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UI.py
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UI.py
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###UI
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - [email protected]
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
#copies of the Software, and to permit persons to whom the Software is furnished
#to do so, subject to the following conditions:
#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
import math
from stats_scripts import statistics
import sys, string
import shutil
import os.path
import unique
import update; reload(update)
import export
import ExpressionBuilder
import time
import webbrowser
import traceback
import AltAnalyze
from sys import argv
"""
import numpy
import scipy
from PIL import Image as PIL_Image
import ImageTk
import matplotlib
import matplotlib.pyplot as pylab
"""
try:
try:
from visualization_scripts import WikiPathways_webservice
except Exception:
#print traceback.format_exc()
if 'URLError' in traceback.format_exc():
print 'No internet connection found'
else:
print 'WikiPathways visualization not supported (requires installation of suds)'
try:
from PIL import Image as PIL_Image
try: import ImageTk
except Exception: from PIL import ImageTk
import PIL._imaging
import PIL._imagingft
except Exception:
print traceback.format_exc()
#print 'Python Imaging Library not installed... using default PNG viewer'
None
try:
### Only used to test if matplotlib is installed
#import matplotlib
#import matplotlib.pyplot as pylab
None
except Exception:
#print traceback.format_exc()
print 'Graphical output mode disabled (requires matplotlib, numpy and scipy)'
None
except Exception:
None
command_args = string.join(sys.argv,' ')
if len(sys.argv[1:])>1 and '-' in command_args and '--GUI' not in command_args:
runningCommandLine = True
else:
runningCommandLine = False
try:
import Tkinter
#import bwidget; from bwidget import *
from Tkinter import *
from visualization_scripts import PmwFreeze
from Tkconstants import LEFT
import tkMessageBox
import tkFileDialog
except Exception: print "\nPmw or Tkinter not found... proceeding with manual input"
mac_print_mode = 'no'
if os.name == 'posix': mac_print_mode = 'yes' #os.name is 'posix', 'nt', 'os2', 'mac', 'ce' or 'riscos'
debug_mode = 'no'
def filepath(filename):
fn = unique.filepath(filename)
return fn
def osfilepath(filename):
fn = filepath(filename)
fn = string.replace(fn,'\\','/')
return fn
def read_directory(sub_dir):
dir_list = unique.read_directory(sub_dir)
return dir_list
def getFolders(sub_dir):
dir_list = unique.read_directory(sub_dir); dir_list2 = []
###Only get folder names
for entry in dir_list:
if entry[-4:] != ".txt" and entry[-4:] != ".csv" and ".zip" not in entry: dir_list2.append(entry)
return dir_list2
def returnDirectoriesNoReplace(dir):
dir_list = unique.returnDirectoriesNoReplace(dir); dir_list2 = []
for entry in dir_list:
if '.' not in entry and 'affymetrix' not in entry:
if 'EnsMart' in entry: dir_list2.append(entry)
return dir_list2
def returnFilesNoReplace(dir):
dir_list = unique.returnDirectoriesNoReplace(dir); dir_list2 = []
for entry in dir_list:
if '.' in entry: dir_list2.append(entry)
return dir_list2
def identifyCELfiles(dir,array_type,vendor):
dir_list = read_directory(dir); dir_list2=[]; full_dir_list=[]
datatype = 'arrays'
types={}
for file in dir_list:
original_file = file
file_lower = string.lower(file); proceed = 'no'
### "._" indicates a mac alias
if ('.cel' in file_lower[-4:] and '.cel.' not in file_lower) and file_lower[:2] != '._':
proceed = 'yes'
elif ('.bed' in file_lower[-4:] or '.tab' in file_lower or '.junction_quantification.txt' in file_lower or '.bam' in file_lower) and file_lower[:2] != '._' and '.bai' not in file_lower:
proceed = 'yes'
datatype = 'RNASeq'
elif array_type == "3'array" and '.cel' not in file_lower[-4:] and '.txt' in file_lower[-4:] and vendor != 'Affymetrix':
proceed = 'yes'
if proceed == 'yes':
if '__' in file and '.cel' not in string.lower(file):
#print file,string.split(file,'__'),file[-4:]
file=string.split(file,'__')[0]+file[-4:]
if '.tab' in original_file: file = string.replace(file,'.txt','.tab')
elif '.bed' in original_file: file = string.replace(file,'.txt','.bed')
if '.TAB' in original_file: file = string.replace(file,'.txt','.TAB')
elif '.BED' in original_file: file = string.replace(file,'.txt','.BED')
dir_list2.append(file)
file = dir+'/'+file
full_dir_list.append(file)
dir_list2 = unique.unique(dir_list2)
full_dir_list = unique.unique(full_dir_list)
dir_list2.sort(); full_dir_list.sort()
if datatype == 'RNASeq':
checkBEDFileFormat(dir) ### Make sure the names are wonky
dir_list3=[]
c = string.lower(string.join(dir_list2,''))
if '.bam' in c and '.bed' in c: #If bed present use bed and not bam
for i in dir_list2:
if '.bam' not in i:
dir_list3.append(i)
dir_list2 = dir_list3
elif '.bam' in c:
for i in dir_list2:
if '.bam' in i:
dir_list3.append(string.replace(i,'.bam','.bed'))
elif '.BAM' in i:
dir_list3.append(string.replace(i,'.BAM','.bed'))
dir_list2 = dir_list3
return dir_list2,full_dir_list
def checkBEDFileFormat(bed_dir):
""" This checks to see if some files have two underscores and one has none or if double underscores are missing from all."""
