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Please help to write a executable script for extracting some parts of a file

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Top Forums Shell Programming and Scripting Please help to write a executable script for extracting some parts of a file
# 8  
Old 05-13-2009
Quote:
Originally Posted by iammitra

Code:
#!/usr/bin/perl -w

$#ARGV==0 or die "Usage: 2ndprocess-script 1st-output-file-as-inputfile\n";

$input=shift;

perl -ne '{$/=""; $i=1;
while (/^Taxonomy:.(.*?)\+{11}/msgi) {
$x = $1; $x =~ s/(^|\n)\s+/$1/g;
open(OUT,">outfile".$i++.".txt"); print OUT $x; close(OUT);
}}' $1; ## it should be $ARGV[0] or $input

and rather than creating perl script wrapper create shell script and put that perl command in it.

here is my perl code ...

Code:
#! env perl
$/ ="" ;
my $i = 1 ; 
my $file = $ARGV[0] ;

open(READ,"<$file") or die "can not open file $! \n" ;
open(WRITE,">${file}.out") or die "can not open file for writing : $!\n" ;
while(<READ>)
{
    chomp ; 
    if ( ^Taxonomy:.(.*?)\+{11}/msgi )
    {
         $x = $1; 
         $x =~ s/(^|\n)\s+/\1/g;
         $i++ ;
         print WRITE "$i\t$x\n" ;
    } 
}
close READ ; 
close WRITE ;

try if it works ...
Last edited by zedex; 05-13-2009 at 09:36 AM.. Reason: changed \1 to $1
# 9  
Old 05-13-2009
Another approach in awk (can write it in one line too of course):
Code:
awk '
     /^Taxonomy:/ {z++}
     /^Taxonomy:/,/\++End/ { if( $0 !~ /^Taxonomy:/ && $0 !~ /\++End/) {sub(/^[[:space:]]*/,""); print > "outfile"z} }
' z=0 infile


$> cat outfile1
Gammaproteobacteria: 2767
Alphaproteobacteria: 4123
Deltaproteobacteria: 1343
Epsilonproteobacteria: 26
Betaproteobacteria: 397
unclassified Proteobacteria: 48
Spirochaetes (class): 15
Nitrospira (class): 1
Bacilli: 25
Not assigned: 1445
No hits: 220253

$> cat outfile2
Gammaproteobacteria: 2809
Alphaproteobacteria: 4001
Deltaproteobacteria: 1208
Epsilonproteobacteria: 15
Not assigned: 299
No hits: 461890

# 10  
Old 05-13-2009
Thank you very much...
It works.. Smilie
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