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_infa: SEQ_DICT[rec.id] =str(rec.seq)#
=int(line[2])-1print(fasta_dict[line[0]][s:e]) bed.close() sys.exit()
Output name (optional, by default is "output"). Strand where are your gene (default: +). Example: bash extractSeq.bash contig0001 500 2000 + myoutput Ecoli.fasta This means that we dive in file Ecoli.fasta, searching the contig "contig0001" and then extract the sequence on the posit...
You can use thewriteFastafunction for that. You just give the function the vector of sequences and the file to output to. Note that you will need to deefine the id lines as thenamesof the vector. E.g. library(ShortRead) ## Load this package first for this code to work consistently ...
Extract a part of a FASTA sequence.Ulrich Wittelsbuerger
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...
python学习——通过命令行参数根据fasta文件中染色体id提取染色体序列 2019-05-15 08:56 −提取fasta文件genome_test.fa中第14号染色体的序列,其内容如下: >chr1 ATATATATAT >chr2 ATATATATATCGCGCGCGCG >chr3 ATATATATATCGCGCGCGCGATATATATAT >chr4 ATATATAT... ...
reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk. If regions are speficified, the subsequences will be retrieved and printed to stdout in the FASTA format...
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP. - wwood/kingfisher-download
“comparison window”. Optimal alignment of the sequences for comparison can be achieved, in addition to manually, by means of the local homology algorithm of Smith and Waterman (1981) [Ad. App. Math. 2:482], by means of the local homology algorithm of Needleman and Wunsch (1970) [J. ...