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Trying to reproduce Rakmakallan's error.

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1 parent 1f24571 commit 7848f8d3d3cea40477addf9b1a0101b40a0e8035 @jhannah committed Jun 7, 2010
Showing with 346 additions and 1 deletion.
  1. +263 −0 Rakmakallan/AQP1_HUMAN.txt
  2. +82 −0 Rakmakallan/PerlLabPart7.pl
  3. +1 −1 wwm/loop.pl
View
263 Rakmakallan/AQP1_HUMAN.txt
@@ -0,0 +1,263 @@
+>AQP1_HUMAN P29972
+MASEFKKKLFWRAVVAEFLATTLFVFISIGSALGFKYPVGNNQTAVQDNVKVSLAFGLSIATLAQSVGHISGAHLNPAVTLGLLLSCQISIFRALMYIIAQCVGAIVATAILSGITSSLTGNSLGRNDLADGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAVITHNFSNHWIFWVGPFIGGALAVLIYDFILAPRSSDLTDRVKVWTSGQVEEYDLDADDINSRVEMKPK
+
+TM1 8 36 LFWRAVVAEFLATTLFVFISIGSALGFKY
+TM2 49 66 VKVSLAFGLSIATLAQSV
+TM3 77 84 AVTLGLLL
+TM4 95 115 MYIIAQCVGAIVATAILSGIT
+TM5 137 155 GLGIEIIGTLQLVLCVLAT
+TM6 167 183 APLAIGLSVALGHLLAI
+TM7 193 200 ARSFGSAV
+TM8 208 228 HWIFWVGPFIGGALAVLIYDF
+0.43
+0.3
+0.175
+0.405
+0.72
+0.79
+1.125
+1.545
+1.7
+1.735
+1.575
+1.58
+1.895
+1.995
+1.765
+1.695
+1.41
+1.52
+1.3
+1.32
+1.21
+1.07
+0.93
+0.565
+0.39
+0.27
+0.34
+-0.06
+-0.195
+-0.595
+-0.365
+-0.52
+-0.4
+-0.63
+-0.42
+-0.47
+-0.135
+-0.0900000000000001
+0.18
+-0.0699999999999999
+0.175
+0.44
+0.58
+0.945
+1.07
+0.805
+0.555
+0.94
+1.095
+1.11
+1.125
+1.28
+1.05
+1.18
+0.83
+0.93
+0.615
+0.555
+0.455
+0.705
+0.445
+0.545
+0.56
+0.56
+0.66
+1.025
+1.025
+0.94
+0.785
+1.17
+0.905
+1.17
+1.33
+1.015
+1.265
+1.265
+1.535
+1.55
+1.685
+1.7
+1.825
+1.46
+1.605
+1.625
+1.415
+1.315
+1.58
+1.665
+1.93
+1.67
+1.8
+1.8
+1.85
+2.035
+1.925
+1.96
+1.83
+1.855
+1.59
+1.555
+1.43
+1.585
+1.285
+1.035
+1.245
+1.135
+0.685
+0.3
+0.0349999999999997
+0.26
+0.26
+-0.14
+-0.35
+-0.1
+-0.255
+-0.52
+-0.505
+-0.64
+-0.62
+-0.62
+-0.605
+-0.36
+-0.36
+-0.0950000000000001
+-0.0600000000000001
+-0.0600000000000001
+0.13
+0.495
+0.495
+0.495
+0.615
+0.98
+1.125
+1.125
+1.49
+1.62
+1.605
+1.745
+1.59
+1.175
+0.97
+0.52
+0.47
+0.0700000000000001
+0.0350000000000001
+0.035
+0.0500000000000002
+-0.18
+0.0850000000000001
+-0.185
+-0.205
+-0.305
+-0.205
+-0.435
+-0.435
+-0.565
+-0.32
+-0.195
+0.17
+0.375
+0.44
+0.855
+1.27
+1.535
+1.57
+1.415
+1.37
+1.375
+1.265
+1.47
+1.26
+1.395
+0.995
+0.935
+0.835
+0.65
+0.4
+0.45
+0.24
+0.22
+0.47
+0.49
+0.525
+0.4
+0.0149999999999999
+0.015
+0.22
+0.215
+0.06
+-0.225
+-0.25
+-0.25
+0.0649999999999999
+0.0999999999999999
+0.22
+0.425
+0.385
+0.385
+0.63
+0.65
+0.54
+0.42
+0.385
+0.51
+0.88
