+ removed end check AVL tree comparisons

emptyewer · Feb 17, 2017 · bb036f9 · bb036f9
1 parent 2e4c834
commit bb036f9
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Showing 4 changed files with 26 additions and 468 deletions.
diff --git a/functions/junctionf_gui.py b/functions/junctionf_gui.py
@@ -127,22 +127,22 @@ def generate_tabulated_blast_results(self, directory, blast_results_folder, blas
             print ">>> Parsing BLAST results file %s ..." % blasttxt
             blast_dict, accession_dict, gene_dict = self._blast_parser(directory, blast_results_folder,
                                                                        blasttxt, gene_list_file)
-            for key in blast_dict.keys():
-                if key not in ['total', 'pos_que']:
-                    stats = {'in_orf'  : 0, 'in_frame': 0, 'downstream': 0,
-                             'upstream': 0, 'not_in_frame': 0,
-                             'intron'  : 0, 'backwards': 0, 'frame_orf': 0, 'total': 0
-                             }
-                    for nm in blast_dict[key].keys():
-                        blast_dict[key][nm] = list(set(blast_dict[key][nm]))
-                        for j in blast_dict[key][nm]:
-                            j.ppm = blast_dict['pos_que'][j.pos_que] * 1000000 / blast_dict['total']
-                            stats[j.frame] += 1
-                            stats[j.orf] += 1
-                            if j.frame_orf:
-                                stats["frame_orf"] += 1
-                            stats['total'] += 1
-                    blast_dict[key]['stats'] = stats
+            # for key in blast_dict.keys():
+            #     if key not in ['total', 'pos_que']:
+            #         stats = {'in_orf'  : 0, 'in_frame': 0, 'downstream': 0,
+            #                  'upstream': 0, 'not_in_frame': 0,
+            #                  'intron'  : 0, 'backwards': 0, 'frame_orf': 0, 'total': 0
+            #                  }
+            #         for nm in blast_dict[key].keys():
+            #             blast_dict[key][nm] = list(set(blast_dict[key][nm]))
+            #             for j in blast_dict[key][nm]:
+            #                 j.ppm = blast_dict['pos_que'][j.pos_que] * 1000000 / blast_dict['total']
+            #                 stats[j.frame] += 1
+            #                 stats[j.orf] += 1
+            #                 if j.frame_orf:
+            #                     stats["frame_orf"] += 1
+            #                 stats['total'] += 1
+            #         blast_dict[key]['stats'] = stats
 
             blast_dict.pop('pos_que')
             blast_query_p = open(os.path.join(directory, blast_results_query_folder,

diff --git a/gene_count_gui.py b/gene_count_gui.py
@@ -53,17 +53,17 @@ def make_read_dictionary(sam_file, chromosomes_list, bin_folder, exon_dict):
         if line != '\n':
             if not re.match(r'^@', split[0]):
                 chromosome = split[2][3:]
-                RUmapped = split[2]
+                r_umapped = split[2]
                 position = int(split[3])
-                if RUmapped != '*' and chromosome in exon_dict.keys():
+                if r_umapped != '*' and chromosome in exon_dict.keys():
                     total_reads += 1
                     iterations += 1
                     read_dict[chromosome].append(position)
 
-                if split[2] not in binoutfile_names.keys():#
-                    handle = open(os.path.join(bin_folder, split[2] + '.bin'), 'wb')#
-                    binoutfile_names[split[2]] = handle#
-                binoutfile_names[split[2]].write('%s:%s\n' % (split[3], split[9]))#
+                if split[2] not in binoutfile_names.keys():
+                    handle = open(os.path.join(bin_folder, split[2] + '.bin'), 'wb')
+                    binoutfile_names[split[2]] = handle
+                binoutfile_names[split[2]].write('%s:%s\n' % (split[3], split[9]))
 
     for f in binoutfile_names.keys():
         binoutfile_names[f].close()

diff --git a/setup.sh b/setup.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-export DEEPN_VERSION=2.5
+export DEEPN_VERSION=2.61
 rm -rf dist/*
 rm -rf build/*
 unzip lists/mm10GeneList.prn.zip ./lists/mm10GeneList.prn
@@ -19,4 +19,6 @@ mv dist/Blast\ Query.app dist/DEEPN.app/Contents/Resources
 mv dist/Read\ Depth.app dist/DEEPN.app/Contents/Resources
 echo "Unzipping Template DMG..."
 bunzip2 -c template_dmg/template.dmg.bz2 > dist/temp.dmg
+cd dist
+tar cvfj Stat_Maker_${DEEPN_VERSION}_macOS.tar.bz2 Stat\ Maker.app
 echo "Mount template_dmg/temp.dmg file, copy the DEEPN.app file to the mounted DEEPN folder, unmount temp.dmg, compress temp.dmg (using Disk Utility) and delete temp .dmg and DEEPN.app file."