dir_list = read_directory(bed_dir)
condition_db={}
for filename in dir_list:
if '.tab' in string.lower(filename) or '.bed' in string.lower(filename) or '.junction_quantification.txt' in string.lower(filename):
condition_db[filename]=[]
if len(condition_db)==0: ### Occurs if BAMs present but not .bed files
for filename in dir_list:
if '.bam' in string.lower(filename):
condition_db[filename]=[]
### Check to see if exon.bed and junction.bed file names are propper or faulty (which will result in downstream errors)
double_underscores=[]
no_doubles=[]
for condition in condition_db:
if '__' in condition:
double_underscores.append(condition)
else:
no_doubles.append(condition)
exon_beds=[]
junctions_beds=[]
if len(double_underscores)>0 and len(no_doubles)>0:
### Hence, a problem is likely due to inconsistent naming
print_out = 'The input files appear to have inconsistent naming. If both exon and\njunction sample data are present, make sure they are named propperly.\n\n'
print_out += 'For example: cancer1__exon.bed, cancer1__junction.bed\n(double underscore required to match these samples up)!\n\n'
print_out += 'Exiting AltAnalyze'
IndicatorWindowSimple(print_out,'Quit')
sys.exit()
elif len(no_doubles)>0:
for condition in no_doubles:
condition = string.lower(condition)
if 'exon' in condition:
exon_beds.append(condition)
if 'junction' in condition:
junctions_beds.append(condition)
if len(exon_beds)>0 and len(junctions_beds)>0:
print_out = 'The input files appear to have inconsistent naming. If both exon and\njunction sample data are present, make sure they are named propperly.\n\n'
print_out += 'For example: cancer1__exon.bed, cancer1__junction.bed\n(double underscore required to match these samples up)!\n\n'
print_out += 'Exiting AltAnalyze'
IndicatorWindowSimple(print_out,'Quit')
sys.exit()
def identifyArrayType(full_dir_list):
#import re
arrays={}; array_type=None ### Determine the type of unique arrays in each directory
for filename in full_dir_list:
fn=filepath(filename); ln=0
for line in open(fn,'rU').xreadlines():
if '\x00' in line: ### Simple way of determining if it is a version 4 file with encoding
line = string.replace(line,'\x00\x00',' ') ### retains spaces
line = string.replace(line,'\x00','') ### returns human readable line
if ln<150:
data = cleanUpLine(line); ln+=1
if 'sq' in data:
try:
#fileencoding = "iso-8859-1"
#txt = line.decode(fileencoding); print [txt];kill ### This works but so does the above
array_info,null = string.split(data,'sq')
array_info = string.split(array_info,' ')
array_type = array_info[-1]
if '.' in array_type: array_type,null = string.split(array_type,'.')
#array_type = string.join(re.findall(r"\w",array_type),'') ### should force only alphanumeric but doesn't seem to always work
arrays[array_type]=[]
#print array_type+'\t'+filename
break
except Exception: pass
elif 'affymetrix-array-type' in data:
null, array_type = string.split(data,'affymetrix-array-type')
if '.' in array_type: array_type,null = string.split(array_type,'.')
arrays[array_type]=[]
"""else: ### some CEL file versions are encoded
fileencoding = "iso-8859-1"
txt = line.decode(fileencoding)
print txt;kill"""
else: break
array_ls = []
for array in arrays:
if len(array)<50: array_ls.append(array) ### Occurs with version 4 encoding (bad entries added)
return array_ls, array_type
def getAffyFilesRemote(array_name,arraytype,species):
global backSelect; global array_type; global debug_mode
debug_mode = 'yes'
backSelect = 'yes'
array_type = arraytype
library_dir, annotation_dir, bgp_file, clf_file = getAffyFiles(array_name,species)
return library_dir, annotation_dir, bgp_file, clf_file
def getAffyFiles(array_name,species):#('AltDatabase/affymetrix/LibraryFiles/'+library_file,species)
sa = supproted_array_db[array_name]; library_file = sa.LibraryFile(); annot_file = sa.AnnotationFile(); original_library_file = library_file
filename = 'AltDatabase/affymetrix/LibraryFiles/'+library_file
fn=filepath(filename); library_dir=filename; bgp_file = ''; clf_file = ''
local_lib_files_present = False
if backSelect == 'yes': warn = 'no'
else: warn = 'yes'
try:
for line in open(fn,'rU').xreadlines():break
### Hence, the library file was found!!!
local_lib_files_present = True
input_cdf_file = filename
if '.pgf' in input_cdf_file:
###Check to see if the clf and bgp files are present in this directory
icf_list = string.split(input_cdf_file,'/'); parent_dir = string.join(icf_list[:-1],'/'); cdf_short = icf_list[-1]
clf_short = string.replace(cdf_short,'.pgf','.clf')
if array_type == 'exon' or array_type == 'junction':
bgp_short = string.replace(cdf_short,'.pgf','.antigenomic.bgp')
else: bgp_short = string.replace(cdf_short,'.pgf','.bgp')
try: dir_list = read_directory(parent_dir)
except Exception: dir_list = read_directory('/'+parent_dir)
if clf_short in dir_list and bgp_short in dir_list:
pgf_file = input_cdf_file; clf_file = string.replace(pgf_file,'.pgf','.clf')
if array_type == 'exon' or array_type == 'junction': bgp_file = string.replace(pgf_file,'.pgf','.antigenomic.bgp')
else: bgp_file = string.replace(pgf_file,'.pgf','.bgp')
else:
try:
print_out = "The directory;\n"+parent_dir+"\ndoes not contain either a .clf or antigenomic.bgp\nfile, required for probeset summarization."
