美国加州大学圣地亚哥分校生信课程练习题week1.1

问题需求：在text中统计pattern重复次数，需要注意的是TGGACTCTG和TGGACTCTGGACTCTG都符合pattern。

text：GGGTTATGGACTCTGGACTCTCAATGGACTCTGGACTCACTGGACTCTGGACTCGGCAATGGACTCATGGACTCTTGGACTCTTGGACTCTACTCGTGGACTCTGGACTCTAATGGACTCAATGGACTCTGGACTCATTTGGACTCGTTGGACTCCTGGACTCGTTGGACTCTGGACTCTTGGACTCCACTCTGGACTCACTGGACTCTGGACTCTTTGGACTCACCGCTGGACTCCTATGGACTCAGTGGACTCGAGTGGACTCCAGTAGTAGGATGTGGACTCTTGGACTCCGGGGACTTAAGCCTGGACTCGGTGGACTCACGATGGACTCTGGACTCTAACTGGACTCGGTGGACTCTGGACTCACCGACAGCGTCTGGACTCCACTGCAGAATGGACTCTGTGGACTCGAACTGGACTCGGCGGGAGATTTGGACTCATGGACTCTGGACTCACTGGACTCCATGGACTCAATTTTGGACTCTGGACTCTCGTGGACTCTGGACTCCCCTGGACTCCTATGGACTCCGTGGACTCTGGACTCTGGACTCTGGACTCTGGACTCGGACTGGACTCATGGACTCTGGACTCTGGACTCCGTTGGACTCTTGGACTCCTCTGGACTCTGTGGACTCAGTGGACTCTTGGACTCGTGGACTCATGGACTCGGTTTTAGTGGACTCGGTATGGACTCTCTGGACTCTGGACTCAGCATGGACTCATGGACTCCCGAGTCATGGACTCTGGACTCGGACGCTGGACTCTGGACTCTATGGACTCATTGGACTCTGGACTCTTTGGACTCAAATGGACTCACTGGACTCTGGACTCCATGGACTCGTGGACTCACTGGACTCGATCCGAATGGACTCTGGACTCACTCCTGGACTCCATGGACTCTTGGACTCGGGTGGACTCGTGGACTCCTCTGGACTCAGATGGACTCAGACCCTGGACTCGTTGGACTCTCTTTGGACTC

pattren：TGGACTCTG

代码实现：

python代码实现:

txt, i= {},1path ="dataset_2_6.txt"
f =open(path,encoding='utf-8')
for line in f:    
  txt[i] = line
  i +=1    
  txt.update(txt)
f.close() 
text = str(txt[1].strip())
pattern = str(txt[2].strip())
def PatternCount(text, pattern):
count=0
for i in range(len(text)-len(pattern)+1):
  if text[i:i+len(pattern)] == pattern:
    count=count+1
return count 
print(PatternCount(text, pattern))

R代码实现:

library(stringr)
data = read.table('dataset_2_6.txt', stringsAsFactors = F)
str = str_split(data[1,1],'') %>%
        as.data.frame()

ncount = 0
for (i in 1:(nrow(str) - nchar(data[2,1]) + 1)) {
        j = i+nchar(data[2,1]) - 1
        rep.1 = paste(str[i:j,1], sep = '')
        
        rep.2 = ''
        
        for (m in 1:length(rep.1)) {
                rep.2 = paste(rep.2,rep.1[m], sep = '')
        }
        
        if (rep.2 == data[2,1]) {
                ncount = ncount + 1
        }
        
        if (i == (nrow(str) - nchar(data[2,1]) + 1)) {
               print(ncount) 
        }
}

shell代码实现:

text=$(sed -n '1p' dataset_2_6.txt)
pattern=$(sed -n '2p' dataset_2_6.txt)
len_text=echo ${#text}
len_pattern=echo ${#pattern}
len_range=$(($len_text-$len_pattern))
count=0
for((i=0;i<=$len_range;i++))
  do
    temp=$(echo ${text:$i:$len_pattern})
    if [ $temp == $pattern ]; then
      count=$(($count+1))
    fi
done
echo $count