问Biopython:将蛋白质片段从PDB导出到FASTA文件EN我正在写PDB蛋白序列片段fasta格式如下所示。Biopython是Py...
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---...
为了处理这样的FASTA格式的数据,我们可以指定Bio.AlignIO.parse()的第三个可选参数seq_count,这一参数将告诉Biopython你所期望的每个序列比对中序列的个数。例如: foralignmentinAlignIO.parse(handle,"fasta",seq_count=2):print"Alignment length%i"%alignment.get_alignment_length()forrecordinalignment:print"%s-...
91001 )的pPCP1质粒全长序列为例,说明从FASTA文件创建SeqRecord的过程。该序列原始文件来自NCBI,可在Biopython单元测试GenBank文件夹下找到,也可点击 NC_005816.fna 下载。 序列以大于号开头,该文件只包含一条序列: >gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtus ... pPCP1, complete sequence ...
我可以从命令行成功调用三个必需的参数:(-sequence [input file],-outseq [output s 浏览9提问于2012-07-09得票数 2 回答已采纳 1回答 使用biopython编写字典到文件 、、、 我是个新手,使用biopython。我正在试着用biopython把字典写到一个文件里。open("file_in.fasta") as original, open("file_out.f...
from Bio import SeqIO records = ... with open("example.faa", "w") as handle: SeqIO.write(records, handle, "fasta") 注意,如果你 Bio.SeqIO.write() 函数要写入的文件已经存在,旧文件将会被覆写,并且不会得到任何警告信息。 例子1:
The Sequence IO object There is one more object that we have to discuss and this theSeqIOobject is like a container for multipleSeqRecordobjects. importosfromBioimportSeqIO'''We use a list here to save the gene records from a FASTA fileIf you have many records a dictionary will make the...
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(...
summarizeheaders Summarize FASTA headers of result DB nrtotaxmapping Create taxonomy mapping for NR database extractdomains Extract highest scoring alignment regions for each sequence from BLAST-tab file countkmer Count k-mers 1. 2. 3. 4.
pymol receptor.pdb -c -d "save receptor.fasta" 2. BioPython from Bio import PDB parser = PDB.PDBParser() structure = parser.get_structure('2FH7', '2FH7.pdb') ppb = PDB.PPBuilder() for pp in ppb.build_peptides(structure): print (pp.get_sequence()) model = structure[0] for pp...