最近从基于高通量测序的16S分析转换到 环境样品的 Metagenome 分析时，需要统计组装后contig的GC含量和N50。于是花了点时间写了个小脚本，方便今后数据处理工作。

#GC_N50.py

print 'Python and Biopython needed for running this script!'

print "Script for calculating N50 of assembly"

fasta = raw_input('Enter your fasta/fa name: ')

# N50 calculation

BaseSum,Length= 0,[]

ValueSum,N50 = 0,0

no_c,no_g,no_a,no_t,no_n = 0,0,0,0,0

from Bio import SeqIO

for record in SeqIO.parse(open(fasta), "fasta"):

   BaseSum += len(record.seq)

   Length.append(len(record.seq))

   seq =record.seq.lower()

   no_c+=seq.count('c')

   no_g+=seq.count('g')

   no_a+=seq.count('a')

   no_t+=seq.count('t')

   no_n+=seq.count('n')

#N50 calcuation

N50_pos = BaseSum / 2.0    

Length.sort()  

Length.reverse()    

for value in Length:

   ValueSum += value

   if N50_pos <= ValueSum:

       N50 = value

       break  

print 'Sequences NO.:'+'t'+str(len(Length))

print 'Sequences Min.:'+'t'+str(min(Length))

print 'Sequences Max.:'+'t'+str(max(Length))

print 'N50: ' + str(N50)

#GC calcuation

print "Total number of bases:", BaseSum

print "percentage of A in given sequences","%.1f"%((float(no_a*100))/BaseSum),'%'

print "percentage of T in given sequences","%.1f"%((float(no_t*100))/BaseSum),'%'

print "percentage of C in given sequences","%.1f"%((float(no_c*100))/BaseSum),'%'

print "percentage of G in given sequences","%.1f"%((float(no_g*100))/BaseSum),'%'

print "percentage of N in given sequences","%.1f"%((float(no_n*100))/BaseSum),'%'

# Program written by Feng Ju，HKU; tested in python and biopython 2.7.3