How to print three consecutive lines after a pattern, which is in different file

Question

I am beginner, hoping somebody can help me out. I would like to use awk (or sed) to do this task.

I have two files,

File 1

@HWI-M01162:73:000000000-A7TPE:1:1101:17896:1432
@HWI-M01162:73:000000000-A7TPE:1:1101:14465:1433

File 2

@HWI-M01162:73:000000000-A7TPE:1:1101:17896:1432 1:N:0:CTTGTA
CCCCAATGTGATCTGTTTACATTCCAACTCAGCTTCCTCTTGTAAATGTTTTTCTTTTTAC
+
8ABC-6F,C<,CFF9FGGAE9FGFF9<EFF9,CEEEEGGGG9E,,,C<FFFGGGGGGGGGG
@HWI-M01162:73:000000000-A7TPE:1:1101:14465:1433 1:N:0:CTTGTA
CCCATGATGGTACGAAAGTACACATTTTATTTCTTATAAGCAATGGGTTTACTCAGCCTGA
+
@CC<CA9F<<FCFE>87@FCFAF?FFGG9FFFFGGCF9,<EA8FC8EFFGEFGG98@FFC8
@HWI-M01162:73:000000000-A7TPE:1:1101:15447:1444 1:N:0:CTTGTA
CTCTATCTAGAGTTGCCTTCATCAGTTTATCAAAAACACAACCTTAAAAAGGCAACCCCTG
+
AACC@FFGA<@9FF9EEFGF9FF9<FFFEFF99,,<B8C<8@FFGD,,,,,:C8<FEFEF8
@HWI-M01162:73:000000000-A7TPE:1:1101:15876:1444 1:N:0:CTTGTA
CTCTTTATTTAGTTTTAACTTATCTCAAAAATTACTCGACCTAAAAAATTTGGCCTGTTTA
+
-8CCCG-EFFA9FFFG98FFF9FEEE9,,,,CFAEFF7,@CF,,,,,+CEF9,CFF8EFF,

The out put what I want is as follows. So if the line in file 1 match with line in the file 2, print the line in file 2 together with three consecutive lines. Lines in file 1 are all unique IDs.

@HWI-M01162:73:000000000-A7TPE:1:1101:17896:1432 1:N:0:CTTGTA
CCCCAATGTGATCTGTTTACATTCCAACTCAGCTTCCTCTTGTAAATGTTTTTCTTTTTAC
+
8ABC-6F,C<,CFF9FGGAE9FGFF9<EFF9,CEEEEGGGG9E,,,C<FFFGGGGGGGGGG
@HWI-M01162:73:000000000-A7TPE:1:1101:14465:1433 1:N:0:CTTGTA
CCCATGATGGTACGAAAGTACACATTTTATTTCTTATAAGCAATGGGTTTACTCAGCCTGA
+
@CC<CA9F<<FCFE>87@FCFAF?FFGG9FFFFGGCF9,<EA8FC8EFFGEFGG98@FFC8

score 2 · Accepted Answer · answered Jun 30 '17 at 03:15

2

$ awk 'NR==FNR{a[$0];next} $1 in a{c=4} c&&c--' file1 file2
@HWI-M01162:73:000000000-A7TPE:1:1101:17896:1432 1:N:0:CTTGTA
CCCCAATGTGATCTGTTTACATTCCAACTCAGCTTCCTCTTGTAAATGTTTTTCTTTTTAC
+
8ABC-6F,C<,CFF9FGGAE9FGFF9<EFF9,CEEEEGGGG9E,,,C<FFFGGGGGGGGGG
@HWI-M01162:73:000000000-A7TPE:1:1101:14465:1433 1:N:0:CTTGTA
CCCATGATGGTACGAAAGTACACATTTTATTTCTTATAAGCAATGGGTTTACTCAGCCTGA
+
@CC<CA9F<<FCFE>87@FCFAF?FFGG9FFFFGGCF9,<EA8FC8EFFGEFGG98@FFC8

answered Jun 30 '17 at 03:15

Ed Morton

172,331
17
70
167

1

Very brilliant use of `c&&c--` – CWLiu Jun 30 '17 at 03:24
1

Thanks you can see more of it at https://stackoverflow.com/a/17914105/1745001 :-). – Ed Morton Jun 30 '17 at 03:26
1

Thank you very much, I really appreciate!! – user2182606 Jun 30 '17 at 03:35

score 1 · Answer 2 · answered Jun 30 '17 at 01:51

1

This awk will do that:

awk 'FNR==NR{k[FNR]=$0; next} 
     {data[FNR]=$0; next}
     END{
       for (i=1;i in k;i++) {
           for (j=1; j in data; j++){
                if (data[j]~k[i]){
                   for (x=0; x<4; x++)
                       print data[j+x]
                   j+=x
                }
           }
        }
      }' f1 f2

answered Jun 30 '17 at 01:51

dawg

90,796
20
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Hi Dawg, Thank you very much!! It works for my files!! – user2182606 Jun 30 '17 at 03:29

How to print three consecutive lines after a pattern, which is in different file

2 Answers2