IndicatorWindow(print_out,'Continue')
except Exception: print print_out; sys.exit()
except Exception:
print_out = "AltAnalyze was not able to find a library file\nfor your arrays. Would you like AltAnalyze to\nautomatically download these files?"
try:
dw = DownloadWindow(print_out,'Download by AltAnalyze','Select Local Files')
warn = 'no' ### If already downloading the library, don't warn to download the csv too
dw_results = dw.Results(); option = dw_results['selected_option']
except Exception: option = 1 ### Occurs when Tkinter is not present - used by CommandLine mode
if option == 1:
library_file = string.replace(library_file,'.cdf','.zip')
filename = 'AltDatabase/affymetrix/LibraryFiles/'+library_file
input_cdf_file = filename
if '.pgf' in input_cdf_file:
pgf_file = input_cdf_file; clf_file = string.replace(pgf_file,'.pgf','.clf')
if array_type == 'exon' or array_type == 'junction': bgp_file = string.replace(pgf_file,'.pgf','.antigenomic.bgp')
else: bgp_file = string.replace(pgf_file,'.pgf','.bgp')
filenames = [pgf_file+'.gz',clf_file+'.gz',bgp_file+'.gz']
if 'Glue' in pgf_file:
kil_file = string.replace(pgf_file,'.pgf','.kil') ### Only applies to the Glue array
filenames.append(kil_file+'.gz')
else: filenames = [input_cdf_file]
for filename in filenames:
var_list = filename,'LibraryFiles'
if debug_mode == 'no': StatusWindow(var_list,'download')
else:
for filename in filenames:
continue_analysis = update.downloadCurrentVersion(filename,'LibraryFiles','')
try: os.remove(filepath(filename)) ### Not sure why this works now and not before
except Exception: pass
else: library_dir = ''
filename = 'AltDatabase/affymetrix/'+species+'/'+annot_file
fn=filepath(filename); annotation_dir = filename
try:
for line in open(fn,'rU').xreadlines():break
except Exception:
if warn == 'yes' and local_lib_files_present == False:
### Indicates that library file wasn't present to prior to this method
print_out = "AltAnalyze was not able to find a CSV annotation file\nfor your arrays. Would you like AltAnalyze to\nautomatically download these files?"
try:
dw = DownloadWindow(print_out,'Download by AltAnalyze','Select Local Files'); warn = 'no'
dw_results = dw.Results(); option = dw_results['selected_option']
except OSError: option = 1 ### Occurs when Tkinter is not present - used by CommandLine mode
else:
try: option = option
except Exception: option = 2
if option == 1 or debug_mode=='yes':
annot_file += '.zip'
filenames = ['AltDatabase/affymetrix/'+species+'/'+annot_file]
for filename in filenames:
var_list = filename,'AnnotationFiles'
if debug_mode == 'no': StatusWindow(var_list,'download')
else:
for filename in filenames:
try: update.downloadCurrentVersionUI(filename,'AnnotationFiles','',Tk())
except Exception:
try: update.downloadCurrentVersion(filename,'AnnotationFiles',None)
except Exception: pass ### Don't actually need Affy's annotations in most cases - GO-Elite used instead
try: os.remove(filepath(filename)) ### Not sure why this works now and not before
except Exception: pass
else: annotation_dir = ''
return library_dir, annotation_dir, bgp_file, clf_file
def cleanUpLine(line):
line = string.replace(line,'\n','')
line = string.replace(line,'\c','')
data = string.replace(line,'\r','')
data = string.replace(data,'"','')
return data
########### Status Window Functions ###########
def copyFiles(file1,file2,root):
print 'Copying files from:\n',file1
data = export.ExportFile(file2) ### Ensures the directory exists
try: shutil.copyfile(file1,file2)
except Exception: print "This file already exists in the destination directory."
root.destroy()
class StatusWindow:
def __init__(self,info_list,analysis_type,windowType='parent'):
try:
if windowType == 'child':
root = Toplevel()
else:
root = Tk()
self._parent = root
root.title('AltAnalyze version 2.1.3')
statusVar = StringVar() ### Class method for Tkinter. Description: "Value holder for strings variables."