+1.245
+1.33
+1.305
+1.305
+1.605
+1.875
+1.84
+1.79
+1.755
+1.32
+1.3
+1.34
+1.025
+0.99
+0.975
+0.82
+0.505
+0.525
+0.24
+0.24
+0.00500000000000011
+-0.255
+-0.23
+-0.0749999999999999
+-0.39
+-0.405
+-0.77
+-1.035
+-1.02
+-0.97
+-0.74
+-0.875
+-0.61
+-0.975
+-1.115
+-0.715
+-0.665
+-0.915
+-0.945
+-0.945
+-1.075
+-0.945
+-1.1
+-1.16
+-1.18
+-1.39
+Q=0.762081784386617
View
82 Rakmakallan/PerlLabPart7.pl
@@ -0,0 +1,82 @@
+open (EPIC,"$ARGV[0]");
+while (<EPIC>)
+ {if ($_=~m/^ID\s{3}(\S*)\s/gi)
+ {$ID=$1;}
+ if ($_=~m/^AC\s{3}(\S*)\;/gi)
+ {$AC=$1;
+ print ">$ID $AC\n";}
+ if ($_=~m/^\s{5}(.*)/gi)
+ {$SEQ.=$1;
+ $SEQ=~s/\s//g;}}
+print "$SEQ\n";
+@res=split("",$SEQ);
+$helcount=0;
+$lala=length($SEQ);
+for ($obcount=0;$obcount<=$lala-1;$obcount++)
+ {@observed[$obcount]='nonhydro';}
+#print "@observed";
+open (EPIC,"$ARGV[0]");
+while (<EPIC>)
+ {if ($_=~m/^FT\s{3}TRANSMEM\s*(\d*)\s*(\d*)/gi)
+ {print "\n";
+ $helcount++;
+ print "TM$helcount $1 $2 ";
+ for ($trans=$1;$trans<=$2;$trans++)
+ {print $res[$trans];
+ @observed[$trans]='hydro';}}}
+#print "@observed";
+print "\n";
+
+
+%KD = ('A'=>'1.8',
+'R'=>'-4.5',
+'N'=>'-3.5',
+'D'=>'-3.5',
+'C'=>'2.5',
+'Q'=>'-3.5',
+'E'=>'-3.5',
+'G'=>'-0.4',
+'H'=>'-3.2',
+'I'=>'4.5',
+'L'=>'3.8',
+'K'=>'-3.9',
+'M'=>'1.9',
+'F'=>'2.8',
+'P'=>'-1.6',
+'S'=>'-0.8',
+'T'=>'-0.7',
+'W'=>'-0.9',
+'Y'=>'-1.3',
+'V'=>'4.2');
+
+@predicted=("nonhydro","nonhydro","nonhydro","nonhydro","nonhydro","nonhydro","nonhydro","nonhydro","nonhydro");
+$arith=0;
+for ($i=10;$i<=$lala-9;$i++)
+ {for ($add=-10;$add<=9;$add++)
+ {$mediator=$res[$i+$add];
+ $arith=$arith+$KD{$mediator};}
+ $hydrocount=$arith/20;
+ print "$hydrocount\n";
+ if ($hydrocount>=0)
+ {push (@predicted,'hydro');}
+ if ($hydrocount<0)
+ {push (@predicted,'nonhydro');}
+ $arith=0;}
+
+for ($compcount=0;$compcount<=$#observed;$compcount++)
+ {if ($predicted[$compcount] eq $observed[$compcount])
+ {if ($observed[$compcount] eq "hydro")
+ {$tp++;}
+ if ($observed[$compcount] eq "nonhydro")
+ {$tn++;}}
+ else
+ {if ($observed[$compcount] eq "hydro")
+ {$fn++;}
+ if ($observed[$compcount] eq "nonhydro")
+ {$fp++;}}}
+$Q=($tp+$tn)/($tp+$tn+$fp+$fn);
+print "Q=$Q\n";
+
+
+#PROBLEM IS EXPECTED TO BE SOMEWHERE IN THE 2 "FOR" LOOPS BUT THIS IS NOT DEFINITE IN ANY WAY
+
View
2 wwm/loop.pl
@@ -1,4 +1,4 @@
-foreach my $n (qw(e_1 e_2 e_7)) {
+foreach my $n (qw(e_1 e_2 foo e_7)) {
next unless ($n =~ /^e_(\d+)$/);
print "$n: $1 \n";
}

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