for file in files: file_path2=file_path+ '/' + file with open(file_path2,"r") as f: 1. 2. 3. 4. 5. 假如文件中都是n行5列数据,我们需要对其进行合并: file_path = ("D:/FDTD/t") files= os.listdir(file_path) time = 0 for file in files: file_path2=file_path+ '/' + ...
为了读取 FASTA 文件,我们可以使用 Python 内建的文件处理功能。以下是一个简单的示例,演示了如何打开和读取 FASTA 文件: defread_fasta(file_path):sequences={}withopen(file_path,'r')asfile:sequence_name=Nonesequence_data=[]forlineinfile:line=line.strip()ifline.startswith('>'):ifsequence_nameisnot...
in_file.close() root@PC1:/home/test#cat a.fasta ## 测试fasta文件>gene1 myc AGCTGCCTAAGC GGCATAGCTAATCG>gene2 jun ACCGAATCGGAGCGATG GGCATTAAAGATCTAGCT>gene3 malat1 AGGCTAGCGAG GCGCGAG GATTAGGCG root@PC1:/home/test#python test.py ## 执行程序>gene1 myc GCTTAGGCAGCT CGATTAGCTATGCC...
代码语言:python 代码运行次数:0 复制 importos# 定义要连接的fasta文件列表fasta_files=['file1.fasta','file2.fasta','file3.fasta']# 定义输出文件名output_file='output.fasta'# 打开输出文件withopen(output_file,'w')asoutput:# 遍历fasta文件列表forfasta_fileinfasta_files:# 打开当前fasta文件withopen...
file_list = ["file1.fasta", "file2.fasta", "file3.fasta"] # 替换为实际的文件名列表 for file in file_list: sequences = SeqIO.parse(file, "fasta") combined_sequences.extend(sequences) 可选:对连接后的序列进行排序或其他处理(根据需要进行操作)。
in_file.close() (base) root@PC1:/home/test2#python test.py ## 执行程序gene1 AGCTGCCTAAGCGGCATAGCTAATCG gene2 ACCGAATCGGAGCGATGGGCATTAAAGATCTAGCT gene3 AGGCTAGCGAGGCGCGAGGATTAGGCG 002、方法2 (base) root@PC1:/home/test2# ls
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 ...
"""importsysimporttimedefusage():print('Usage: python seq_abstract.py [fasta_file] [index_file] [out_indexfile] [out_remainfile]')deffasta2dict(inf):# 按行读取序列# 输入fasta文件,返回名称,序列globalnamedict={}forlineininf:line=line.strip()ifline.startswith('>'):name=line[1:]dict[...
方案一: from pyfaidx import Fasta #读取fasta文件 pep = Fasta('./pep.fa') #新文件 pep_len = open("pep_len.fa", "w") #写入文件 for n in pep.keys(): print(">{} {}\n{}".format(n, len(pep[n]), pep[n]), file=pep_len) ...
from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord # 序列的输入和输出 # 1、读取 Fasta 格式文件(也可以读取genbank文件) print("---read fasta file") # 数据放到了data目录下 for seq_record in SeqIO.parse("data/ls_orchid.fasta", "fasta"): print(seq_record...