height = 300; width = 700
if os.name != 'nt': height+=100; width+=50
self.sf = PmwFreeze.ScrolledFrame(self._parent,
labelpos = 'n', label_text = 'Download File Status Window',
usehullsize = 1, hull_width = width, hull_height = height)
self.sf.pack(padx = 5, pady = 1, fill = 'both', expand = 1)
self.frame = self.sf.interior()
group = PmwFreeze.Group(self.sf.interior(),tag_text = 'Output')
group.pack(fill = 'both', expand = 1, padx = 10, pady = 0)
Label(group.interior(),width=180,height=1000,justify=LEFT, bg='black', fg = 'white',anchor=NW,padx = 5,pady = 5, textvariable=statusVar).pack(fill=X,expand=Y)
status = StringVarFile(statusVar,root) ### Captures the stdout (or print) to the GUI instead of to the terminal
self.original_sys_out = sys.stdout ### Save the original stdout mechanism
#ProgressBar('Download',self._parent)
except Exception: None
if analysis_type == 'download':
filename,dir = info_list
try: sys.stdout = status; root.after(100,update.downloadCurrentVersionUI(filename,dir,None,self._parent))
except Exception:
update.downloadCurrentVersion(filename,dir,None)
if analysis_type == 'copy':
file1,file2 = info_list
try: sys.stdout = status; root.after(100,copyFiles(file1,file2,self._parent))
except Exception: copyFiles(file1,file2,None)
if analysis_type == 'getOnlineDBConfig':
file_location_defaults = info_list
try: sys.stdout = status; root.after(100,getOnlineDBConfig(file_location_defaults,self._parent))
except Exception,e: getOnlineDBConfig(file_location_defaults,None)
if analysis_type == 'getOnlineEliteDatabase':
file_location_defaults,db_version,new_species_codes,update_goelite_resources = info_list
try: sys.stdout = status; root.after(100,getOnlineEliteDatabase(file_location_defaults,db_version,new_species_codes,update_goelite_resources,self._parent))
except Exception,e: getOnlineEliteDatabase(file_location_defaults,db_version,new_species_codes,update_goelite_resources,None)
if analysis_type == 'getAdditionalOnlineResources':
species_code,additional_resources = info_list
try: sys.stdout = status; root.after(100,getAdditionalOnlineResources(species_code,additional_resources,self._parent))
except Exception,e: getAdditionalOnlineResources(species_code,additional_resources,None)
if analysis_type == 'createHeatMap':
filename, row_method, row_metric, column_method, column_metric, color_gradient, transpose, contrast = info_list
try: sys.stdout = status; root.after(100,createHeatMap(filename, row_method, row_metric, column_method, column_metric, color_gradient, transpose, contrast, self._parent))
except Exception,e: createHeatMap(filename, row_method, row_metric, column_method, column_metric, color_gradient, transpose,contrast,None)
if analysis_type == 'performPCA':
filename, pca_labels, dimensions, pca_algorithm, transpose, geneSetName, species, zscore, colorByGene, reimportModelScores, maskGroups = info_list
try: sys.stdout = status; root.after(100,performPCA(filename, pca_labels, pca_algorithm, transpose, self._parent, plotType = dimensions, geneSetName=geneSetName, species=species, zscore=zscore, colorByGene=colorByGene, reimportModelScores=reimportModelScores, maskGroups=maskGroups))
except Exception,e: performPCA(filename, pca_labels, pca_algorithm, transpose, None, plotType = dimensions, geneSetName=geneSetName, species=species, zscore=zscore, colorByGene=colorByGene, reimportModelScores=reimportModelScores, maskGroups=maskGroups)
if analysis_type == 'runLineageProfiler':
fl, filename, vendor, custom_markerFinder, geneModel_file, modelDiscovery = info_list
try: sys.stdout = status; root.after(100,runLineageProfiler(fl, filename, vendor, custom_markerFinder, geneModel_file, self._parent, modelSize=modelDiscovery))
except Exception,e: runLineageProfiler(fl, filename, vendor, custom_markerFinder, geneModel_file, None, modelSize=modelDiscovery)
if analysis_type == 'MergeFiles':
files_to_merge, join_option, ID_option, output_merge_dir = info_list
try: sys.stdout = status; root.after(100,MergeFiles(files_to_merge, join_option, ID_option, output_merge_dir, self._parent))
except Exception,e: MergeFiles(files_to_merge, join_option, ID_option, output_merge_dir, None)
if analysis_type == 'VennDiagram':
files_to_merge, output_venn_dir = info_list
try: sys.stdout = status; root.after(100,vennDiagram(files_to_merge, output_venn_dir, self._parent))
except Exception,e: vennDiagram(files_to_merge, output_venn_dir, None)
if analysis_type == 'AltExonViewer':
species,platform,exp_file,gene,show_introns,analysisType = info_list
try: sys.stdout = status; root.after(100,altExonViewer(species,platform,exp_file,gene,show_introns,analysisType,self._parent))
except Exception,e: altExonViewer(species,platform,exp_file,gene,show_introns,analysisType,None)
if analysis_type == 'network':
inputDir,inputType,outputdir,interactionDirs,degrees,expressionFile,gsp = info_list
try: sys.stdout = status; root.after(100,networkBuilder(inputDir,inputType,outputdir,interactionDirs,degrees,expressionFile,gsp, self._parent))
except Exception,e: networkBuilder(inputDir,inputType,outputdir,interactionDirs,degrees,expressionFile,gsp, None)
if analysis_type == 'IDConverter':
filename, species_code, input_source, output_source = info_list
try: sys.stdout = status; root.after(100,IDconverter(filename, species_code, input_source, output_source, self._parent))
except Exception,e: IDconverter(filename, species_code, input_source, output_source, None)
if analysis_type == 'predictGroups':
try: expFile, mlp_instance, gsp, reportOnly = info_list
except Exception: expFile, mlp_instance, gsp, reportOnly = info_list
try: sys.stdout = status; root.after(100,predictSampleExpGroups(expFile, mlp_instance, gsp, reportOnly, self._parent))
except Exception,e: predictSampleExpGroups(expFile, mlp_instance, gsp, reportOnly, None)
if analysis_type == 'preProcessRNASeq':
species,exp_file_location_db,dataset,mlp_instance = info_list
try: sys.stdout = status; root.after(100,preProcessRNASeq(species,exp_file_location_db,dataset,mlp_instance, self._parent))
except Exception,e: preProcessRNASeq(species,exp_file_location_db,dataset,mlp_instance, None)
try:
self._parent.protocol("WM_DELETE_WINDOW", self.deleteWindow)
self._parent.mainloop()
self._parent.destroy()
except Exception: None ### This is what typically get's called
try:
sys.stdout = self.original_sys_out ### Has to be last to work!!!
