Question

我有一个看起来像这样的RNA-seq数据：

@J00157:85:HNNJLBBXX:5:1101:2869:15047 1:N:0:ATTACTCG+TATAGCCT
CGACGCTCTTCCGATCTGAGCTGCAGCCTCGGCCCCAGGATCCCCCTGGGGGACTGGACGCTGCTATTGATTCACGAGGCGCTCAGATCGGAAGAGCACAC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJFJJJJJJJJFJJJFJFJJJJJJJJJJJJJJJJ
--
@J00157:85:HNNJLBBXX:5:1101:12550:15574 1:N:0:ATTACTCG+TATAGCCT
GCTCTTCCGATCTGCTATTGATGACTGTCCTCTGTTCTTTCTTTCACAGTAGACGAGGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTACTC
+
AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
--

如果我们将@之后的所有内容视为一个部分，您只能看到第二行是真实的排序信息，1,3,4,5是逻辑/质量信息。

目标 提取在每行的前N（N = 35）个字符中包含“GCTGCA”的序列（第二行信息），以及同时输出周围的线（前面1行，匹配线后3行）。

答案示例是

@J00157:85:HNNJLBBXX:5:1101:2869:15047 1:N:0:ATTACTCG+TATAGCCT
CGACGCTCTTCCGATCTGAGCTGCAGCCTCGGCCCCAGGATCCCCCTGGGGGACTGGACGCTGCTATTGATTCACGAGGCGCTCAGATCGGAAGAGCACAC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJFJJJJJJJJFJJJFJFJJJJJJJJJJJJJJJJ
--

我试过的是

awk 'substr($0, 1, 35) ~ "GCTGCA"' filename.fastq > newfile.fastq
grep -B 1 -A 2 -E GCTGCA filename.fastq > newfile.fastq
awk '{a[++i]=$0;}{substr(a[++i], 1, 35) ~ "GCTGCA"}{for(j=NR-1;j<=NR+2;j++)print a[j];}' filename.fastq > newfile.fastq

第一个不能输出周围的线条。第二个不能限制每行的前35个字母中的模式匹配。第三行应该可以工作，但它给了我有线输出（显然这是不正确的）：

@J00157:85:HNNJLBBXX:5:1101:14235:1367 1:N:0:ATTACTCG+TATAGCCT
@J00157:85:HNNJLBBXX:5:1101:14235:1367 1:N:0:ATTACTCG+TATAGCCT
TCTNCTCTTCCGATCTACCCCACACACCCCCGCCGCCGCCGCCGCCGCCGCCCTCCGACGCACACCACACGCGCGCGCGCGCGCGCCGCCCCCGCCGCTCC
TCTNCTCTTCCGATCTACCCCACACACCCCCGCCGCCGCCGCCGCCGCCGCCCTCCGACGCACACCACACGCGCGCGCGCGCGCGCCGCCCCCGCCGCTCC
+
+
AAF#FJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJAJJJJJFJJJJ7JJ
AAF#FJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJAJJJJJFJJJJ7JJ
--
--

Answer 1

gawk多字符RS支持。

awk -v RS='\n--' -F'\n' 'substr($2,0,35)~"GCTGCA"{print $0 RS}' file

使用记录分隔符定义记录。

Answer 2

awk使用getline：

search.awk ：

substr($0,0,35)~"GCTGCA"  {
    print p # Print the previous line ...
    print # ... , current line ...
    for(i=0;i<=2;i++) { # ... and the 3 lines following it
        getline
        print
    }
}

# Store the previous line
{ p = $0 }

这样称呼：

awk -f search.awk input_file

或没有正则表达式和参数：

search.awk

index(substr($0,0,35), search)  {
    print l
    print
    for(i=0;i<=2;i++) {
        getline
        print
    }
}

{ l = $0 }

称之为

awk -v search="GCTGCA" -f search.awk input_file

GREP或AWK：搜索每一行的前N个字符，并输出与模式匹配的周围行

2 个答案: