added bayespairing2 development

bayespairing/dev/Carnaval_rins.ipynb

@@ -4,6 +4,7 @@
    "cell_type": "code",
    "execution_count": 4,
    "metadata": {
+    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -26,6 +27,7 @@
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {
+    "collapsed": false,
     "scrolled": false
    },
    "outputs": [
@@ -46,6 +48,7 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {
+    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -347,6 +350,7 @@
    "cell_type": "code",
    "execution_count": 30,
    "metadata": {
+    "collapsed": false,
     "scrolled": false
    },
    "outputs": [
@@ -393,6 +397,7 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {
+    "collapsed": false,
     "scrolled": false
    },
    "outputs": [
@@ -522,6 +527,7 @@
    "cell_type": "code",
    "execution_count": 10,
    "metadata": {
+    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -3223,6 +3229,7 @@
    "cell_type": "code",
    "execution_count": 18,
    "metadata": {
+    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -7801,6 +7808,7 @@
    "cell_type": "code",
    "execution_count": 19,
    "metadata": {
+    "collapsed": false,
     "scrolled": false
    },
    "outputs": [
@@ -7853,6 +7861,7 @@
    "cell_type": "code",
    "execution_count": 12,
    "metadata": {
+    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -8901,13 +8910,7 @@
       "137 8\n",
       "39 Exterior Loop\n",
       "40 Exterior Loop\n",
-      "41 Exterior Loop\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "41 Exterior Loop\n",
       "42 Exterior Loop\n",
       "102 Exterior Loop\n",
       "103 Exterior Loop\n",
@@ -10561,6 +10564,7 @@
    "cell_type": "code",
    "execution_count": 10,
    "metadata": {
+    "collapsed": false,
     "scrolled": false
    },
    "outputs": [
@@ -10601,6 +10605,7 @@
    "cell_type": "code",
    "execution_count": 11,
    "metadata": {
+    "collapsed": false,
     "scrolled": false
    },
    "outputs": [
@@ -10639,7 +10644,10 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "metadata": {},
+   "metadata": {
+    "collapsed": false,
+    "scrolled": false
+   },
    "outputs": [
     {
      "name": "stderr",
@@ -10679,7 +10687,10 @@
   {
    "cell_type": "code",
    "execution_count": 16,
-   "metadata": {},
+   "metadata": {
+    "collapsed": false,
+    "scrolled": false
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -10697,7 +10708,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "scrolled": false
    },
    "outputs": [],
    "source": []
@@ -10719,7 +10731,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.6.0"
   }
  },
  "nbformat": 4,

scanning @ 510ea632

+Subproject commit 510ea632270109d5941f1e7c54b68c7fb8225b2b

bayespairing/src/parse_sequences.py

@@ -268,6 +268,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                 #print(input[index:index + w])
                 bf = max(0, index)
                 maxs = run_BP(input[index:index + w], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
+                if interm:
+                    print('PURE SEQUENCE RESULTS:',maxs)
                 for mod in modules_to_parse:
                     corrected_maxes = []
                     for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
@@ -275,11 +277,13 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                             corrected_maxes.append([i + bf for i in cand])
                         else:
                             corrected_maxes.append(cand)
-                    all_maxes.append((mod, index, corrected_maxes))
+                    all_maxes.append((mod, *corrected_maxes))
                 index = index + s
             #print("Running Bayespairing on sequence part:", index, len(input))
             #print(input[index:])
             maxs = run_BP(input[index:], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
+            if interm:
+                print('PURE SEQUENCE RESULTS:',maxs)
             for mod in modules_to_parse:
                 corrected_maxes = []
                 for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
@@ -287,7 +291,9 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                         corrected_maxes.append([i + index for i in cand])
                     else:
                         corrected_maxes.append(cand)
-                all_maxes.append((mod, index, corrected_maxes))
+                all_maxes.append((mod, *corrected_maxes))
+                #print("ALL MAXES FINAL:",all_maxes)
+
             fOUTPUT=fOUTPUT+present_output(all_maxes, t)+"\n"
             pickle.dump(all_maxes,open("../output/"+o+".pickle","wb"))
     return fOUTPUT,sequences