except Exception: None
def deleteWindow(self):
#tkMessageBox.showwarning("Quit Selected","Use 'Quit' button to end program!",parent=self._parent)
self._parent.destroy(); sys.exit()
def quit(self):
try: self._parent.destroy(); sys.exit() #self._parent.quit();
except Exception: sys.exit() #self._parent.quit();
def SysOut(self):
return self.original_sys_out
def preProcessRNASeq(species,exp_file_location_db,dataset,mlp_instance,root):
for dataset in exp_file_location_db:
flx = exp_file_location_db[dataset]
if root == None: display=False
else: display=True
runKallisto = False
try:
import RNASeq
from build_scripts import ExonArray
expFile = flx.ExpFile()
count = verifyFileLength(expFile)
try: fastq_folder = flx.RunKallisto()
except Exception: fastq_folder = []
try: customFASTA = flx.CustomFASTA()
except Exception: customFASTA = None
try: matrix_file = flx.ChromiumSparseMatrix()
except Exception: matrix_file = []
if len(matrix_file)>0:
print 'Exporting Chromium sparse matrix file to tab-delimited-text'
try:
#print expFile, 'expFile'
#print flx.RootDir(), 'root_dir'
output_dir = export.findParentDir(expFile)
try: os.mkdir(output_dir)
except Exception: pass
matrix_dir = export.findParentDir(matrix_file)
genome = export.findFilename(matrix_dir[:-1])
parent_dir = export.findParentDir(matrix_dir[:-1])
from import_scripts import ChromiumProcessing
ChromiumProcessing.import10XSparseMatrix(matrix_file,genome,dataset,expFile=expFile)
except Exception:
print 'Chromium export failed due to:',traceback.format_exc()
try: root.destroy()
except Exception: pass
return None
elif len(fastq_folder)>0 and count<2:
print 'Pre-processing input files'
try:
parent_dir = export.findParentDir(expFile)
flx.setRootDir(parent_dir)
RNASeq.runKallisto(species,dataset,flx.RootDir(),fastq_folder,mlp_instance,returnSampleNames=False,customFASTA=customFASTA)
except Exception:
print 'Kallisto failed due to:',traceback.format_exc()
try: root.destroy()
except Exception: pass
return None
elif len(fastq_folder)>0 and count>1:
try: root.destroy()
except Exception: pass
return None ### Already run
elif count<2:
print 'Pre-processing input BED/BAM files\n'
analyzeBAMs=False
bedFilesPresent=False
dir_list = unique.read_directory(flx.BEDFileDir())
for file in dir_list:
if '.bam' in string.lower(file):
analyzeBAMs=True
if '.bed' in string.lower(file):
bedFilesPresent=True
if analyzeBAMs and bedFilesPresent==False:
print 'No bed files present, deriving from BAM files'
from import_scripts import multiBAMtoBED
bam_dir = flx.BEDFileDir()
refExonCoordinateFile = filepath('AltDatabase/ensembl/'+species+'/'+species+'_Ensembl_exon.txt')
outputExonCoordinateRefBEDfile = bam_dir+'/BedRef/'+species+'_'+string.replace(dataset,'exp.','')
analysisType = ['exon','junction','reference']
#analysisType = ['junction']
try: multiBAMtoBED.parallelBAMProcessing(bam_dir,refExonCoordinateFile,outputExonCoordinateRefBEDfile,analysisType=analysisType,useMultiProcessing=flx.multiThreading(),MLP=mlp_instance,root=root)
except Exception:
print traceback.format_exc()
try: biotypes = RNASeq.alignExonsAndJunctionsToEnsembl(species,exp_file_location_db,dataset,Multi=mlp_instance)
except Exception:
print traceback.format_exc()
biotypes = getBiotypes(expFile)
else:
biotypes = getBiotypes(expFile)
array_linker_db,array_names = ExonArray.remoteExonProbesetData(expFile,{},'arraynames',flx.ArrayType())
steady_state_export = expFile[:-4]+'-steady-state.txt'
normalize_feature_exp = flx.FeatureNormalization()
try: excludeLowExpressionExons = flx.excludeLowExpressionExons()
except Exception: excludeLowExpressionExons = True
if flx.useJunctionsForGeneExpression():
if 'junction' in biotypes:
feature = 'junction'
else:
feature = 'exon'
else:
### Use all exons either way at this step since more specific parameters will apply to the next iteration
if 'exon' in biotypes:
feature = 'exon'
else:
feature = 'junction'
probeset_db = getAllKnownFeatures(feature,species,flx.ArrayType(),flx.Vendor(),flx)
print 'Calculating gene-level expression values from',feature+'s'
RNASeq.calculateGeneLevelStatistics(steady_state_export,species,probeset_db,normalize_feature_exp,array_names,flx,excludeLowExp=excludeLowExpressionExons,exportRPKMs=True)
#if display == False: print print_out
#try: InfoWindow(print_out, 'Continue')
#except Exception: None
try: root.destroy()
except Exception: pass
except Exception:
error = traceback.format_exc()
#print error
try:
logfile = filepath(fl.RootDir()+'Error.log')
log_report = open(logfile,'a')
log_report.write(traceback.format_exc())
except Exception:
None
print_out = 'Expression quantification failed..\n',error
if runningCommandLine==False:
try: print print_out
except Exception: pass ### Windows issue with the Tk status window stalling after pylab.show is called
