这条序列来自于NCBI的RefSeq数据库,所有来自于NCBI的序列都有一个gi号,是具有唯一性的数据库流水号,gb|AF349571.1是genebank编号的信息,后面是序列信息的详细描述(Homo sapiens hemoglobin alpha-1 globin chain (HBA1) mRNA, complete cds) RefSeq(reference sequence database) 基因参考序列数据库:是美国国家医学图书...
13 @filedata = get_file_data(); 14 #得到序列 15 $dna = extract_sequence_from_fasta_data(@filedata); 16 17 #六框阅读翻译 18 19 print "\n---Reading Frame 1---\n"; 20 $protein=translate_frame($dna,1); 21 print_sequence($protein,70); 22 23 print "\n---Reading Frame 2---...
Biopython可以直接读取FASTA(.txt或者.fasta),GenBank(.gbk或者.gb),以及其他格式的序列。 from Bio import SeqIO seq_record = SeqIO.read("sequence.fasta", "fasta") print(seq_record.id) print(seq_record.seq) 输出结果: gi|2765658|emb|Z78533.1|CIZ78533 AGTGGCACCGCGGTGATGATTTGGAACTGC ...
("clustalw2", infile="sequences.fasta") clustalw_cline() # 计算F统计量 data = GenePop.read("population.gen") f_stats = data.calculate_f_statistics() print(f_stats) # 突变检测 seq1 = Seq("ACCGT") seq2 = Seq("AACCT") alignments = pairwise2.align.globalxx(seq1, seq2) for ...
SeqIO.write(bseq, bseq_file, "fasta") # build needle commnad if needle_path is None: needle_cmd = NeedleCommandline( asequence=aseq_file, bsequence=bseq_file, gapopen=10, gapextend=0.5, outfile=needle_file) else: assert os.path.isfile(needle_path) needle_cmd = NeedleCommandline(...
open_database(driver='mysql', user='user', passwd='passwd', host='localhost', db='biosql') # 获取Sequence数据库 db = server['sequence_db'] # 保存序列数据到FASTA文件 with open('seq.fasta', 'w') as f: for seq_id in db.keys(): seq_obj = db.lookup(seq_id) f.write('>{}\...
from Bio import SeqIO for record in SeqIO.parse("sequence.fasta", "fasta"): print(record.id, len(record.seq)) 序列比对: Biopython-序列提供了快速而灵活的序列比对工具,可以进行全局或局部比对,计算序列相似性和差异等。 from Bio import Align aligner = Align.PairwiseAligner() alignments = aligner...
from Bio import SeqIO # 导入Biopython库中的SeqIO模块,用于读取和解析序列文件 from Bio.SeqRecord import SeqRecord # 导入SeqRecord类,用于表示序列记录 def extract_CDS(gene_name, gb_path='sequence.gb', extract_type='CDS'): # 读取GenBank文件中的所有记录ID并存储在列表中 ...
from Bio import SeqIO fastas = SeqIO.parse(fasta_file, 'fasta') for fasta in fastas: print fasta.id # 如果序列名有空格,只识别第一个空格前的内容 print fasta.description # 整个序列名 print fasta.seq 生成的序列固定长度 while len(sequence) > 0: ...
from Bio import SeqIO record_iterator = SeqIO.parse("ls_orchid.gbk", "genbank") first_record = record_iterator.next() print first_record 输出结果: ID: Z78533.1 Name: Z78533 Description: C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA. Number of features: 5 /sequence_version=1...