echo -e "\nConvert contig in UCSC chromosome names using :\n ${pathToConvert}\n On the files:\n${gff_path}\n and\n${fasta_path}\n" grep -v "#" ${pathToConvert} | awk 'BEGIN{OFS="|"}{print $7,$11}' > tmp_convert.txt OLDIFS=$IFS IFS=$'\n' for line in $(cat tmp...
# 需要导入模块: from Bio import SeqIO [as 别名]# 或者: from Bio.SeqIO importconvert[as 别名]defconvertQ2A( qd, qname):qpath = qd +"/"+ qname +".fastq"cpath = qd +"/"+ qname +".fasta"SeqIO.convert(qpath,"fastq", cpath,"fasta")print"converted file to fasta"returncpath ...
Formats: FASTA, SCF, SEQ, TXT, GBK, ABI Doesn't need to be installed/uninstalled Very small (less than 1MB) Portable Quick links How to write DOS scripts Similar molecular biology format converters Order now All programs have been scanned againstviruses ...
(fna_fp,convert_to_id('preprocessed_fasta','filepath_type')), (qual_fp,convert_to_id('preprocessed_fastq','filepath_type'))] preprocessed_data = PreprocessedData.create( Study(1),"preprocessed_sequence_illumina_params",1, filepaths, data_type="18S") params = ProcessedSortmernaParams(1) ...
line(input=fasta_infile)#Create mafft command linestdout,stderr=mafft_cline()#save mafft output into variablewithopen(msa_fasta,'w')ashandle:handle.write(stdout)#write mafft output in fasta formatAlignIO.convert(msa_fasta,"fasta",msa_phy,"phylip-relaxed")#convert mafft output from fasta to ...
Supports any ASCII text based genome such as FASTA, GBK, .txt, .gff etc, if it has text like GTAGCCTAGTCGATTCAG or maybe UUGCUTGUTGUTGUTGTUCUT then AminoSee can render up a set of images of it! The triplet for Lyson AAA would render to this indigo colour at 313 A node command ...