try: WarningWindow(print_out,'Continue')
except Exception: pass
try: root.destroy()
except Exception: pass
def getBiotypes(filename):
biotypes={}
firstRow=True
if 'RawSpliceData' in filename: index = 2
else: index = 0
try:
fn=filepath(filename)
for line in open(fn,'rU').xreadlines():
t = string.split(line,'\t')
if firstRow:
firstRow = False
else:
if '-' in t[index]:
biotypes['junction']=[]
else:
biotypes['exon']=[]
except Exception: pass
return biotypes
def getAllKnownFeatures(feature,species,array_type,vendor,fl):
### Simple method to extract gene features of interest
from build_scripts import ExonArrayEnsemblRules
source_biotype = 'mRNA'
if array_type == 'gene': source_biotype = 'gene'
elif array_type == 'junction': source_biotype = 'junction'
if array_type == 'AltMouse':
import ExpressionBuilder
probeset_db,constitutive_gene_db = ExpressionBuilder.importAltMerge('full')
source_biotype = 'AltMouse'
elif vendor == 'Affymetrix' or array_type == 'RNASeq':
if array_type == 'RNASeq':
source_biotype = array_type, fl.RootDir()
dbs = ExonArrayEnsemblRules.getAnnotations('no','Ensembl',source_biotype,species)
probeset_db = dbs[0]; del dbs
probeset_gene_db={}
for probeset in probeset_db:
probe_data = probeset_db[probeset]
gene = probe_data[0]; external_exonid = probe_data[-2]
if len(external_exonid)>2: ### These are known exon only (e.g., 'E' probesets)
proceed = True
if feature == 'exon': ### Restrict the analysis to exon RPKM or count data for constitutive calculation
if '-' in probeset and '_' not in probeset: proceed = False
else:
if '-' not in probeset and '_' not in probeset: proceed = False ### Use this option to override
if proceed:
try: probeset_gene_db[gene].append(probeset)
except Exception: probeset_gene_db[gene] = [probeset]
return probeset_gene_db
def RemotePredictSampleExpGroups(expFile, mlp_instance, gsp, globalVars):
global species
global array_type
species, array_type = globalVars
predictSampleExpGroups(expFile, mlp_instance, gsp, False, None, exportAdditionalResults=False)
return graphic_links
def getICGSNMFOutput(root,filename):
if 'exp.' in filename:
filename = string.replace(filename,'exp.','')
umap_scores_file=''
for file in unique.read_directory(root):
if '-UMAP_coordinates.txt' in file and filename in file:
umap_scores_file = file
return root+'/'+umap_scores_file
def exportAdditionalICGSOutputs(expFile,group_selected,outputTSNE=True):
### Remove OutlierRemoved files (they will otherwise clutter up the directory)
if 'OutliersRemoved' in group_selected and 'OutliersRemoved' not in expFile:
try: os.remove(expFile[:-4]+'-OutliersRemoved.txt')
except Exception: pass
try: os.remove(string.replace(expFile[:-4]+'-OutliersRemoved.txt','exp.','groups.'))
except Exception: pass
try: os.remove(string.replace(expFile[:-4]+'-OutliersRemoved.txt','exp.','comps.'))
except Exception: pass
### Create the new groups file but don't over-write the old
import RNASeq
new_groups_dir = RNASeq.exportGroupsFromClusters(group_selected,expFile,array_type,suffix='ICGS')
from import_scripts import sampleIndexSelection; reload(sampleIndexSelection)
### Look to see if a UMAP file exists in ICGS-NMF
if 'ICGS-NMF' in group_selected or 'NMF-SVM' in group_selected:
root = export.findParentDir(export.findParentDir(expFile)[:-1])+'/ICGS-NMF'
umap_scores_file = getICGSNMFOutput(root,export.findFilename(expFile)[:-4])
tSNE_score_file = umap_scores_file
extension = '-UMAP_scores.txt'
elif outputTSNE:
try:
### Build-tSNE plot from the selected ICGS output (maybe different than Guide-3)
tSNE_graphical_links = performPCA(group_selected, 'no', 'UMAP', False, None, plotType='2D',
display=False, geneSetName=None, species=species, zscore=True, reimportModelScores=False,
separateGenePlots=False,returnImageLoc=True)
if 'SNE' in tSNE_graphical_links[-1][-1]:
tSNE_score_file =tSNE_graphical_links[-1][-1][:-10]+'-t-SNE_scores.txt'
extension = '-t-SNE_scores.txt'
else:
tSNE_score_file =tSNE_graphical_links[-1][-1][:-9]+'-UMAP_scores.txt'
extension = '-UMAP_scores.txt'
except Exception:
print traceback.format_exc()
pass
if '-steady-state' in expFile:
newExpFile = string.replace(expFile,'-steady-state','-ICGS-steady-state')
ICGS_order = sampleIndexSelection.getFilters(new_groups_dir)
sampleIndexSelection.filterFile(expFile,newExpFile,ICGS_order)
### Copy the steady-state files for ICGS downstream-specific analyses
ssCountsFile = string.replace(expFile,'exp.','counts.')
newExpFile = string.replace(expFile,'-steady-state','-ICGS-steady-state')
newssCountsFile = string.replace(newExpFile,'exp.','counts.')
exonExpFile = string.replace(expFile,'-steady-state','')
exonCountFile = string.replace(exonExpFile,'exp.','counts.')
newExonExpFile = string.replace(newExpFile,'-steady-state','')
newExonCountsFile = string.replace(newExonExpFile,'exp.','counts.')
