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extracting lines from a file1 which maches a pattern in file2

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# 1  
Old 07-29-2008
extracting lines from a file1 which maches a pattern in file2
Hi guys,
Can you help me in solving ths problem?
I have two files file1 and file2 as following:
===FILE1====
>LOC21
MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
>LOC05
MASSKFSTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
GRAFYSAPIQIWDSTTGKVASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
AKVLITYDSSTKLLVASLVYPSGS
>LOC48
MASLQTQMISFYAIFLSILLTTILFFKVNSTGEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVK

====FILE2====
LOC21
LOC48

I want to write the complete record form FILE1 (which starts from '>' sign) which matches the pattern in FILE2 into a new file FILE3 which shold look like -
>LOC21
MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
>LOC48
MASLQTQMISFYAIFLSILLTTILFFKVNSTGEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVK


your help is highly appretiated Smilie

Thanks
Last edited by smriti_shridhar; 07-29-2008 at 04:30 AM.. Reason: to make it more informative
# 2  
Old 07-29-2008
Try this awk program :
Code:
awk '
NR==FNR { keys[">" $1]++ ; next }
/^>/    { selected = ($1 in keys) }
selected
' FILE2 FILE1

Jean-Pierre.
# 3  
Old 07-29-2008
I could get 'aigles' code to work on my cygwin

Anyway, this is my version:
Code:
#! /bin/sh

if [ $# -ne 2 ]; then
        echo "Usage: $0 <file1> <file2>"
        exit 1
fi

awk -v f2=$2 '
BEGIN {
        ok=0
        count=1
        while ( getline < f2 ) {
                file2[count]=sprintf(">%s",$0)
                ++count
        }
}
/^>LOC/ {
        for (i=1;i<count;++i) {
                if ($0 == file2[i]) {
                        print $0
                        ok=1
                        next
                }
        }
        ok=0
}
ok==1 {
        print
}' $1

Run it
Code:
$ ./file.sh file1 file2
>LOC21
MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
>LOC48
MASLQTQMISFYAIFLSILLTTILFFKVNSTGEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVK

Last edited by chihung; 07-29-2008 at 07:03 AM..
# 4  
Old 07-30-2008
thanks!
Thanks Jean-Pierre..

I tried to run ur code but it didn't produce any output or error.

smriti.
# 5  
Old 07-30-2008
Thanks! chihung but
Thanks for your help.. the code is running perfect but i hv one more problem.

actually the line begining with '>' contain other words also and i have different files in which LOC can be smthn els like ABC or GNL but the first three letters after '>' will be same. I solved that by replacing the line
/^>LOC/ {
with
/^>/ {

my file is like this..
>LOC21 ths is a seq of protein bla-bla-bla
MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP

so whn i tried it on my actual file it could't work as far as i understood words with spaces in header line(begining with '>') is causing a trouble.

I will be thankful if you can help me to solve this out.

cheers!
Smilie
smriti
# 6  
Old 07-30-2008
Quote:
Originally Posted by smriti_shridhar
Thanks Jean-Pierre..

I tried to run ur code but it didn't produce any output or error.

smriti.
The script works fine on my box with your example data files.
Code:
> cat -n smriti1.dat
     1  >LOC21
     2  MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
     3  VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
     4  >LOC05
     5  MASSKFSTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
     6  GRAFYSAPIQIWDSTTGKVASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
     7  AKVLITYDSSTKLLVASLVYPSGS
     8  >LOC48
     9  MASLQTQMISFYAIFLSILLTTILFFKVNSTGEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVK
> cat -n smriti2.dat
     1  LOC21
     2  LOC48
> cat -n smriti.sh
     1  awk '
     2  NR==FNR { keys[">" $1]++ ; next }
     3  /^>/    { selected = ($1 in keys) }
     4  selected
     5  ' smriti2.dat smriti1.dat
     6
> smriti.sh
>LOC21
MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
>LOC48
MASLQTQMISFYAIFLSILLTTILFFKVNSTGEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVK
>

Beware, the order for input files is FILE2 FILE1.
if you specify FILE1 FILE2, the script doesn't product any result.


Jean-Pierre.
# 7  
Old 07-30-2008
Thanks a lot!
Hi aigles,

Its working now although I hd put the order of files correctly before as well.

Actually i tried to run it as single line on command line. I think it shudn't make any
difference.
But anyways its working fine nw and it solved my other problem also as it works even if my header line (the one begining with '>' ) contain more words.

Thanks Jean Smilie
smriti
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