+ Minor bug fixes

functions/junctionf_gui.py

@@ -1,28 +1,15 @@
 import os
 import sys
-import time
 import struct
 import cPickle
 import subprocess
-from PyQt4 import QtCore
 from sys import platform as _platform
 from collections import Counter
 
 import libraries.joblib.parallel as Parallel
 import functions.process as process
-import functions.spinbar as spinbar
 import functions.structures as sts
 
-def timeit(method):
-    def timed(*args, **kw):
-        ts = time.time()
-        result = method(*args, **kw)
-        te = time.time()
-        print '>>> Function %r finished %2.2f sec' % (method.__name__.upper().replace("_", " "), te-ts)
-        sys.stdout.flush()
-        return result
-    return timed
-
 class junctionf():
     def __init__(self, f, p):
         self.fileio = f
@@ -59,7 +46,6 @@ def _get_unprocessed_files(self, list, suffix1, processed_list, suffix2):
                     break
         return list
 
-    @timeit
     def junction_search(self, directory, junction_folder, input_data_folder, blast_results_folder,
                         blast_results_query, junction_sequence, exclusion_sequence):
         # junction_sequence = self._getjunction(">junctionseq")
@@ -92,7 +78,6 @@ def _multi_convert(self, directory, infolder, outfolder, blast_results_query):
             self.fileio.make_FASTA(os.path.join(directory, infolder, f),
                                    os.path.join(directory, outfolder, f[:-4] + ".fa"))
 
-    @timeit
     def blast_search(self, directory, db_name, blast_results_folder):
         platform_specific_path = 'osx'
         suffix = ''
@@ -126,14 +111,10 @@ def blast_search(self, directory, db_name, blast_results_folder):
             # blast_command = " ".join(blast_command_list)
             print ">>> Running BLAST search for file: " + file_name
             sys.stdout.flush()
-            self._spin = spinbar.SpinCursor(msg="Please wait for BLAST to finish...", speed=2)
-            self._spin.start()
             # os.system(blast_command)
             self.blast_pipe = subprocess.Popen(blast_command_list, shell=False)
             self.blast_pipe.wait()
-            self._spin.stop()
 
-    @timeit
     def generate_tabulated_blast_results(self, directory, blast_results_folder, blast_results_query_folder, gene_list_file):
         blast_list = self.fileio.get_file_list(directory, blast_results_folder, ".txt")
         processed_file_list = self.fileio.get_file_list(directory, blast_results_query_folder, ".bqa")

functions/printio_gui.py

@@ -86,7 +86,7 @@ def get_text_block_as_array(self, tag):
 
     def print_progress(self, infile, x, y, z, a):
         if a == 1:
-            sys.stdout.write('>>> Processing {}:'.format(infile))
+            sys.stdout.write('>>> Processing {}:\n'.format(infile))
             sys.stdout.flush()
         if a == 2:
             sys.stdout.write('>>> Counting. {} sequences with blast hits in file: {}'.format(x, infile))

gene_count_gui.py

@@ -1,15 +1,13 @@
 import os
 import re
 import sys
-import glob
 import time
 import cPickle as pickle
 import libraries.joblib.parallel as Parallel
 
 # Custom Functions
 import functions.fileio_gui as f
 import functions.printio_gui as p
-import functions.spinbar as spinbar
 
 input_folder = 'mapped_sam_files'
 # Creates the folder that will hold the Genecounts summaries
@@ -27,17 +25,6 @@
     input_folder = 'sam_files'
 
 
-def timeit(method):
-    def timed(*args, **kw):
-        ts = time.time()
-        result = method(*args, **kw)
-        te = time.time()
-        sys.stdout.write('>>> Function %r finished %2.2f sec' % (method.__name__, te-ts))
-        sys.stdout.flush()
-        return result
-    return timed
-
-
 def get_dictionary(fileName):
     dictionary = pickle.load(open(fileName, 'rb'))
     return dictionary
@@ -97,12 +84,14 @@ def query(chromosome, geneName, Dict, totalReads, output_file, summary_file):
     for exonTuple in Dict[chromosome]:
         if exonTuple[4] == geneName:
             counts = Dict[chromosome][exonTuple]
-            PPM = counts * float(1000000) / totalReads
+            PPM = 0
+            if totalReads > 0:
+                PPM = counts * float(1000000) / totalReads
             RPKM = PPM * float(1000) / (exonTuple[1] - exonTuple[0])
             output_file.write("\n" + str(exonTuple) + " Counts:" + str(counts) + " PPM:" + str(PPM) + " RPKM:" + str(RPKM))
             Ctotal += counts
             Ptotal += PPM
-            length += (exonTuple[1] - exonTuple[0])
+            length += exonTuple[1] - exonTuple[0]
             accession = exonTuple[5]
     Rtotal = Ptotal * float(1000) / length        
     output_file.write("\n" + "TOTALS" + "\n" + "Counts:" + str(Ctotal) + " PPM:" + str(Ptotal) + " RPKM:" + str(Rtotal) + " Length:" + str(length) + "\n")
@@ -131,7 +120,7 @@ def write_all_to_file(directory, Dictionary, totalReads, totalReads2, f, sumfold
 
