python 中统计fasta文件scaffolds平均长度、最长scaffolds、最短scaffolds

 

001、利用列表实现

(base) root@PC1:/home/test# ls
a.fasta  test.py
(base) root@PC1:/home/test# cat a.fasta         ## 测试数据
>scaffold_1
CCCGGGTAAAACGGGTCTTCAAGAAAACGCTCCTCCGTTAATGCCGGCCGATTCAAATAA
CCTCTGGCAACACCCGCTCCGGCAATGTATAGTTCACCGATACATCCAACAGGCAGCATC
GGCCCNN
>scaffold_2
CTGTTGCTCCTGTTGCTCCTGTTGATCCCGTTGCACCTGTTGGTCCAGTCGGTCCAATTC
nnn
>scaffold_3
TTGATCCAGTGGCTCCGGTTACTCCAGTTGATCCTGTTGCGCCTGTTGCTCCAGTTTCTC
CGGTTGGTCCGGTTGATCCGGTTGCACCTGTTACTCCAGTGGCTCCGGTTACTCCCGTCG
CTGTTGCTCCTGTTGCTCCTGTTGATCCCGTTGCACCTGTTGGTCCAGTCGGTCCAATTC
(base) root@PC1:/home/test# cat test.py         ## 测试脚本
#!/usr/bin/python

in_file = open("a.fasta", "r")
out_file = open("result.txt", "w")

total_list = []
total_len = 0

for i in in_file:
    i = i.strip()
    if i[0] == ">":
        total_list.append(total_len)
        total_len = 0
    else:
        total_len += len(i)
total_list.append(total_len)
total_list = total_list[1::]

print("mean_sca", "max_sca", "min_sca", file = out_file, sep = "\t")
print(sum(total_list)/len(total_list), max(total_list), min(total_list), file = out_file, sep = "\t")

in_file.close()
out_file.close()
(base) root@PC1:/home/test# python test.py         ## 执行脚本
(base) root@PC1:/home/test# ls
a.fasta  result.txt  test.py
(base) root@PC1:/home/test# cat result.txt          ## 查看统计结果
mean_sca        max_sca min_sca
123.33333333333333      180     63

 

002、利用字典实现

(base) root@PC1:/home/test# ls
a.fasta  test.py
(base) root@PC1:/home/test# cat a.fasta         ## 测试数据
>scaffold_1
CCCGGGTAAAACGGGTCTTCAAGAAAACGCTCCTCCGTTAATGCCGGCCGATTCAAATAA
CCTCTGGCAACACCCGCTCCGGCAATGTATAGTTCACCGATACATCCAACAGGCAGCATC
GGCCCNN
>scaffold_2
CTGTTGCTCCTGTTGCTCCTGTTGATCCCGTTGCACCTGTTGGTCCAGTCGGTCCAATTC
nnn
>scaffold_3
TTGATCCAGTGGCTCCGGTTACTCCAGTTGATCCTGTTGCGCCTGTTGCTCCAGTTTCTC
CGGTTGGTCCGGTTGATCCGGTTGCACCTGTTACTCCAGTGGCTCCGGTTACTCCCGTCG
CTGTTGCTCCTGTTGCTCCTGTTGATCCCGTTGCACCTGTTGGTCCAGTCGGTCCAATTC
(base) root@PC1:/home/test# cat test.py     ## 测试脚本
#!/usr/bin/python

in_file = open("a.fasta", "r")
out_file = open("result.txt", "w")

dict1 = dict()

for i in in_file:
    i = i.strip()
    if i[0] == ">":
        key = i
        dict1[key] = 0
    else:
        dict1[key] += len(i)

print("max", "min", "mean", file = out_file, sep = "\t")
print(max(dict1.values()), min(dict1.values()), sum(dict1.values())/len(dict1.values()), file = out_file, sep = "\t")

in_file.close()
out_file.close()
(base) root@PC1:/home/test# python test.py       ## 执行程序
(base) root@PC1:/home/test# ls
a.fasta  result.txt  test.py
(base) root@PC1:/home/test# cat result.txt       ## 查看统计结果
max     min     mean
180     63      123.33333333333333