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I want to edit a file called trial.fastq with the following format:

@NAME123.15.1 15 length=151
GTAGCNTACGGGAGGCAGCAGTGGGGAATTTTCC
+NAME123.15.1 15 length=151
AAABB#>>AABDGCEGGGFGGGHHHGGGFHHGHH
@NAME123.14.1 14 length=150
TTCGCNTACGGGAGGCAGCAGTAGGGAATCTTCC
+NAME123.14.1 14 length=150
ABBBB#>>ABBBGGGGGEGGGGHDGFFFHHGHHH

I want to change the format to this:

@Inst:1:FID:LANE:TILE:15:Y 1:Y:0:NAME123
+GTAGCNTACGGGAGGCAGCAGTGGGGAATTTTCC
@Inst:1:FID:LANE:TILE:14:Y 1:Y:0:NAME123
+TTCGCNTACGGGAGGCAGCAGTAGGGAATCTTCC

I've tried many formats of sed including:

sed -i -E 's/@(\w+).(\d+).(\d)\s\d+\slength=\d+\n.*/@Inst:1:FID:LANE:TILE:\2:Y \3:Y:0:\1\n/g' trial.fastq > trial_new.fastq

which I found from copying my TextWrangler find and replace grep search. As well as:

sed -e 's/\(@\w\).\(\d..+\).\(\d\)\s\d..*\slength\=\d..*\n.*$(\w..*)\(.*\)$\+.*$.*$/@Inst\:1\:FID\:LANE\:TILE\:\2\:Y \3\:Y\:0\:\1\n\4/g' trial.fastq

I am pretty sure I am going about this the wrong way. Can someone help me understand what I'm doing wrong and how to fix this problem?

  • Note that depending on your sed flavor \d is not a digit. That's a typical pitfall for people used to regexp in other tools – Philippos Mar 7 '17 at 21:40
0

I hope I understood you desired output correctly!

$ sed -nr '/#/d;s/@([^\.]+)[^ ]+ ([0-9]+) .*/@Inst:1:FID:LANE:TILE:\2:Y 1:Y:0:\1/p;s/^[A-Z]/\+&/p' file
@Inst:1:FID:LANE:TILE:15:Y 1:Y:0:NAME123
+GTAGCNTACGGGAGGCAGCAGTGGGGAATTTTCC
@Inst:1:FID:LANE:TILE:14:Y 1:Y:0:NAME123
+TTCGCNTACGGGAGGCAGCAGTAGGGAATCTTCC

Explanation

  • -n don't print until we ask for it
  • -r use ERE
  • /#/d delete lines with #
  • ([^\.]+) save some characters that are not.` for later
  • [^ ]+ ([0-9]+) .* save some numbers between spaces
  • \1 backreference to saved pattern in replacement
  • ; separates commands, like in the shell
  • s/^[A-Z]/\+&/ replace lines that start with a capital letter with themselves prefixed with +
  • p print the lines we worked on

Use the -i flag if you want to edit the file in place, after testing the output is what you want (repeat the command with sed -nri ....)

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