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How to grep B file according to A file?

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# 1  
Old 07-09-2013
How to grep B file according to A file?
Hi, i have two files: A.txt and B.txt. How can i get C.txt from B.txt according to A.txt?

Here are two examples of A.txt and B.txt:

A.txt
Code:
Contig1
Contig3
ESVER1N
ESVER1M

B.txt
Code:
>Contig1
ATTTTAGACTACATTTTAAGGCCGACT

>Contig2
GATCCCCAAATACCCAAAAGGGTTTTCCCCAAATATAATAT

>Conitg3
GATCAGCATGGGGACCCCTTTAA

>ESVER1L
ATTTATTGCCCCGGGTTTACT

>Contig8
AATCGTACCGGAC

>ESVER1N length=1 description
GATGGGGGCCCTACTTTTAAACC

>ESVER1M
TCCCCAAAGGGGCCCTTTTATAGGGATTCAT

C.txt
Code:
>Contig1
ATTTTAGACTACATTTTAAGGCCGACT

>Conitg3
GATCAGCATGGGGACCCCTTTAA

>ESVER1N length=1 description
GATGGGGGCCCTACTTTTAAACC

>ESVER1M
TCCCCAAAGGGGCCCTTTTATAGGGATTCAT

Thanks!!
Last edited by Scott; 07-09-2013 at 08:32 PM.. Reason: Use code tags, please...
# 2  
Old 07-09-2013
Code:
$ grep -A1 -f A.txt B.txt
>Contig1
ATTTTAGACTACATTTTAAGGCCGACT
--
>Contig3
GATCAGCATGGGGACCCCTTTAA
--
>ESVER1N length=1 description
GATGGGGGCCCTACTTTTAAACC
--
>ESVER1M
TCCCCAAAGGGGCCCTTTTATAGGGATTCAT

This assumes only one line follows the matched item in B.txt.

If your grep doesn't support -A, a similar thing can be done in AWK.
# 3  
Old 07-09-2013
Thanks.
However, there are more than one line follows the matched item in B.txt, and the line numbers are different.

Quote:
Originally Posted by Scott
Code:
$ grep -A1 -f A.txt B.txt
>Contig1
ATTTTAGACTACATTTTAAGGCCGACT
--
>Contig3
GATCAGCATGGGGACCCCTTTAA
--
>ESVER1N length=1 description
GATGGGGGCCCTACTTTTAAACC
--
>ESVER1M
TCCCCAAAGGGGCCCTTTTATAGGGATTCAT

This assumes only one line follows the matched item in B.txt.

If your grep doesn't support -A, a similar thing can be done in AWK.
# 4  
Old 07-09-2013
That grep was rubbish, anyway!

Code:
$ awk 'NR==FNR {
  A[">"$1]=">"$1
  next
}

A[$1] {
  print
  while( $1 && getline !=0 )
    print
}' A.txt B.txt                       
>Contig1
ATTTTAGACTACATTTTAAGGCCGACT

>Contig3
GATCAGCATGGGGACCCCTTTAA
SOME BLAH
MORE BLAH

>ESVER1N
GATGGGGGCCCTACTTTTAAACC
BLAH
BLAH
BLAH

>ESVER1M
TCCCCAAAGGGGCCCTTTTATAGGGATTCAT

Use /usr/xpg4/bin/awk or nawk on Solaris.
# 5  
Old 07-09-2013
Thanks,Scott,

It works perfectly.



Quote:
Originally Posted by Scott
That grep was rubbish, anyway!

Code:
$ awk 'NR==FNR {
  A[">"$1]=">"$1
  next
}

A[$1] {
  print
  while( $1 && getline !=0 )
    print
}' A.txt B.txt                       
>Contig1
ATTTTAGACTACATTTTAAGGCCGACT

>Contig3
GATCAGCATGGGGACCCCTTTAA
SOME BLAH
MORE BLAH

>ESVER1N
GATGGGGGCCCTACTTTTAAACC
BLAH
BLAH
BLAH

>ESVER1M
TCCCCAAAGGGGCCCTTTTATAGGGATTCAT

Use /usr/xpg4/bin/awk or nawk on Solaris.
# 6  
Old 07-09-2013
Better
Code:
while ( NF && getline !=0 )

that continues if $1 is 0.
Further little improvements:
A[">"$1]=1 is sufficient for the test A[$1]
and
A[">"$1](no value) for the smart test ($1 in A)
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