#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')
