根據GFF3文件統計外顯子大小和數量以及內含子大小

### 根據GFF3文件統計外顯子大小和數量以及內含子大小

with open('TSG.gff3', 'r') as f:
    for line in f:
        lin = line.strip().split('\t')
        name = lin[8].split(';')[1].split('=')[-1]
        if lin[2] == 'gene':
            print '\n',
            print name, lin[0], lin[3], lin[4],lin[6],
        if lin[2] == 'exon':
            print lin[3], lin[4],

# 上述程序統計每個基因的外顯子起始與結束的位置，保存爲1.txt,注意需要打開1.txt編輯刪除第一行的空行
with open('1.txt', 'r') as f:
    for line in f:
        lin = line.strip().split()
        a = len(lin)
        for i in range(6, a, 2):
            exon = int(lin[i]) - int(lin[i-1]) + 1
            print lin[0], exon

#上述程序則是計算每個外顯子的大小

with open('1.txt', 'r') as f:
    for line in f:
        lin = line.strip().split()
        a = len(lin)
        if a == 7:
            print lin[0], '0'
        if a > 7:
            if lin[4] == '+':
                for i in range(7, a, 2):
                    intron = abs(int(lin[i]) - int(lin[i-1]) - 1)
                    print lin[0], intron
            if lin[4] == '-':
                for i in range(8, a, 2):
                    intron = abs(int(lin[i]) + 1 - int(lin[i - 3]))
                    print lin[0], intron

#上述這個程序則是計算每個內含子的大小 

with open('1.txt', 'r') as f:
    for line in f:
        lin = line.strip().split()
        a = len(lin)
        n = (a - 5)/2
        print lin[0], n


#上述這個程序則是統計每個基因外顯子的數量