统计个数

for i in `cat file3 | awk -F " " '{print $1}' | sort | uniq`
do

    fc_count=`grep ${i} file3 | wc -l `
    for y in `cat file3 | awk -F " " '{print $2}' | sort | uniq`
    do
        sample_count=`grep ${y} file3 | wc -l `
        sample_fc_count=`grep ${y} file3 | grep ${i} | wc -l `
        echo ${i} ${y} ${sample_fc_count} >>count.txt
        echo ${y} ${sample_count} >>count.txt
    done
    echo ${i} ${fc_count} >>count.txt
done

另一种写法

cat file3 | awk -F " " '{print $2}' | sort -u | uniq -c

cat file3 | sort -u | uniq -c

python脚本

#!/usr/bin/env python
#-*-coding:utf-8-*-

import os
import re

file=open("file3","r")

# FC 和 sample 各存一个字典
dictfc = {}
dictsample = {}
dictfcsam= {}
# 按照行 读文件；
fileline=file.readlines()

for line in fileline:
    key = line.strip().split("\t")
#    dict[key[0]]=key[1]
    fc = key[0]
    sample = key[1]
# fc存入字典
    if fc not in dictfc:
        dictfc[fc] = 1
    else:
        dictfc[fc] += 1
# sample存入字典        
    if sample not in dictsample:
        dictsample[sample] = 1
    else:
        dictsample[sample] += 1
    if line not in dictfcsam:
        dictfcsam[line] = 1
    else:
        dictfcsam[line] += 1

print(dictfc)  
print(dictsample)  
print(dictfcsam)    
 
file.close()