UNIX for Dummies Questions & Answers

Hi all,

I need to extract lines between the lines 'RD' and 'QA' from a text file (following). there are more that one of such pattern in the file and I need to extract all of them. however, the number of lines between them is varied in the file. Therefore, I can not just use 'grep -A' command. Any suggestion would be appreciated.

Many thanks

---------------------------------------------------------
........
RD FTLH3RB02II3DW 333 0 0
GG**A***AC*AC*ACACACACAC*ACACACACACATGCTTGCACACAAT
CT*GAAATCTTCACTAA*TCTTTATCTTAAATC*AGTT*GGA*T*GTAGA
CAGACACCTGAG*TCATTTAGTCTAATGATGGC*GT*CCCTCACTC*AGG
GCAAGAAATGCTTTCCTCCA*T*GG*A*GAGGTT*AC*AG*TC*TGTT*G
*CC*TCAA*C*TCC*TGTCAGCCTCCAGCTGCTGACA*GG*A**T*CCTG
T*GCCC*TCTC*TT*GT*AGGATGGAGA*GA*TGT*GGTCCTCTATCAAT
TGTACCATCTGTGCTTGTGTGAAAGGCAGG*AC

QA 1 333 1 333
DS CHROMAT_FILE: none PHD_FILE: none TIME: Mon Jan 01 00:00:00 000
........
--------------------------------------------------

try this:

Code:

sed -n '/^RD/,/^QA/p' filename | grep -v -e '^RD' -e '^QA' > newfile

The grep bit is because you did not want the QA and RD lines. There are other more terse ways to do this with awk, but they would be hard for non-awk people to generalize to other solutions. IMO.

Just easy as the sed commands

Including the RD and QA lines:

Code:

awk '/^RD/{p=1}/^QA/{p=0;print}p' file

Without the RD and QA lines:

Code:

awk '/^RD/{p=1;next}/^QA/{p=0}p' file

See? That's what I meant. Great code Franklin! I love it.

I love awk, too, but I don't think a DNA researcher is going to going to fall in love with awk's implied and somewhat arecane logic like the trailing {....}p trick.
I think its neat, too, but the OP probably probably doesn't. And cannot maintain it, either, which is the whole point.

if i want these two in run time input

Code:

#!/bin/sh
file=~/test/imm_del.txt
read -p "provide your first input" read1
read -p "provide your 2nd input" read2
awk -v var1="$read1" -v var2="$read2" "/^var1/{p=1}/^var2/{p=0;print }p" $file

But it not working

With awk variables it should be like:

Code:

#!/bin/sh

file=~/test/imm_del.txt
read -p "provide your first input" read1
read -p "provide your 2nd input" read2

awk -v var1="$read1" -v var2="$read2" '$1==var1{p=1}$1==var2{p=0;print}p' $file

Thank both of you, Jim and Franklin, very much. You are so kind.