我有一个 RNA-seq 数据,如下所示:
@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
--
如果我们把@后面的所有内容都当成一个section,可以看到只有第二行才是真正的测序信息,1,3,4,5是logistic/quality信息。
目标是提取每行前N(N=35)个字符中包含“GCTGCA”的序列(第二行信息),并且同时输出周围的行(前面1行,匹配行后面3行)。
一个示例答案是
@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。第二个不能限制每行前 35 个字母的模式匹配。第三行应该可以工作,但它给了我有线输出(这显然是不正确的):
@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
--
--
最佳答案
使用 gawk
多字符 RS 支持。
awk -v RS='\n--' -F'\n' 'substr($2,0,35)~"GCTGCA"{print $0 RS}' file
您使用记录分隔符定义记录。
关于linux - GREP 或 AWK : Search in the first N characters of each line, 并输出匹配模式的周围行,我们在Stack Overflow上找到一个类似的问题: https://stackoverflow.com/questions/50008431/