Create specific output

Shell Programming and Scripting
1

I have a file that looks like the below and only need certain lines, but am not sure how to do that. It is basically everything from the @HD up to the @RG. Thank you :).

file.txt - input

@HD    VN:1.4    GO:none    SO:coordinate @SQ    SN:chr1    LN:249250621 @SQ    SN:chr2    LN:243199373 @SQ    SN:chr3    LN:198022430 @SQ    SN:chr4    LN:191154276 @SQ    SN:chr5    LN:180915260 @SQ    SN:chr6    LN:171115067 @SQ    SN:chr7    LN:159138663 @SQ    SN:chr8    LN:146364022 @SQ    SN:chr9    LN:141213431 @SQ    SN:chr10    LN:135534747 @SQ    SN:chr11    LN:135006516 @SQ    SN:chr12    LN:133851895 @SQ    SN:chr13    LN:115169878 @SQ    SN:chr14    LN:107349540 @SQ    SN:chr15    LN:102531392 @SQ    SN:chr16    LN:90354753 @SQ    SN:chr17    LN:81195210 @SQ    SN:chr18    LN:78077248 @SQ    SN:chr19    LN:59128983 @SQ    SN:chr20    LN:63025520 @SQ    SN:chr21    LN:48129895 @SQ    SN:chr22    LN:51304566 @SQ    SN:chrX    LN:155270560 @SQ    SN:chrY    LN:59373566 @SQ    SN:chrM    LN:16569 @RG    ID:8AH6U.IonXpress_009    PL:IONTORRENT    PU:Unspecified/P1.1.17/IonXpress_009    FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG    DT:2015-06-03T14:03:02-0700    SM:E1    PG:tmap    KS:TCAGTGAGCGGAACGAT    CN:TorrentServer/Proton

Desired output

@HD    VN:1.4    GO:none    SO:coordinate @SQ    SN:chr1    LN:249250621 @SQ    SN:chr2    LN:243199373 @SQ    SN:chr3    LN:198022430 @SQ    SN:chr4    LN:191154276 @SQ    SN:chr5    LN:180915260 @SQ    SN:chr6    LN:171115067 @SQ    SN:chr7    LN:159138663 @SQ    SN:chr8    LN:146364022 @SQ    SN:chr9    LN:141213431 @SQ    SN:chr10    LN:135534747 @SQ    SN:chr11    LN:135006516 @SQ    SN:chr12    LN:133851895 @SQ    SN:chr13    LN:115169878 @SQ    SN:chr14    LN:107349540 @SQ    SN:chr15    LN:102531392 @SQ    SN:chr16    LN:90354753 @SQ    SN:chr17    LN:81195210 @SQ    SN:chr18    LN:78077248 @SQ    SN:chr19    LN:59128983 @SQ    SN:chr20    LN:63025520 @SQ    SN:chr21    LN:48129895 @SQ    SN:chr22    LN:51304566 @SQ    SN:chrX    LN:155270560 @SQ    SN:chrY    LN:59373566 @SQ    SN:chrM    LN:16569
2

What do you mean "I have a file that looks like the below and only need certain lines"? You have shown us same input that is a single line. And the output you want is also a single (although shorter) line.

Are you saying that some lines don't contain one or both of @HD and @RG and that you want to eliminate those lines?

You said: "It is basically everything from the @HD up to the @RG.", but you didn't keep the space(s) before the %RG that were present in your input.

Please given us a clearer description of what you are trying to do and show us what you have tried.

What operating system and shell are you using?

3

Hi cmccabe,

Don is absolutely right.
However, you can try this if it helps

 sed -n 's/^\(@HD.*\)@RG.*/\1/p' file.txt
4

It depends on the split point. What is the rule you want to use?

  • Line length (truncate)
  • Number of fields
  • Specific delimiter - single character or string
  • Multiple delimiters e.g. after the 10th @
  • Something else :confused:

If you can explain how you want to work with the data, then we can work something out, but a single line input doesn't give us the rule clearly.

Thanks, in advance,
Robin