EN与Biopython的Turtles Are Cute类似，但使用Bio.SeqIO.to_dict()，并按序列长度对fasta进行排序：...
from Bio import Entrez, SeqIO, SeqRecord Entrez.email = "your@email.here" hdl = Entrez.efetch(db='nucleotide', id=['NM_002299'], rettype='gb') # Lactase gene gb_rec = SeqIO.read(hdl, 'gb') 现在我们有了 GenBank 记录,让我们提取基因序列。记录还不止这些,但让我们先找到基因的精确...
1. 引入第三方库 from Bio import SeqIO import matplotlib.pyplot as plt 2. 写函数 def sequence(file_name): info_dict = {} # 绘图数据 # 检查后缀 raw = open(file_name, err
from Bio import SeqIO import argparse records_new = SeqIO.parse(args.in_raw, "fasta") Pretreated_fa = SeqIO.to_dict(SeqIO.parse(args.input, "fasta"& fastq fasta uniq 去重复 原创2016-11-04 14:55:003353阅读 python中 for ... else ... 的用法 ...
records = SeqIO.parse("My_fasta_file.aa", 'fasta') for record in records: subtab=tab[tab['query']==record.id] subtab=subtab.drop_duplicates(subset ="New_query",keep = "first") if subtab.empty == True: #it means that the seq was not in the tab, so I do not rename the ...
//pypi.org/project/pip...3.2 直接用安装包安装二、Biopython 基础用法 1 读取常见的序列文件格式(fasta,gb) from Bio import SeqIO # 读取包含单个序列 Fasta 格式文件 fa_seq...seqs = [fa.seq for fa in SeqIO.parse("res/multi.fasta", "fasta")] print (seqs) # 如果不想要seq对象中的字母表...
fromBioimportSeqIOclassDataParser:defparse_data(self,data:str)->list:return[recordforrecordinSeqIO.parse(data,"fasta")] 1. 2. 3. 4. 5. 3. 数据存储模块 将解析后的数据存储到本地JSON文件。 importjsonclassDataStorage:defstore_data(self,data:list,filename:str)->None:withopen(filename,'w'...
import pandas as pd import numpy as np from Bio import SeqIO from Bio.SeqUtils.ProtParam import ProteinAnalysis # read fasta re = {} with open ('***.fasta') as f: for line in f: seq = [] if line.startswith('>'): id = line.split(' ')[0].split('_') #切片分割序列名称 id...
分享回复赞 biopython吧 色彩档案 比较Bio.SeqIO.to_dict(),.index(),.index_db()可以使用不可变的Python对象作为字典键而不仅仅是字符串(e.g. 如字符串元组、不可变容器(frozen set))如果被建立索引的序列文件改变,不需要担心索引数据库过期。选择Bio.SeqIO.index_db() 而不选择 Bio.SeqIO.index() 的原...
MG1655_GENBANK=os.path.join(GENOMES_DIR,'mg1655','mg1655.genbank')GENE_DICT={'prfA':{'types':('CDS','gene')}}withopen(MG1655_GENBANK)asfh:genome_record=SeqIO.read(fh,'genbank')remove_gene_features(genome_record,GENE_DICT)forfeatureingenome_record.features:if('gene'infeature.qualifi...