 
 def letsCount(directory, summary_folder, chromosomes_folder, input_folder, chromosomes_list, filename):
-    sys.stdout.write(">>> Started processing file %s" % filename)
+    sys.stdout.write(">>> Started processing file %s\n" % filename)
     sys.stdout.flush()
     exonDict = get_dictionary(os.path.join('dictionaries', gene_dictionary))
     infile = os.path.join(directory, input_folder, filename)
@@ -142,7 +131,7 @@ def letsCount(directory, summary_folder, chromosomes_folder, input_folder, chrom
     # else:
     #     bin_folder = os.path.join(directory, input_folder, filename[:-4])
     (readDict, totalReads) = make_read_dictionary(infile, chromosomes_list, gene_count_bin_folder, exonDict)
-    sys.stdout.write(">>> %d Total Reads (%s)" % (totalReads, filename))
+    sys.stdout.write(">>> %d Total Reads (%s)\n" % (totalReads, filename))
     sys.stdout.flush()
     totalReads2 = 0
     exon_index = 0
@@ -160,25 +149,20 @@ def letsCount(directory, summary_folder, chromosomes_folder, input_folder, chrom
                     elif read > exon[1]:
                         exon_index += 1
                         # exonList.remove(exon)
-            sys.stdout.write('>>> Finished Chromosome %s%s for File (%s)' % (chrom[:20], '' if len(chrom) <= 20 else '...',
+            sys.stdout.write('>>> Finished Chromosome %s%s for File (%s)\n' % (chrom[:20], '' if len(chrom) <= 20 else '...',
                                                                              filename))
             sys.stdout.flush()
             time.sleep(1)
-    sys.stdout.write('>>> Creating files and cleaning up... ( %s )' % filename)
+    sys.stdout.write('>>> Creating files and cleaning up... ( %s )\n' % filename)
     sys.stdout.flush()
     write_all_to_file(directory, exonDict, totalReads, totalReads2, filename, summary_folder, chromosomes_folder)
 
-@timeit
 def gene_count(directory, summary_folder, chromosomes_folder, input_folder, chromosomes_list, sam_file_list):
     num_cores = Parallel.cpu_count()
     print ">>> Using %d Processor Cores" % (num_cores - 1)
-    _spin = spinbar.SpinCursor(msg="Processing mapped .sam files ...", speed=2)
-    _spin.start()
     Parallel.Parallel(n_jobs=num_cores-1)(Parallel.delayed(letsCount)(directory, summary_folder, chromosomes_folder,
                                                                       input_folder, chromosomes_list, f) for f in
                                                                       sam_file_list)
-    _spin.stop()
-
 
 def initialize_folders(directory):
     # Creates the folder that will hold the Genecounts summaries

setup_statistics.py

@@ -54,7 +54,7 @@ def find_data_files(sources, targets, patterns):
            }
 DATA_FILES = find_data_files(['ui', '', 'statistics', 'libraries', ''],
                              ['ui', 'lib/python2.7', 'statistics', 'libraries', ''],
-                             ['Stat_Maker.ui', 'DragDropListView.py', '*.pkg', '*.py', 'install_deepn.sh'])
+                             ['Stat_Maker.ui', 'DragDropListView.py', '*.pkg', '*.py', '*.sh'])
 
 if sys.platform == 'darwin':
     setup(

stat_maker_gui.py

@@ -163,12 +163,15 @@ def on_verify_installation_btn_clicked(self):  #####################   new defin
                 subprocess.Popen(['bash install_deepn.sh ' + self.r_path], shell=True)
                 while not self.check_deepn_installed():
                     time.sleep(0.5)
+            else:
+                self.statusbar.showMessage("Updating DEEPN...")
+                subprocess.Popen(['bash update_deepn.sh ' + self.r_path], shell=True)
 
         self.set_interaction_state(True)
         self.run_btn.setEnabled(False)
         self.verify_installation_btn.setEnabled(False)
         self.verify_installation_btn.setText("Installations are Correct")
-        self.statusbar.showMessage("R, JAGS, and DEEPN Installation is Correct")
+        self.statusbar.showMessage("R, JAGS, and DEEPN Installations is Correct")
 
     def which(self, program):
         try:
@@ -308,9 +311,8 @@ def bait2_nonsel_fileDropped_2(self, path):
             self.fileDropped(self.bait2_nonsel_list_2, path, "Bait2_Non-Selected_2")
 
     def write_four_columns_from_csv(self, csv_file):
-
         filehandle = open(csv_file, 'r')
-        outhandle = open(csv_file[:-4] + "_temp.csv", 'w')
+        outhandle = open(csv_file.replace("_summary.csv", "_stats.csv"), 'w')
         count = 0
         for line in filehandle.readlines():
             if count > 3:
@@ -322,9 +324,9 @@ def write_four_columns_from_csv(self, csv_file):
 
     def write_r_input(self):
         output = open(os.path.join(self.directory, 'r_input.params'), 'w')
-        for key in self.data.keys():
+        for key in sorted(self.data.keys()):
             self.write_four_columns_from_csv(self.data[key])
-            output.write("%-25s = %s_temp.csv\n" % (key, self.data[key][:-4]))
+            output.write("%-25s = %s\n" % (key, self.data[key].replace("_summary.csv", "_stats.csv")))
         output.write("%-25s = %d\n" % ("Threshold", self.threshold_sbx.value()))
         # output.write("%-25s = %s\n" % ("R Path", self.r_path))
         # output.write("%-25s = %s" % ("JAGS Path", self.jags_path))