root221 [~/gcg]>ls
a28086.pep         gdec.pep           gdpg.blastp        glut28.strings
gcgtest.pl         gdec.pepsort       gdpg.fasta         orf15.pep
gdec.bestfit       gdec.pir1          gdpg.gap           test.list
gdec.coilscan      gdec.seg           gdpg.netblastp     test5.pep
gdec.gap           gdec.spscan        gi-79882.pep       tests.pep
gdec.hmmerpfam     gdec.tfa           glut104.strings    txec.motifs
gdec.hthscan       gdechwheel.png     glut27.msf
gdec.motifs        gdecp2s.png        glut27.strings
gdec.p2s           gdpg.bestfit       glut27pileup.png
root222 [~/gcg]>ls *.composition
ls: No match.
root223 [~/gcg]>more gcgtest.pl
#!/opt/local/bin/perl -w

#program to run gcg modules

# gcg is assumed to be initialized

$testfile = "tests.pep";

$output = `fromfasta $testfile`;  #run fromfasta gcg command
@lines = split (/\n/, $output);

# create a gcg format .list file

$newlines[0]="!!";
$count = 1;

foreach $i (@lines)
  { if ($i =~/.pep/)
    { $newlines[$count] = $i; $count ++;
    }
  }

$filename = "test.list";

#open file and associate it with a "filehandle"
open (LISTFILE, ">$filename");

foreach $i (@newlines)
  { print LISTFILE $i,"\n";
  }

close (LISTFILE);

#run the composition gcg module for each protein

foreach $i (@newlines)
 { if ($i ne "!!") 
      {$index = index ($i, ".pep") + 4;
       $pepname = substr ($i, 0, $index);
       $output = `composition $pepname -Default `;
       print $output;
      }
 }
exit;

root224 [~/gcg]>perl gcgtest.pl
root225 [~/gcg]>ls *.composition
a28086.composition     gi-79882.composition   orf15.composition
root226 [~/gcg]>ls *.list
test.list
root227 [~/gcg]>more test.list
!!
 a28086.pep  104 aa.
 gi-79882.pep  161 aa.
 orf15.pep  485 aa.
root228 [~/gcg]>more a28086.composition
 (Peptide) COMPOSITION of: a28086.pep  Check: 7776  from: 1  to: 104

 October 8, 2002 11:26

                            *****
 
     A: 8            C: 5            D: 7            E: 10           
     F: 10           G: 5            H: 1            I: 5            
     K: 13           L: 6            M: 2            N: 4            
     P: 3            Q: 4            S: 6            T: 3            
     V: 11           W: 1            
 
                          Other: 0
 
                          Total: 104
 
                            *****
                            *****
                            *****
root229 [~/gcg]>