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I have a text file which looks like this(I am showing few lines of it)

INDEX : 1
snRNA_seq:TTTTGGAGCAGGGAGATGGAAT

miRNA_seq:CTCCTGACTCCAGGTCCTGTGT

target: RNU2-1,RNU2-64P,RNU2-37P,RNU2-61P,RNU2-68P,RNU2-26P,RNU2-57P,RNU2-59P
length: 22
miRNA: hsa-miR-378a-5p*MI0000786
length: 22


mfe: -21.3 kcal/mol

p-value: 0.015469



position  1

target 5'        U             A 3'

                  UUUGGAG CAGGG    

                  GGACCUC GUCCU    

miRNA  3' UGUGUCCU       A     C 5'





INDEX : 10
snRNA_seq:TTGGAGCAGGGAGATGGAAT

miRNA_seq:ATCCTCTCTTCCCTCCTCCCAG

target: RNU2-1,RNU2-64P,RNU2-37P,RNU2-61P,RNU2-68P,RNU2-26P,RNU2-57P,RNU2-59P
length: 20
miRNA: hsa-miR-7111-3p*MI0022962
length: 22


mfe: -24.0 kcal/mol

p-value: 0.001695



position  2

target 5'   U    C        U    A 3'

             GGAG AGGG AGA  GGA    

             CCUC UCCC UCU  CCU    

miRNA  3' GAC    C    U   CU   A 5'

I have list of identifiers namely 1,10,20,30 etc This identifier in the above file is right next to INDEX part. All I want to do is if the identifier matches the above file print that line + next 28 lines basically some thing like this grep -A 28 "INDEX : identifier"

How can i do this in shell??

Regards

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  • grep -A 28 "INDEX : identifier" is exactly how you would do this in a shell script. Is this what you are asking? Commented Feb 25, 2015 at 18:41
  • Yes that is exactly what i want Commented Feb 25, 2015 at 19:03

3 Answers 3

1

When you have fixed entries for the identifiers you like, you can use

for identifier in 1 10 20 30; do
   grep -A 28 "INDEX : ${identifier}$" Test.txt
done

When you do not have fixed identifiers, you might grep without specifying the identifier:

grep -A 28 "^INDEX : " Test.txt

I use ^ here for matching INDEX lines at the beginning of the line.

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  • I have Identifiers like 1,2,3,4,5,10,100 No they are arranged in the input file as 1,10,100,101 Since grep goes line by line I am purposely using this for i in 1 10;do grep -A 28 "INDEX : ${i}" done It gives me 101 102 103 104 etc why so?? Let's say I want 1 and 2 How will I get that?? Commented Feb 25, 2015 at 19:09
  • I added an end-of-line character $. Without the dollar grep will find INDEX : 1 as a substring of INDEX : 101
    – Walter A
    Commented Feb 25, 2015 at 19:16
  • for identifier in 1 2; do grep -A 28 "INDEX : ${identifier}$" done < Test.txt Does not give INDEX : 2 output Why so??? Commented Feb 25, 2015 at 19:21
  • See edited answer: Test.txt should be inside the loop, so each call to grep in the loop will know where to grep.
    – Walter A
    Commented Feb 25, 2015 at 19:42
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You could use grep with -f:

   -f FILE, --file=FILE
          Obtain patterns from FILE, one per line.

but for that you need to format your identifiers file accordingly, e.g. it should read:

INDEX : 1
INDEX : 10
..........
INDEX : 100

instead of:

1,10....100

If you use - as FILE grep will read patterns from stdin so, one way, with awk (and also using grep with -x to match the whole line):

awk -F, '{for (i=1; i<=NF; i++) print "INDEX : "$i}' identifiers | grep -A28 -x -f - file

Unless you want to use your favorite tool to edit identifiers in place and then run:

grep -A28 -x -f identifiers file
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  • I undeleted this (and a couple of other As you deleted) because they provide useful information. One of them was also the only answer on the Q so deleting it sets the Q as unanswered. If you really, really want to, you can delete them again but I would much prefer you leave them.
    – terdon
    Commented Mar 30, 2015 at 12:09
  • Sure, flag away. The thing is that consecutive question deletions raises an automatic flag (to protect against rage quitting I guess). That's why I noticed. As for ignoring, no. Unfortunately.
    – terdon
    Commented Mar 30, 2015 at 16:51
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If you want to avoid a multi-pass through your data with a fixed subset of IDs given, this is one possible way (for sample indexes 1, 2, 10):

sed -n '/INDEX : \(1\|2\|10\)$/,+28p'

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