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How to grep paragraph?

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# 1  
Old 08-28-2013
How to grep paragraph?
Hi, I have A file like this:

Code:
>Contig1
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEATATATAT
>Contig2
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTCCCA
ATCCCAAATATATAT
>Contig3
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTCCCA
ATCCCAAATAAATTTTTTCCCAATAT
ATGATATATATAEAATTTTTAATTTTT
TCCCAATCCCAAATATATATATATAT
AATATATATA
>contig1 length=130 dkfldf
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTC
>contig2 length=500 ldjfdlfjfdls
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTCCCA
ATCCCAAATAAATTTTTTCCCAATAT
ATGATATATATAEAATTTTTAATTTTT
TCCCAATCCCAAATATATATATATAT
AATATATATA
....

If i have B file like this:
Code:
Contig2
Contig3
contig2
....

How could i get a C file like this:
Code:
>Contig2
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTCCCA
ATCCCAAATATATAT
>Contig3
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTCCCA
ATCCCAAATAAATTTTTTCCCAATAT
ATGATATATATAEAATTTTTAATTTTT
TCCCAATCCCAAATATATATATATAT
AATATATATA
>contig2 length=500 ldjfdlfjfdls
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTCCCA
ATCCCAAATAAATTTTTTCCCAATAT
ATGATATATATAEAATTTTTAATTTTT
TCCCAATCCCAAATATATATATATAT
AATATATATA

Thanks!!!

Moderator's Comments:
Mod Comment Use code tags please, see PM.
Last edited by zaxxon; 08-28-2013 at 11:21 AM.. Reason: code tags
# 2  
Old 08-28-2013
Code:
awk 'END {
  if (substr(f, 2) in idx)
    print r
  }
NR == FNR {
  idx[$0]; next
  }
/^>/ {
  if (length(r)) {
    if (substr(f, 2) in idx)
      print r
    r = x; f = $1      
    }
  }  
{
  r = r ? r ORS $0 : $0
  }' file_b file_a

# 3  
Old 08-29-2013
Thanks, but it seems not work.


Quote:
Originally Posted by radoulov
Code:
awk 'END {
  if (substr(f, 2) in idx)
    print r
  }
NR == FNR {
  idx[$0]; next
  }
/^>/ {
  if (length(r)) {
    if (substr(f, 2) in idx)
      print r
    r = x; f = $1      
    }
  }  
{
  r = r ? r ORS $0 : $0
  }' file_b file_a

# 4  
Old 08-29-2013
You're welcome! Could you be more specific? Do you get wrong output? No output at all?
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