e_value: str bit_score: float def filter_overlap(sort_data, score=False): i = 0 if sort_data: if sort_data[0].s_start <= sort_data[0].s_end: start = "s_start" end = "s_end" else: start = "s_end" end = "s_start" while i <= len(sort_data) - 2: if getattr(sort_data[i+1], start) < getattr(sort_data[i], end) and \ sort_data[i+1].s_id == sort_data[i].s_id: if not score: if abs(sort_data[i+1].s_start - sort_data[i+1].s_end) > \ abs(sort_data[i].s_start - sort_data[i].s_end): del sort_data[i] else: del sort_data[i+1] else: if sort_data[i+1].bit_score > sort_data[i].bit_score: del sort_data[i] else: del sort_data[i+1] else: i += 1 class RegionIO: def __init__(self, file_path): self.file_path = file_path self.sort_rf = [] self.sort_rv = [] self.recs_forward = [] self.recs_reverse = [] with open(self.file_path, "r") as f: for rec in f: rec = rec.strip().split("\t") bit_score = float(rec[11]) rec_dict = Rec( *rec[0:8], int(rec[8]), int(rec[9]), rec[10], int(bit_score) if bit_score == int(bit_score) else bit_score) if rec_dict.s_start <= rec_dict.s_end: self.recs_forward.append(rec_dict) else: self.recs_reverse.append(rec_dict) def extend_region(self, up=0, down=0, genome_path=""): if genome_path == "": for n in range(len(self.recs_forward)): start = self.recs_forward[n].s_start - up end = self.recs_forward[n].s_end + down self.recs_forward[n] = \ replace(self.recs_forward[n], s_start=start) \ if start >= 1 \ else replace(self.recs_forward[n], s_start=1) self.recs_forward[n] = \ replace(self.recs_forward[n], s_end=end) \ if start >= 1 \ else replace(self.recs_forward[n], s_end=abs(start)+end+1) for n in range(len(self.recs_reverse)): start = self.recs_reverse[n].s_end - up end = self.recs_reverse[n].s_start + down self.recs_reverse[n] = \ replace(self.recs_reverse[n], s_end=start) \ if start >= 1 \ else replace(self.recs_reverse[n], s_end=1) self.recs_reverse[n] = \ replace(self.recs_reverse[n], s_start=end) \ if start >= 1 \ else replace(self.recs_reverse[n], s_start=abs(start)+end+1) else: id_len = {} with open(genome_path,"r") as in_handle: for title, seq in SimpleFastaParser(in_handle): id_len[title.split(" ")[0]] = len(seq) for n in range(len(self.recs_forward)): start = self.recs_forward[n].s_start - up end = self.recs_forward[n].s_end + down self.recs_forward[n] = \ replace(self.recs_forward[n], s_start=start) \ if start >= 1 \ else replace(self.recs_forward[n], s_start=1) if end <= id_len[self.recs_forward[n].s_id]: self.recs_forward[n] = \ replace(self.recs_forward[n], s_end=end) \ if start >= 1 \ else replace(self.recs_forward[n], s_end=abs(start) + end + 1 if abs(start) + end + 1 <= id_len[self.recs_forward[n].s_id] else id_len[self.recs_forward[n].s_id]) else: self.recs_forward[n] = \ replace(self.recs_forward[n], s_end=id_len[self.recs_forward[n].s_id]) self.recs_forward[n] = \ replace(self.recs_forward[n], s_start=self.recs_forward[n].s_start -(end-id_len[self.recs_forward[n].s_id]) if self.recs_forward[n].s_start -(end-id_len[self.recs_forward[n].s_id]) >= 1 else 1) for n in range(len(self.recs_reverse)): start = self.recs_reverse[n].s_end - up end = self.recs_reverse[n].s_start + down self.recs_reverse[n] = \ replace(self.recs_reverse[n], s_end=start) \ if start >= 1 \ else replace(self.recs_reverse[n], s_end=1) if end <= id_len[self.recs_reverse[n].s_id]: self.recs_reverse[n] = \ replace(self.recs_reverse[n], s_start=end) \ if start >= 1 \ else replace(self.recs_reverse[n], s_start=abs(start) + end + 1 if abs(start) + end + 1 <= id_len[self.recs_forward[n].s_id] else id_len[self.recs_forward[n].s_id]) else: self.recs_reverse[n] = \ replace(self.recs_reverse[n], s_start=id_len[self.recs_reverse[n].s_id]) self.recs_reverse[n] = \ replace(self.recs_reverse[n], s_end=self.recs_reverse[n].s_end -(end - id_len[self.recs_reverse[n].s_id]) if (self.recs_reverse[n].s_end -(end - id_len[self.recs_reverse[n].s_id])) >= 1 else 1) def region_sort(self): self.sort_rf = sorted(self.recs_forward, key=attrgetter("s_id", "s_start", "s_end")) self.sort_rv = sorted(self.recs_reverse, key=attrgetter("s_id", "s_end", "s_start")) def filter_threshold(self, threshold): if int(threshold) > 0: self.sort_rf = [record for record in self.sort_rf if abs(record.s_start-record.s_end)+1 >= threshold] self.sort_rv = [record for record in self.sort_rv if abs(record.s_start-record.s_end)+1 >= threshold] def write(self, output_path): with open(output_path, "w") as o: for rec in self.sort_rf+self.sort_rv: o.write(f"{rec.q_id}\t{rec.s_id}" f"\t{rec.identity}\t{rec.alignment_length}" f"\t{rec.mismatches}\t{rec.gap_openings}" f"\t{rec.q_start}\t{rec.q_end}" f"\t{rec.s_start}\t{rec.s_end}" f"\t{rec.e_value}\t{rec.bit_score}\n") class StepError(Exception): def __init__(self, error): self.error = error if __name__ == "__main__": path, up, down, filt, genome, output, threshold, score = "", 0, 0, False, "", "", 0, False try: opts, args = getopt.getopt(sys.argv[1:], "-i:-g:-o:-u:-d:-f-t:-s") for opt_name, opt_value in opts: if opt_name == "-i": path = opt_value if opt_name == "-u": up = int(opt_value) if opt_name == "-d": down = int(opt_value) if opt_name == "-f": filt = True if opt_name == "-t": threshold = int(opt_value) if opt_name == "-g": genome = opt_value if opt_name == "-o": output = opt_value if opt_name == "-s": score = True except getopt.GetoptError as e: for error in e.args: print("".join(error)) results = RegionIO(path) if up or down: if genome: results.extend_region(up=up, down=down, genome_path=genome) else: results.extend_region(up=up, down=down) results.region_sort() if filt: filter_overlap(results.sort_rf, score) filter_overlap(results.sort_rv, score) if threshold > 0: results.filter_threshold(threshold) if output: results.write(output) else: results.write(path+"_region_tools")
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