convert fasta format to phylip format #!/usr/bin/pythonimportsysfromBioimportSeqIO# usageUSAGE ="\nusage: python convert_fasta2phylip.py [input fasta file] [output phy file]\n"iflen(sys.argv) !=3:printUSAGE sys.exit() infile = sys.argv[1] outfile = sys.argv[2] sequence_list = []...
# import a converter from bioconvert.fastq2fasta import FASTQ2FASTA # Instanciate with infile/outfile names convert = FASTQ2FASTA(infile, outfile) # the conversion itself: convert() Setting up and maintaining Bioconvert has been possible thanks to users and contributors. Thanks to all: ...
def create_msa(fasta_infile, msa_fasta,msa_phy): "Creates a multiple sequence alignment with mafft in phylip format" mafft_cline = MafftCommandline(input=fasta_infile) #Create mafft command line stdout,stderr = mafft_cline() #save mafft output into variable with open(msa_fasta, 'w') as...
# 需要导入模块: from Bio import AlignIO [as 别名]# 或者: from Bio.AlignIO importconvert[as 别名]defcreate_msa(fasta_infile, msa_fasta,msa_phy):"Creates a multiple sequence alignment with mafft in phylip format"mafft_cline = MafftCommandline(input=fasta_infile)#Create mafft command linestdou...
FastaToPhylip.pyconverts FASTA to PHYLIP. FastaToTab.pyconverts FASTA to tab-delimited file with columns: Chr, Pos, REF. filterByNs_callsTab.pyremoves all sites that consists of more than a given amount of missing data (Ns). find_popSpecificAlleles_in_callsTab.pyoutputs only unique allele...
phylipAn alignment format. Truncates names at 10 characters. pirA FASTA like' format introduced by the National Biomedical Research Foundation (NBRF) for the Protein Information Resource (PIR) database, now part of UniProt. seqxmlSimple sequence XML file format. ...
SeqIO.convert(workingFile +"_seqgen_out.phylip","phylip", workingFile +".fasta","fasta") shutil.copy(workingFile +".fasta", srp_hap_file) 开发者ID:stevenhwu,项目名称:SrpPython,代码行数:32,代码来源:generateData.py 示例5: main
I only keep the program namedsreformat, which can convert various file formats likefasta,a2m(aligned fasta)and so on. Help information insreformat Output format choices: Unaligned Aligned --- --- fasta stockholm embl msf genbank a2m gcg phylip gcgdata clustal pir selex raw eps Available opti...