python - 从基因组创建树状图

Question

我想尝试一下基因组数据:

Species_A = ctnngtggaccgacaagaacagtttcgaatcggaagcttgcttaacgtag
Species_B = ctaagtggactgacaggaactgtttcgaatcggaagcttgcttaacgtag
Species_C = ctacgtggaccgacaagaacagtttcgactcggaagcttgcttaacgtag
Species_D = ctacgtggaccgacaagaacagtttcgactcggaagcttgcttaacgccg
Species_E = ctgtgtggancgacaaggacagttccaaatcggaagcttgcttaacacag

根据上面的基因组序列，我想根据这些生物体彼此之间的相关程度来创建一个树状图。我首先做的是计算每个物种的 a、c、t 和 g 的数量，然后创建一个数组，然后绘制树状图:

gen_size1 = len(Species_A)
a1 = float(Species_A.count('a'))/float(gen_size1)
c1 = float(Species_A.count('c'))/float(gen_size1)
g1 = float(Species_A.count('g'))/float(gen_size1)
t1 = float(Species_A.count('t'))/float(gen_size1)
.
.
.
gen_size5 = len(Species_E)
a5 = float(Species_E.count('a'))/float(gen_size5)
c5 = float(Species_E.count('c'))/float(gen_size5)
g5 = float(Species_E.count('g'))/float(gen_size5)
t5 = float(Species_E.count('t'))/float(gen_size5)

my_genes = np.array([[a1,c1,g1,t1],[a2,c2,g2,t2],[a3,c3,g3,t3],[a4,c4,g4,t4],[a5,c5,g5,t5]])
plt.subplot(1,2,1)
plt.title("Mononucleotide")
linkage_matrix = linkage(my_genes, "single")
print linkage_matrix
dendrogram(linkage_matrix,truncate_mode='lastp', color_threshold=1, labels=[Species_A, Species_B, Species_C, Species_D, Species_E], show_leaf_counts=True)
plt.show()

物种 A 和 B 是同一生物体的变体，我预计两者都应该从根部的共同进化枝中分化出来，物种 C 和 D 也应该从根部的另一个共同进化枝中分化出来，然后是物种 E与主根 fork ，因为它与物种 A 到 D 无关。不幸的是，树状图结果与从一个共同分支 fork 的物种 A 和 E 混合在一起，然后是另一个分支中的物种 C、D 和 B(相当困惑)。

我读过关于基因组序列的层次聚类，但我观察到它只适应二维系统，不幸的是我有 4 个维度，即 a、c、t 和 g。还有其他策略吗？谢谢您的帮助!

Answer 1

这是生物信息学中相当常见的问题，因此您应该使用像 BioPython 这样的生物信息学库内置了此功能。

首先，使用您的序列创建一个多 FASTA 文件:

import os
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_dna


sequences = ['ctnngtggaccgacaagaacagtttcgaatcggaagcttgcttaacgtag',
             'ctaagtggactgacaggaactgtttcgaatcggaagcttgcttaacgtag',
             'ctacgtggaccgacaagaacagtttcgactcggaagcttgcttaacgtag',
             'ctacgtggaccgacaagaacagtttcgactcggaagcttgcttaacgccg',
             'ctgtgtggancgacaaggacagttccaaatcggaagcttgcttaacacag']

my_records = [SeqRecord(Seq(sequence, generic_dna),
              id='Species_{}'.format(letter), description='Species_{}'.format(letter))
              for sequence, letter in zip(sequences, 'ABCDE')]

root_dir = r"C:\Users\BioGeek\Documents\temp"
filename = 'my_sequences'
fasta_path = os.path.join(root_dir, '{}.fasta'.format(filename))

SeqIO.write(my_records, fasta_path, "fasta")

这将创建文件C:\Users\BioGeek\Documents\temp\my_sequences.fasta，如下所示:

>Species_A
ctnngtggaccgacaagaacagtttcgaatcggaagcttgcttaacgtag
>Species_B
ctaagtggactgacaggaactgtttcgaatcggaagcttgcttaacgtag
>Species_C
ctacgtggaccgacaagaacagtttcgactcggaagcttgcttaacgtag
>Species_D
ctacgtggaccgacaagaacagtttcgactcggaagcttgcttaacgccg
>Species_E
ctgtgtggancgacaaggacagttccaaatcggaagcttgcttaacacag

接下来，使用命令行工具ClustalW进行多序列比对:

from Bio.Align.Applications import ClustalwCommandline
clustalw_exe = r"C:\path\to\clustalw-2.1\clustalw2.exe"
assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
clustalw_cline = ClustalwCommandline(clustalw_exe, infile=fasta_path)
stdout, stderr = clustalw_cline()    
print stdout

打印:

 CLUSTAL 2.1 Multiple Sequence Alignments


Sequence format is Pearson
Sequence 1: Species_A     50 bp
Sequence 2: Species_B     50 bp
Sequence 3: Species_C     50 bp
Sequence 4: Species_D     50 bp
Sequence 5: Species_E     50 bp
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score:  90
Sequences (1:3) Aligned. Score:  94
Sequences (1:4) Aligned. Score:  88
Sequences (1:5) Aligned. Score:  84
Sequences (2:3) Aligned. Score:  90
Sequences (2:4) Aligned. Score:  84
Sequences (2:5) Aligned. Score:  78
Sequences (3:4) Aligned. Score:  94
Sequences (3:5) Aligned. Score:  82
Sequences (4:5) Aligned. Score:  82
Guide tree file created:   [C:\Users\BioGeek\Documents\temp\my_sequences.dnd]

There are 4 groups
Start of Multiple Alignment

Aligning...
Group 1: Sequences:   2      Score:912
Group 2: Sequences:   2      Score:921
Group 3: Sequences:   4      Score:865
Group 4: Sequences:   5      Score:855
Alignment Score 2975

CLUSTAL-Alignment file created  [C:\Users\BioGeek\Documents\temp\my_sequences.aln]

ClustalW 创建的 my_sequences.dnd 文件是一个标准 Newick tree file Bio.Phylo 可以解析这些:

from Bio import Phylo
newick_path = os.path.join(root_dir, '{}.dnd'.format(filename))
tree = Phylo.read(newick_path, "newick")
Phylo.draw_ascii(tree)

打印内容:

       ____________ Species_A
  ____|
 |    |_____________________________________ Species_B
 |
_|          ____ Species_C
 |_________|
 |         |_________________________ Species_D
 |
 |__________________________________________________________________ Species_E

或者，如果您安装了 matplotlib 或 pylab，则可以使用 draw 函数创建图形:

tree.rooted = True
Phylo.draw(tree, branch_labels=lambda c: c.branch_length)

产生:

该树状图清楚地说明了您所观察到的情况:物种 A 和 B 是同一生物体的变体，并且都从根部的共同进化枝中分化出来。物种 C 和 D 也是如此，两者都从根源上偏离了另一个共同进化枝。最后，物种 E 与主根分离，因为它与物种 A 到 D 没有关系。