Shell Programming and Scripting

$i=0;
while (<>){
 chomp;
 if (/\+*End of summary for file/ ){
    $f=0;close(FH);next;
 }    
 if (/Taxonomy:/ ) { 
     open(FH,">>","output_".$i++) or die "Cannot open for writing:$!\n";
     $f=1; next;
 }
 if ($f) { 
    s/^\s+//g; #get rid of spaces in front
    print FH $_."\n";
  }
}

# perl myscript.pl file

open $fh,"<","a.txt";
my ($flag,$n)=(0,0);
while(<$fh>){
	if(/Taxonomy:/){
		$n++;
		$file=sprintf("outfile%s.txt",$n);
		open FH,"+>$file";
		$flag=1;
		next;
	}
	if(/\++/){
		$flag=0;
		next;
	}
	print FH $_ if $flag==1;
}

#!/usr/bin/perl -w

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

$name=shift;

$inputfile="`pwd`/$name";

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);
  }}' inputfile;

#!/usr/bin/perl -w

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

$name=shift;

$inputfile="`pwd`/$name";

open $fh,"<", $inputfile;
my ($flag,$n)=(0,0);
while(<$fh>){
	if(/Taxonomy:/){
		$n++;
		$file=sprintf("outfile%s.txt",$n);
		open FH,"+>$file";
		$flag=1;
		next;
	}
	if(/\++/){
		$flag=0;
		next;
	}
	print FH $_ if $flag==1;
}

  Gammaproteobacteria: 2767
        Alphaproteobacteria: 4123
          Deltaproteobacteria: 1343
          Epsilonproteobacteria: 26
        Betaproteobacteria: 397
        unclassified Proteobacteria: 48
          Elusimicrobium: 2
        candidate division WWE1: 9
          Flavobacteria: 2358
          Sphingobacteria: 136
          Bacteroidia: 162
          environmental samples: 21
          Chlorobia: 77
        Planctomycetacia: 40
        Spirochaetes (class): 15
        Nitrospira (class): 1
        Bacilli: 25
  Not assigned: 1445
  No hits: 220253

#!/usr/bin/perl -w

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

$i=1;
while (<>){
chomp;
   
 if (/Taxonomy:/ ) { 
     $x = $1; $x =~ s/^\s+|\s+$//g;
     open(OUT,">>","output_".$i++) or die "Cannot open for writing:$!\n";
     $f=1; next;
 }
 
 if (/\+*End of summary for file/ ){
    $f=0;close(OUT);next;
 }
 if ($f) { print OUT $_."\n";}
}

awk '{$1=$1}1' file