转换代码 Converting other formats to GFF3;只需要在脚本里面改成你的文件就可以了。 fromBCBioimportGFFfromBioimportSeqIOin_file="your_file.gb"out_file="your_file.gff"in_handle=open(in_file)out_handle=open(out_file,"w")GFF.write(SeqIO.parse(in_handle,"genbank"),out_handle)in_handle.close...
to get a list of valid method of conversions. Taking the example of a conversion from a FastQ file into a FastA file, you could do the conversion as follows: bioconvert fastq2fasta input.fastq output.fasta bioconvert fastq2fasta input.fq output.fasta bioconvert fastq2fasta input.fq.gz out...
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...
GenBank to Fasta Converter is a afreewaremolecular biology tool that can convert GenBank (gb/gbk) file format to FASTA format. How to use it Start GenBank to Fasta Converter Converter module (located inDNA Baser). Locate the GBK files you want to convert and press the CONVERT button. A ...
SeqIO.convert(seqin,'genbank', seqout,'fasta') seqin.close()# Write the fasta string to a new window at position 0self.view.window().new_file().insert( edit,0, seqout.getvalue())else: sublime.error_message("Selected text does not look like Genbank: no 'LOCUS'")return ...
--inputfile The input sample. The following input formats are supported: SCF, ABI, FASTA, SEQ, TXT, GBK. --outputfolderThe folder where the output file will be written. Default=application's folder. --trimendsThe program will automatically trim low quality ends (if the input sample has ...
barcode_filepath_id =convert_to_id('raw_barcodes','filepath_type') fps = [(fp1, forward_filepath_id), (fp2, barcode_filepath_id)] filetype_id = get_filetypes()['per_sample_FASTQ'] raw_data = RawData.create(filetype_id, [prep_template], fps) ...
requirements.txt fix Jun 29, 2022 vcf.py pylint and sourcery.ai suggested changes p1 Nov 11, 2021 Repository files navigation README MIT licenseConvert GWAS summary statistics to VCFTool to map GWAS summary statistics to VCF with on-the-fly harmonisation to a supplied reference FASTAProduces...
-f : fasta file -r : spectra raw file folder -mcf : MaxQuant default configure path (if given, Can add new modifications) -m : via matching between runs to boosts number of identifications -pef : posterior error probability calculation based on target-decoy search -prf : protein score =...
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 ...