ACC_DICT[pdID] = ptID# id vs seq dictpd_infa = SeqIO.parse(open(sys.argv[2]),'fasta') pt_infa = SeqIO.parse(open(sys.argv[3]),'fasta')# 创建以 FASTA 文件的 ID 为 keys, sequence 为 values 的字典SEQ_DICT = {}forrecinpd_infa: SEQ_DICT[rec.id] =str(rec.seq)forrecinpt...
fasta=open(FASTA,'U') fasta_dict= {} for line in fasta: line= line.strip() if line =='': continue if line.startswith('>'): seqname= line.lstrip('>') seqname= re.sub('\..*','', seqname) fasta_dict[seqname]=''else: fasta_dict[seqname] += line fasta.close() bed=open...
extracSeq is a bash script (awk embedded), that giving a contig name and positions (start and end), return the corresponding sequence from your fasta. Usage extractSeq need five (and intuitive), parameters (order is important): The contig name where are the coordinates that you want. Start...
uniquesToFasta(mergers[[i]], paste0("F:/MHC_VR/Dada2/output", i, ".fasta")) } Error in getUniques(unqs, collapse = FALSE) : Unrecognized format: Requires named integer vector, fastq filename, dada-class, derep-class, sequence matrix, or a data.frame with $sequence and $abundance...
FeatureExtract--extracts sequences and feature annotation from genbank format file 最近一直在看和植物叶绿体基因组有关的知识,其中有一项内容是分析叶绿体基因组的密码子偏向性,这就要求我们首先要拿到基因的CDS序列,在NCBI的organelle genome数据库中我们通常可以下载到叶绿体全基因组的fasta文件,genbank文件;gff3...
Extract a part of a FASTA sequence.Ulrich Wittelsbuerger
$outputfile = $_.".seq"; open (OUT,'>',"$outputfile") or die "Can't open $outputfile! Check FASTA file sequence name, which may contain illegal characters in file system!\n"; print OUT ">$_\n$hash{$_}"; close OUT;
你可以使用 blastdbcmd 从fasta 文件构造的 blastdb 中提取 fasta 序列,blastdbcmd 应该在安装 makeblastdb 时安装。 blastdbcmd -entry all -db <database label> -out <outfile> 如果你有一个名为 my_database 的数据库,其中包含文件 my_database.nhr,my_database.nsq,my_database.nin,并且你希望将...
根据位置信息提取 fasta 文件中的序列 -- extract fasta sequence by their position 2015-08-08 16:46 −... liuhui_pine 0 1999 统计fasta 文件序列长度及 GC 含量 2017-01-14 03:25 −注:该脚本适用于序列不断开的情况 可用一下命令将折行的序列合并为一行 ``` awk '/^>/ {printf("\n%s\t...
(GAP, BESTFIT, FASTA and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis., or by the BLAST N or BLAST P comparison software). The percentage identity between two nucleic sequences is determined by comparing these two optimally aligned...