#7.5.2.WebLogo_example_1.py from Bio.motifs import Motif from Bio import motifs from Bio.Seq import Seq instances = [ Seq("TACAA"), Seq("TACGC"), Seq("TACAC"), Seq("TACCC"), Seq("AACCC"), Seq("AATGC"), Seq("AATGC"), ] m = motifs.create(instances) print(m.counts) Motif.weblogo(m, 'test.png')
#13.5.WebLogo.py from Bio.motifs import Motif from Bio import motifs from Bio.Seq import Seq instances = [ Seq("AATTAAA"), Seq("AAAAAGA"), Seq("AAATAGC"), Seq("AATCAAC"), Seq("AATTTAA"), Seq("TATCAGA"), Seq("ATATAGC"), Seq("ATATTAA"), ] m = motifs.create(instances) print(m.counts) Motif.weblogo(m, '13.5.png')
from Bio import motifs from Bio.Seq import Seq instances = [ Seq("TACAA"), Seq("TACGC"), Seq("TACAC"), Seq("TACCC"), Seq("AACCC"), Seq("AATGC"), Seq("AATGC") ] m = motifs.create(instances) print(m.counts) Motif.weblogo(m, 'test.png') from Bio.Alphabet import IUPAC # multiple sequence alignment 파일 읽기 alignment = AlignIO.read( "C:/" "Users/" "SD NOH/" "PycharmProjects/" "First/" "Bioinformatics_Biopython-master/" "Bioinformatics_Biopython-master/" "Section1/" "Chap7/" "HBA.aln", "clustal")
sample_2 = SeqIO.read(open("/mnt/hgfs/shared_folder/AJ011405.gb"), "genbank") sample_3 = SeqIO.read(open("/mnt/hgfs/shared_folder/AJ011408.gb"), "genbank") list = [sample_1, sample_2, sample_3] aln_fasta="" for sample in list: title = sample.name+" "+sample.description aln_fasta+=">"+title+"\n"+sample.seq+"\n" fr = open("aln_fasta", "w") fr.write(str(aln_fasta)) fr.close() from Bio.Align.Applications import MuscleCommandline muscle_exe = "~/muscle64" cmd_line = MuscleCommandline(muscle_exe, input="aln_fasta", out="7.8.aln", clw=" ") print (cmd_line) stdout, stderr = cmd_line() from Bio import AlignIO from Bio.motifs import Motif from Bio import motifs from Bio.Seq import Seq from Bio.Alphabet import IUPAC alignment = AlignIO.read("7.8.aln", "clustal") instance=[] for record in alignment: s = Seq(str(record.seq), IUPAC.unambiguous_dna) instance.append(s) m =motifs.create(instance) Motif.weblogo(m, '7.8_weblogo.png')