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isabelrem · Aug 1, 2023 · 619b023 · 619b023
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diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/modules.xml b/.idea/modules.xml
diff --git a/.idea/stp_tutorials.iml b/.idea/stp_tutorials.iml
diff --git a/Python exercises 1.pdf b/Python exercises 1.pdf
diff --git a/Python exercises 2.pdf b/Python exercises 2.pdf
diff --git a/Python exercises 3.pdf b/Python exercises 3.pdf
diff --git a/Python exercises 4.pdf b/Python exercises 4.pdf
diff --git a/chunking.log b/chunking.log
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,6 @@
+name: stp_tutorials
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python==3.10.10
diff --git a/examples/1abc.sec b/examples/1abc.sec
@@ -0,0 +1,141 @@
+    1 A   1    VAL V -
+    2 A   2    LEU L -
+    3 A   3    SER S -
+    4 A   4    ALA A H
+    5 A   5    ALA A H
+    6 A   6    ASP D H
+    7 A   7    LYS K H
+    8 A   8    THR T H
+    9 A   9    ASN N H
+   10 A  10    VAL V H
+   11 A  11    LYS K H
+   12 A  12    GLY G H
+   13 A  13    VAL V H
+   14 A  14    PHE F H
+   15 A  15    SER S H
+   16 A  16    LYS K H
+   17 A  17    ILE I H
+   18 A  18    SER S -
+   19 A  19    GLY G -
+   20 A  20    HIS H -
+   21 A  21    ALA A H
+   22 A  22    GLU E H
+   23 A  23    GLU E H
+   24 A  24    TYR Y H
+   25 A  25    GLY G H
+   26 A  26    ALA A H
+   27 A  27    GLU E H
+   28 A  28    THR T H
+   29 A  29    LEU L H
+   30 A  30    GLU E H
+   31 A  31    ARG R H
+   32 A  32    MET M H
+   33 A  33    PHE F H
+   34 A  34    THR T H
+   35 A  35    ALA A H
+   36 A  36    TYR Y -
+   37 A  37    PRO P G
+   38 A  38    GLN Q G
+   39 A  39    THR T G
+   40 A  40    LYS K G
+   41 A  41    THR T G
+   42 A  42    TYR Y G
+   43 A  43    PHE F -
+   44 A  44    PRO P -
+   45 A  45    HIS H -
+   46 A  46    PHE F -
+   47 A  47    ASP D -
+   48 A  48    LEU L -
+   49 A  49    GLN Q -
+   50 A  50    HIS H -
+   51 A  51    GLY G -
+   52 A  52    SER S -
+   53 A  53    ALA A H
+   54 A  54    GLN Q H
+   55 A  55    ILE I H
+   56 A  56    LYS K H
+   57 A  57    ALA A H
+   58 A  58    HIS H H
+   59 A  59    GLY G H
+   60 A  60    LYS K H
+   61 A  61    LYS K H
+   62 A  62    VAL V H
+   63 A  63    VAL V H
+   64 A  64    ALA A H
+   65 A  65    ALA A H
+   66 A  66    LEU L H
+   67 A  67    VAL V H
+   68 A  68    GLU E H
+   69 A  69    ALA A H
+   70 A  70    VAL V H
+   71 A  71    ASN N -
+   72 A  72    HIS H -
+   73 A  73    ILE I -
+   74 A  74    ASP D -
+   75 A  75    ASP D -
+   76 A  76    ILE I H
+   77 A  77    ALA A H
+   78 A  78    GLY G H
+   79 A  79    ALA A H
+   80 A  80    LEU L H
+   81 A  81    SER S H
+   82 A  82    LYS K H
+   83 A  83    LEU L H
+   84 A  84    SER S H
+   85 A  85    ASP D H
+   86 A  86    LEU L H
+   87 A  87    HIS H H
+   88 A  88    ALA A H
+   89 A  89    GLN Q -
+   90 A  90    LYS K -
+   91 A  91    LEU L -
+   92 A  92    ARG R -
+   93 A  93    VAL V -
+   94 A  94    ASP D -
+   95 A  95    PRO P G
+   96 A  96    VAL V G
+   97 A  97    ASN N G
+   98 A  98    PHE F G
+   99 A  99    LYS K G
+  100 A 100    PHE F G
+  101 A 101    LEU L G
+  102 A 102    GLY G G
+  103 A 103    HIS H G
+  104 A 104    CYS C G
+  105 A 105    PHE F G
+  106 A 106    LEU L G
+  107 A 107    VAL V G
+  108 A 108    VAL V G
+  109 A 109    VAL V G
+  110 A 110    ALA A G
+  111 A 111    ILE I G
+  112 A 112    HIS H G
+  113 A 113    HIS H -
+  114 A 114    PRO P -
+  115 A 115    SER S -
+  116 A 116    ALA A -
+  117 A 117    LEU L -
+  118 A 118    THR T -
+  119 A 119    ALA A H
+  120 A 120    GLU E H
+  121 A 121    VAL V H
+  122 A 122    HIS H H
+  123 A 123    ALA A H
+  124 A 124    SER S H
+  125 A 125    LEU L H
+  126 A 126    ASP D H
+  127 A 127    LYS K H
+  128 A 128    PHE F H
+  129 A 129    LEU L H
+  130 A 130    CYS C H
+  131 A 131    ALA A H
+  132 A 132    VAL V H
+  133 A 133    GLY G H
+  134 A 134    THR T H
+  135 A 135    VAL V H
+  136 A 136    LEU L -
+  137 A 137    THR T -
+  138 A 138    ALA A -
+  139 A 139    LYS K -
+  140 A 140    TYR Y -
+  141 A 141    ARG R