2012-03-05_15_30_01_01_00 :: 0 :: M => 1

bin/fastaCut.pl

@@ -11,7 +11,7 @@ my $finish = $ARGV[3];
 my $name   = $ARGV[4];
 
 
-my $verbose = 1;
+my $verbose = 0;
 die "NO INPUT FASTA"        if ! defined $fasta;
 die "INPUT FASTA $fasta DOES NOT EXISTS" if ! -f $fasta;
 die "INPUT FASTA $fasta IS EMPTY"        if ! -s $fasta;
@@ -21,7 +21,15 @@ die "NO FINISH DEFINED"     if ! defined $finish;
 die "NO NAME DEFINED"       if ! defined $name;
 
 die "START $start NOT NUMERIC" if $start  !~ /^\d+$/;
-die "END $finish NOT NUMERIC"     if $finish !~ /^\d+$/;
+die "END $finish NOT NUMERIC"  if $finish !~ /^\d+$/;
+
+print STDERR "
+    INFASTA '$fasta'
+    CHR     '$chrom'
+    START   '$start'
+    FINISH  '$finish'
+    NAME    '$name'
+";
 
 my $gene = &readFasta($fasta, $chrom, $start, $finish, $name);
 #&returner($gene, $start, $end, $name);
@@ -40,22 +48,6 @@ my $gene = &readFasta($fasta, $chrom, $start, $finish, $name);
 # ./cut.pl WM276GBFF10_06.fasta CP000298_CGB_M1520C_Translation_elongation_factor_EF1_alpha__putative_323075_324730 673 1371 tef1 > tef1.276.txt
 
 
-sub returner
-{
-    my $gene  = $_[0];
-    my $start = $_[1];
-    my $end   = $_[2];
-    my $name  = $_[3];
-
-    #$start = $start - 500;
-    #$end   = $end   + 500;
-
-    print ">$fasta\_$chrom\_$start\_$end\_$name\n";
-
-    print join("", @$gene[($start-1) .. $end]);
-}
-
-
 
 sub readFasta
 {
@@ -88,7 +80,7 @@ sub readFasta
     while (<FILE>)
     {
             chomp;
-            if (( /^>/) && ($on))
+            if (( /^\>/) && ($on))
             {
                 $on   = 0;
             }
@@ -105,27 +97,27 @@ sub readFasta
                 my $cut2   = -1;
                 if ( ! $seq && $seqBeg <= $begin && $seqEnd >= $begin) {
                     $cut1 = $begin - $seqBeg;
-                    printf "subtracting CUT1 %3d - %3d = %d\n", $seqBeg, $begin, $cut1 if $verbose;
+                    printf STDERR "subtracting CUT1 %3d - %3d = %d\n", $seqBeg, $begin, $cut1 if $verbose;
                 }
 
                 if ( $end >= $seqBeg && $seqEnd >= $end ) {
                     $cut2 = $end - $seqBeg + 1;
-                    printf "subtracting CUT2 %3d - %3d = %d\n", $end, $seqBeg, $cut2 if $verbose;
+                    printf STDERR "subtracting CUT2 %3d - %3d = %d\n", $end, $seqBeg, $cut2 if $verbose;
                 }
 
-                printf "LINE %80s LENGTH %2d POS %5d END POS %5d CUT1 %3d CUT2 %3d ", $_, $seqLen, $seqBeg, $seqEnd, $cut1, $cut2 if $verbose;
+                printf STDERR "LINE %80s LENGTH %2d POS %5d END POS %5d CUT1 %3d CUT2 %3d ", $_, $seqLen, $seqBeg, $seqEnd, $cut1, $cut2 if $verbose;
                 if    ( $cut1 != -1 && $cut2 == -1 ) { if ($verbose) { printf "T1 %3d - %3d ", $cut1, $seqEnd                   } ; $_ = substr( $_, $cut1                       )  } # get from end
                 elsif ( $cut1 == -1 && $cut2 != -1 ) { if ($verbose) { printf "T2   0 - %3d ", $cut2                            } ; $_ = substr( $_, 0          ,  $cut2         )  } # get from begining 
                 elsif ( $cut1 != -1 && $cut2 != -1 ) { if ($verbose) { printf "T3 %3d - %3d ", $cut1, ( $cut2 - $cut1 )         } ; $_ = substr( $_, $cut1, ($cut2 - $cut1)      )  } # indside
-                else                                 { if ($verbose) { print  "T4 ALL "                                                 } ;                                                           } # all
+                else                                 { if ($verbose) { print  "T4 ALL "                                         } ;                                                 } # all
 
-                if    ( $seqBeg < $begin && $seqEnd < $begin ) { if ($verbose) { print " NEXTING ($seqBeg < $seqEnd < $begin)\n"; } next };
+                if    ( $seqBeg < $begin && $seqEnd < $begin ) { if ($verbose) { print STDERR " NEXTING ($seqBeg < $seqEnd < $begin)\n"; } next };
 
                 if ( ! defined $_ ) {
                     die "NO LINE\n";
                 }
                 $seq .= $_;
-                print "$_\n" if ($verbose);
+                print STDERR "$_\n" if $verbose;
 
                 last if $seqEnd >= $end;
                 #push(@gene, split("",$_));
@@ -137,7 +129,7 @@ sub readFasta
                 #}
             }
     
-            if (/^>$chrom/)
+            if (/^\>$chrom/)
             {
                #print ">$chrom\n";
                 $on         = 1;
@@ -145,18 +137,18 @@ sub readFasta
     }
     print "$begin $seq $end (" , length($seq), "/",($end - $begin + 1),")\n" if ($verbose);
     if ( length($seq) != ($end - $begin + 1) ) {
-        print "COULD NOT EXTRACT FULL SEQUENCE LENGTH\n";
-        print "  REQUESTED SIZE   ", ($end - $begin + 1)  , "\n";
-        print "  OBSERVED SIZE    ", length($seq)         , "\n";
-        print "  TOTAL SEQ LENGTH ", $totalSeqLen         , "\n";
-        print "  FOUND CHROMOSOME ", ($on ? 'yes' : 'no') , "\n";
+        print STDERR "COULD NOT EXTRACT FULL SEQUENCE LENGTH\n";
+        print STDERR "  REQUESTED SIZE   ", ($end - $begin + 1)  , "\n";
+        print STDERR "  OBSERVED SIZE    ", length($seq)         , "\n";
+        print STDERR "  TOTAL SEQ LENGTH ", $totalSeqLen         , "\n";
+        print STDERR "  FOUND CHROMOSOME ", ($on ? 'yes' : 'no') , "\n";
         exit 2;
     }
 
     if ( $seq ) {
         $seq =~ s/(.{60})/$1\n/g;
 
-        print "$seq\n";
+        print $seq, "\n";
     } else {
         die "NOT ABLE TO EXTRACT SEQUENCE\n";
     }
@@ -164,5 +156,5 @@ sub readFasta
     undef $chromo;
     close FILE;
 #    print "GOT GENE\n";
-    return \@gene;
+    #return \@gene;
 }