Shell Programming and Scripting

I tried the same script on a little modified file where headre line is
>LOC_Os01g57570.1|12001.m11908|protein minor allergen Alt a 7, putative, [expressed]
MAVKVYVVYYSMYGHVAKLAEEIKKGASSIEGVEAKIWQVPETLHEEVLGKMGAPPKPDV
PTITPQELTEADGILFGFP

in place of

>LOC575
MAVKVYVVYYSMYGHVAKLAEEIKKGASSIEGVEAKIWQVPETLHEEVLGKMGAPPKPDV
PTITPQELTEADGILFGFP

script is not working on ths.. can you please help me out??

Thanks
Smriti

What is the contents of FILE2 ?

Hi aigles,

here are the file details -

===FILE1===
>LOC_Os01g57570.1|12001.m11908|protein minor allergen Alt a 7, [expressed]
MAVKVYVVYYSMYGHVAKLAEEIKKGASSIEGVEAKIWQVPETLHEEVLGKMGAPPKPDV
PTITPQELTEADGILFGFP
>LOC_Os01g57640.1|12001.m11908|protein lectin 7, (putative), expressed
MAVKVYVVYYSMYGHVAKLAEEIKKGASSIEGVEAKIWQVPETLHEEVLGKMGAPPKPDV
PTITPQELTEADGILFGFPTRFGMMAAQMKAFFDATGGLWSEQSLAGKPAGIFFS
>LOC_Os01g57000.2|12001.m43222|protein minor allergen Alt a 7
MAVKVYVVYYSMYGHVAKLAEEIKKGASSIEGVEAKIWQVPETLHEEVLGKMGAPPKPDV
PTITPQELTEADGILFGFPTRFGMMAAQMKAFFDATGGLWSEQSL

====FILE2====
LOC_Os01g57570
LOC_Os01g57000

and ths LOC can be any three letters such as ABC or GNL but they will be same in every header (line with a '>' symbol)

Thanks
smriti

If the first character '.' in records of FILE1 can act as a field separator :

Code:

awk -F. '
NR==FNR { keys[">" $1]++ ; next }
/^>/    { selected = ($1 in keys) }
selected
' FILE2 FILE1

If it is not the case, if all values in FILE2 have the same length :

Code:

awk '
NR==1   { key_length = length($1)+1 }
NR==FNR { keys[">" $1]++ ; next }
/^>/    { selected = (substr($0, 1, key_length) in keys) }
selected
' FILE2 FILE1

Otherwise :

Code:

awk '
NR==FNR { keys[">" $1] = length($1)+1 ; next }
/^>/    {
   selected = 0;
   for (k in keys) {
      if (substr($0,1,keys[k]) == k) {
         selected = 1;
         break;
      }
   }
}
selected
' FILE2 FILE1

Jean-Pierre.

The code is running perfect. Thanks a lot.

smriti