python 统计fasta文件每条scalfold的碱基长度

 

001、

root@PC1:/home/test# cat test.fasta        ## 测试数据
>scaffold_1
CCCGGGTAAAACGGGTCTTCAAGAAAACGCTCCTCCGTTAATGCCGGCCGATTCAAATAA
CGCTGATTCTGATTCAGGATATACAATCTGACATGATGAACAGGTTTTCCAATTGGAATC
CGTT
>scaffold_2
CACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCGATAAATGGATCACAGGTT
AAGTTCACCGCATCCTGCGGCGACACCTGTGTGGCCTGCGTCGTGCAGGCCCTAGTTTGA
>scaffold_3
TTGATCCAGTGGCTCCGGTTACTCCAGTTGATCCTGTTGCGCCTGTTGCTCCAGTTTCTC
CGGTTGGTCCGGTTGATCCGGTTGCACCTGTTACTCCAGTGGCTCCGGTTACTCCCGTCG
CACCAGTTTCTCCTGTCGCACCAGTTGATCCTGTTGCGCCTGTTGGTCCTGTATCTCCAG
>scaffold_4
CCTGAGCCAGGATCAAACTCTCCGATA
root@PC1:/home/test# cat test.py           ## 测试脚本
#!/usr/bin/python
in_file = open("test.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] = ""
    else:
        dict1[key] = dict1[key] + i
print("id", "length", file = out_file, sep = "\t")
for i in dict1:
    print(i, len(dict1[i]), file = out_file, sep = "\t")
in_file.close()
out_file.close()
root@PC1:/home/test# python test.py
root@PC1:/home/test# ls
result.txt  test.fasta  test.py
root@PC1:/home/test# cat result.txt    ## 结果文件
id      length
>scaffold_1     124
>scaffold_2     120
>scaffold_3     180
>scaffold_4     27