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up vote 1 down vote favorite

I am trying to write a bash script. In a directory I have 2 fastq files:

A-122-3.BH7WBVADXX.lane_1_P1_I24.hg19.sequence.fastq

A-122-3.BH7WBVADXX.lane_1_P2_I24.hg19.sequence.fastq

I just want to loop on P1 lets say something like this 

for f in *_P1*
do
   SOMETHING
done

Now In SOMETHING part I want to define some varables which i would be using later in my code I need to extract these values from my string: A-122-3.BH7WBVADXX.lane_1_P1_I24.hg19.sequence.fastq

I need ID = A-122-3-BH7WBVADXX-1

I need PU = BH7WBVADXX

I need LB = A-122-3

Then I will solve it further.

NOTE : FILENAME ARE NOT OF SAME LENGTH. A-122-3 PART VARIES FOR DIFFERENT SAMPLES AND ALSO THIS PART I24 VARIES. Thanks

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1 Answer 1

up vote 2 down vote accepted

Assuming that each filename you are processing has the same length and that each substring has the same length, you can split based on this. Also, sure where the -1 part on the ID comes from, so I assume you get it from lane_1.

for file in *_P1*
do
  id=${file:0:18}-${file:24:1}
  pu=${file:8:10}
  lb=${file:0:7}

  echo "id=$id pu=$pu lb=$lb"
done

Update

This should work provided certain dots and underscores remain consistent:

for file in *_P1*
do
  lb=${file%%.*}

  pu=${file%%.lane_*}
  pu=${pu#*.}

  num=${file%%_P*}
  num=${num##*_}

  id="$lb-$pu-$num"

  echo "id=$id pu=$pu lb=$lb"
done
share|improve this answer
    
Hi, I am afraid but each filename does not have same length. I should have mentioned that before. Fixing. You are correct, 1 comes from lane_1 –  user3138373 Apr 8 '14 at 20:48
1  
@user3138373, updated. –  Graeme Apr 8 '14 at 21:13

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