sampleIndexSelection.filterFile(ssCountsFile,newssCountsFile,ICGS_order)
sampleIndexSelection.filterFile(exonExpFile,newExonExpFile,ICGS_order)
sampleIndexSelection.filterFile(exonCountFile,newExonCountsFile,ICGS_order)
exonExpFile = exonExpFile[:-4]+'-ICGS.txt'
else:
newExpFile = expFile[:-4]+'-ICGS.txt'
ICGS_order = sampleIndexSelection.getFilters(new_groups_dir)
sampleIndexSelection.filterFile(expFile,newExpFile,ICGS_order)
exonExpFile = newExpFile
if outputTSNE:
try:
status = verifyFile(tSNE_score_file)
if status=='no':
tSNE_score_file = string.replace(tSNE_score_file,'Clustering-','')
### Copy the t-SNE scores to use it for gene expression analyses
if 'DataPlots' not in tSNE_score_file:
outdir = export.findParentDir(export.findParentDir(tSNE_score_file)[:-1])+'/DataPlots'
else:
outdir = export.findParentDir(tSNE_score_file)
exp_tSNE_score_file = outdir+'/'+export.findFilename(exonExpFile)[:-4]+extension
import shutil
export.customFileCopy(tSNE_score_file,exp_tSNE_score_file)
except Exception:
#print traceback.format_exc()
pass
return exonExpFile,newExpFile,new_groups_dir
def predictSampleExpGroups(expFile, mlp_instance, gsp, reportOnly, root, exportAdditionalResults=True):
global graphic_links; graphic_links=[];
if root == None: display=False
else: display=True
import RNASeq,ExpressionBuilder; reload(RNASeq) ### allows for GUI testing with restarting
try:
if gsp.FeaturestoEvaluate() != 'AltExon':
from stats_scripts import ICGS_NMF
reload(ICGS_NMF)
scaling = True ### Performs pagerank downsampling if over 2,500 cells - currently set as a hard coded default
dynamicCorrelation=True
status = verifyFile(expFile)
if status=='no':
expFile = string.replace(expFile,'-steady-state','') ### Occurs for Kallisto processed
graphic_links=ICGS_NMF.runICGS_NMF(expFile,scaling,array_type,species,gsp,enrichmentInput='',dynamicCorrelation=True)
#graphic_links = RNASeq.singleCellRNASeqWorkflow(species, array_type, expFile, mlp_instance, parameters=gsp, reportOnly=reportOnly)
if gsp.FeaturestoEvaluate() != 'Genes':
### For splice-ICGS (needs to be updated in a future version to ICGS_NMF updated code)
graphic_links2,cluster_input_file=ExpressionBuilder.unbiasedComparisonSpliceProfiles(fl.RootDir(),species,array_type,expFile=fl.CountsFile(),min_events=gsp.MinEvents(),med_events=gsp.MedEvents())
gsp.setCountsCutoff(0);gsp.setExpressionCutoff(0)
graphic_links3 = RNASeq.singleCellRNASeqWorkflow(species, 'exons', cluster_input_file, mlp_instance, parameters=gsp, reportOnly=reportOnly)
graphic_links+=graphic_links2+graphic_links3
print_out = 'Predicted sample groups saved.'
if exportAdditionalResults:
### Optionally automatically generate t-SNE and MarkerFinder Results
guide3_results = graphic_links[-1][-1][:-4]+'.txt'
exportAdditionalICGSOutputs(expFile,guide3_results)
if len(graphic_links)==0:
print_out = 'No predicted sample groups identified. Try different parameters.'
if display == False: print print_out
try: InfoWindow(print_out, 'Continue')
except Exception: None
try: root.destroy()
except Exception: pass
except Exception:
error = traceback.format_exc()
if 'score_ls' in error:
error = 'Unknown error likely due to too few genes resulting from the filtering options.'
if 'options_result_in_no_genes' in error:
error = 'ERROR: No genes differentially expressed with the input criterion'
print_out = 'Predicted sample export failed..\n'+error
try: print print_out
except Exception: pass ### Windows issue with the Tk status window stalling after pylab.show is called
try: WarningWindow(print_out,'Continue')
except Exception: pass
try: root.destroy()
except Exception: pass
try: print error
except Exception: pass
def openDirectory(output_dir):
if runningCommandLine:
pass
elif os.name == 'nt':
try: os.startfile('"'+output_dir+'"')
except Exception: os.system('open "'+output_dir+'"')
elif 'darwin' in sys.platform: os.system('open "'+output_dir+'"')
elif 'linux' in sys.platform: os.system('xdg-open "'+output_dir+'"')
def networkBuilder(inputDir,inputType,outputdir,interactionDirs_short,degrees,expressionFile,gsp,root):
species = gsp.Species()
Genes = gsp.GeneSelection()
PathwaySelect = gsp.PathwaySelect()
OntologyID = gsp.OntologyID()
GeneSet = gsp.GeneSet()
IncludeExpIDs = gsp.IncludeExpIDs()
if 'Ontology' in GeneSet: directory = 'nested'
else: directory = 'gene-mapp'
interactionDirs=[]
obligatorySet=[] ### Always include interactions from these if associated with any input ID period
secondarySet=[]
print 'Species:',species, '| Algorithm:',degrees, ' | InputType:',inputType, ' | IncludeExpIDs:',IncludeExpIDs
print 'Genes:',Genes
print 'OntologyID:',gsp.OntologyID(), gsp.PathwaySelect(), GeneSet
print ''
if interactionDirs_short == None or len(interactionDirs_short)==0:
interactionDirs_short = ['WikiPathways']
for i in interactionDirs_short:
if i == None: None
else:
if 'common-' in i:
i = string.replace(i,'common-','')
secondarySet.append(i)
if 'all-' in i:
i = string.replace(i,'all-','')
obligatorySet.append(i)
fn = filepath('AltDatabase/goelite/'+species+'/gene-interactions/Ensembl-'+i+'.txt')
interactionDirs.append(fn)
print "Interaction Files:",string.join(interactionDirs_short,' ')
import InteractionBuilder
try:
output_filename = InteractionBuilder.buildInteractions(species,degrees,inputType,inputDir,outputdir,interactionDirs,Genes=Genes,
geneSetType=GeneSet,PathwayFilter=PathwaySelect,OntologyID=OntologyID,directory=directory,expressionFile=expressionFile,
