一、输入文件
cat test.txt
>sequence_1
AAAA
GGGG
CCCC
TTTT
>sequence_2
aaaa
gggg
cccc
tttt
二、python3代码
#!/usr/bin/env python3
import os, sys, re
ms, infile, outfile = sys.argv
with open(infile) as f:
Dict = {}
for line in f:
if line[0] == ">":
key = re.sub('>', '', line.strip())
Dict[key] = []
else:
Dict[key].append(line.strip())
with open(outfile, 'w') as o:
o.write("id\tGC_percent\n")
for key, value in Dict.items():
seq = ''.join(value)
nG = seq.count("G") + seq.count("g")
nC = seq.count("C") + seq.count("c")
gc_percent = (nG + nC)/len(seq)
o.write("{}\t{}\n".format(key, gc_percent))
三、运行结果
python3 ../fasta_gc_percent.py test.txt out.txt
cat out.txt
id GC_percent
sequence_1 0.5
sequence_2 0.5
