python中统计基因组所含scaffolds总数、碱基总个数

001、

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

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

import re
total_sca = 0
total_len = 0
total_len_gc = 0

for i in in_file:
    i = i.strip()
    if i[0] == ">":
        total_sca += 1
    else:
        total_len += len(i)
        total_len_gc += len(re.findall("[GCgc]", i))

print("n_scofflod", "total_len", "total_len_gc", "proportion_gc", file = out_file, sep = "\t")
print(total_sca, total_len, total_len_gc, total_len_gc/total_len, 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
n_scofflod      total_len       total_len_gc    proportion_gc
3       365     203     0.5561643835616439

参考：https://mp.weixin.qq.com/s?__biz=MzIxNzc1Mzk3NQ==&mid=2247491482&idx=1&sn=596fd0f0e7d41757e1e539f3223a8c8c&chksm=97f5af82a08226943da69bca8228480d4b708ca2c89f8008281f140682e8814b43cf49d60762&scene=178&cur_album_id=2403674812188688386#rd

标签：python,基因组,len,gc,file,test,home,total,scaffolds
来源： https://www.cnblogs.com/liujiaxin2018/p/16561436.html