obligatorySet=obligatorySet,secondarySet=secondarySet,IncludeExpIDs=IncludeExpIDs)
if output_filename==None:
print_out = 'Network creation/visualization failed..\nNo outputs produced... try different options.\n'
print_out += traceback.format_exc()
if root != None and root != '':
try: InfoWindow(print_out, 'Continue')
except Exception: None
else:
if root != None and root != '':
try: openDirectory(outputdir)
except Exception: None
else:
print 'Results saved to:',output_filename
if root != None and root != '':
GUI(root,'ViewPNG',[],output_filename) ### The last is default attributes (should be stored as defaults in the option_db var)
except Exception:
error = traceback.format_exc()
if 'queryGeneError' in error:
print_out = 'No valid gene IDs present in the input text search\n(valid IDs = FOXP1,SOX2,NANOG,TCF7L1)'
else: print_out = 'Network creation/visualization failed..\n',error
if root != None and root != '':
try: InfoWindow(print_out, 'Continue')
except Exception: None
try: root.destroy()
except Exception: None
def vennDiagram(files_to_merge, output_venn_dir, root, display=True):
from visualization_scripts import VennDiagram
if root == None and display==False: display=False
else: display=True
try:
VennDiagram.compareInputFiles(files_to_merge,output_venn_dir,display=display)
if display == False: print 'VennDiagrams saved to:',output_venn_dir
except Exception:
error = traceback.format_exc()
print_out = 'Venn Diagram export failed..\n',error
if root != None and root != '':
try: InfoWindow(print_out, 'Continue')
except Exception: None
try: root.destroy()
except Exception: None
def altExonViewer(species,platform,exp_file,gene,show_introns,analysisType,root):
from visualization_scripts import QC
transpose=True
if root == None: display = False
else: display = True
if analysisType == 'Sashimi-Plot':
showEvent = False
try:
### Create sashimi plot index
from visualization_scripts import SashimiIndex
print 'Indexing splicing-events'
SashimiIndex.remoteIndexing(species,exp_file)
from visualization_scripts import SashimiPlot
#reload(SashimiPlot)
print 'Running Sashimi-Plot...'
genes=None
if '.txt' in gene:
events_file = gene
events = None
else:
gene = string.replace(gene,',',' ')
genes = string.split(gene,' ')
events_file = None
if len(genes)==1:
showEvent = True
SashimiPlot.remoteSashimiPlot(species,exp_file,exp_file,events_file,events=genes,show=showEvent) ### assuming the bam files are in the root-dir
if root != None and root != '':
print_out = 'Sashimi-Plot results saved to:\n'+exp_file+'/SashimiPlots'
try: InfoWindow(print_out, 'Continue')
except Exception: None
except Exception:
error = traceback.format_exc()
print_out = 'AltExon Viewer failed..\n',error
if root != None and root != '':
try: WarningWindow(print_out, 'Continue')
except Exception: None
try: root.destroy()
except Exception: None
else:
#print [analysisType, species,platform,exp_file,gene,transpose,display,show_introns]
try: QC.displayExpressionGraph(species,platform,exp_file,gene,transpose,display=display,showIntrons=show_introns,analysisType=analysisType)
except Exception:
error = traceback.format_exc()
print_out = 'AltExon Viewer failed..\n',error
if root != None and root != '':
try: WarningWindow(print_out, 'Continue')
except Exception: None
try: root.destroy()
except Exception: None
def MergeFiles(files_to_merge, join_option, ID_option, output_merge_dir, root):
from import_scripts import mergeFiles
try: outputfile = mergeFiles.joinFiles(files_to_merge, join_option, ID_option, output_merge_dir)
except Exception:
outputfile = 'failed'
error = traceback.format_exc()
if outputfile == 'failed':
print_out = 'File merge failed due to:\n',error
else:
print_out = 'File merge complete. See the new file:\n'+outputfile
if root != None and root!= '':
try: InfoWindow(print_out, 'Continue')
except Exception: None
try: root.destroy()
except Exception: None
if outputfile != 'failed': ### Open the folder
try: openDirectory(output_merge_dir)
except Exception: None
def IDconverter(filename, species_code, input_source, output_source, root):
import gene_associations
try: outputfile = gene_associations.IDconverter(filename, species_code, input_source, output_source)
except Exception:
outputfile = 'failed'
error = traceback.format_exc()
if outputfile == 'failed':
print_out = 'Translation failed due to:\n',error
print print_out
else:
print_out = 'ID translation complete. See the new file:\n'+outputfile
if root != None and root!= '':
try: InfoWindow(print_out, 'Continue')
except Exception: None
try: root.destroy()
except Exception: None
if outputfile != 'failed': ### Open the folder
try: openDirectory(export.findParentDir(filename))
except Exception: None
def remoteLP(fl, expr_input_dir, vendor, custom_markerFinder, geneModel, root, modelSize=None,CenterMethod='centroid'):
global species; global array_type
species = fl.Species()
array_type = fl.PlatformType()
runLineageProfiler(fl, expr_input_dir, vendor, custom_markerFinder, geneModel, root, modelSize=modelSize,CenterMethod=CenterMethod)
def runLineageProfiler(fl, expr_input_dir, vendor, custom_markerFinder, geneModel, root, modelSize=None,CenterMethod='centroid'):
try:
global logfile
root_dir = export.findParentDir(expr_input_dir)
time_stamp = AltAnalyze.timestamp()
logfile = filepath(root_dir+'/AltAnalyze_report-'+time_stamp+'.log')
except: pass