def sashmi_plot_list(bamdir,eventsToVisualizeFilename,PSIFilename,events=None):
import gene_associations
gene_to_symbol = gene_associations.getGeneToUid(species,('hide','Ensembl-Symbol'))
import OBO_import; symbol_to_gene = OBO_import.swapKeyValues(gene_to_symbol)
if events==None:
splicing_events,expandedSearch = importSplicingEventsToVisualize(eventsToVisualizeFilename)
else:
### Replace any ":" from the input events
#for i in range(len(events)): events[i] = string.replace(events[i],':','__')
expandedSearch = True
for i in range(len(events)):
gene = string.split(events[i],'__')[0]
if gene in gene_to_symbol:
symbol = gene_to_symbol[gene][0]
elif 'ENS' not in gene or 'G0000' in gene:
if gene in symbol_to_gene:
ensID = symbol_to_gene[gene][0]
symbol = gene
events[i] = ensID ### translate this ID to an Ensembl gene ID for propper SashimiPlot lookup
splicing_events = events ### optionally get from supplied variable
if len(splicing_events)==0:
print eventsToVisualizeFilename
forceNoCompatibleEventsInFile
print 'Exporting plots',
### Determine Groups for Coloring
groups_file = 'None'
dir_list = unique.read_directory(root_dir+'/ExpressionInput')
for file in dir_list:
if 'groups.' in file:
groups_file = root_dir+'/ExpressionInput/'+file
if groups_file != None:
try:
import ExpressionBuilder
sample_group_db = ExpressionBuilder.simplerGroupImport(groups_file)
groups=[]
for sample in sample_group_db:
if sample_group_db[sample] not in groups:
groups.append(sample_group_db[sample]) ### create an ordered list of unique group
except Exception:
groups = ['None']
#print traceback.format_exc()
pass
processed_events = formatAndSubmitSplicingEventsToSashimiPlot(PSIFilename, bamdir, splicing_events, sample_group_db, groups, False)
mopup_events = getMopUpEvents(splicing_events, processed_events)
### Do the same for supplied gene queries or junctions that didn't map above using the gene expression values as a guide
#print len(splicing_events),len(processed_events),len(mopup_events)
processed_events = formatAndSubmitSplicingEventsToSashimiPlot(steady_state_exp_file,bamdir,mopup_events,sample_group_db,groups,expandedSearch)
if len(processed_events)>0:
mopup_events = getMopUpEvents(mopup_events, processed_events)
processed_events = formatAndSubmitSplicingEventsToSashimiPlot(PSIFilename, bamdir, mopup_events, sample_group_db, groups, True)
return gene_to_symbol
def matrixImport(filename):
matrix={}
original_data={}
headerRow=True
for line in open(filename,'rU').xreadlines():
original_line = line
data = line.rstrip()
values = string.split(data,'\t')
if headerRow:
group_db={}
groups=[]
if ':' in data:
group_sample_list = map(lambda x: string.split(x,':'),values[1:])
index=1
for (g,s) in group_sample_list:
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
index+=1
if g not in groups: groups.append(g)
else:
import ExpressionBuilder
search_dir = string.split(filename,'AltResults')[0]+'ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'groups.' in file:
sample_group_db = ExpressionBuilder.simplerGroupImport(search_dir+'/'+file)
index=0
for s in values[1:]:
g = sample_group_db[s]
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
index+=1
if g not in groups: groups.append(g)
headerRow = False
grouped_values=[]
original_data['header'] = original_line
else:
key = values[0]
grouped_floats=[]
float_values = []
for g in groups: ### string values
gvalues_list=[]
for i in group_db[g]:
if values[i] != '0':
try: gvalues_list.append(float(values[i]))
except Exception: pass
else:
try: gvalues_list.append('') ### Thus are missing values
except Exception: pass
grouped_floats.append(gvalues_list)
matrix[key] = grouped_floats
if '\n' not in original_line:
original_line+='\n'
original_data[key] = original_line
last_line = line
return matrix,original_data
def remoteSashimiPlot(Species,
fl,
bamdir,
eventsToVisualizeFilename,
events=None,
show=False):
global PSIFilename
global outputdir
global root_dir
global steady_state_exp_file
global species
species = Species
try:
countinp = fl.CountsFile()
root_dir = fl.RootDir()
except Exception:
root_dir = fl
search_dir = root_dir + '/ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'counts.' in file and 'steady-state.txt' not in file:
countinp = search_dir + '/' + file
PSIFilename = root_dir + '/AltResults/AlternativeOutput/' + species + '_RNASeq_top_alt_junctions-PSI.txt'
import ExpressionBuilder
dir_list = unique.read_directory(root_dir + '/ExpressionInput')
for file in dir_list:
if 'exp.' in file and 'steady-state' not in file:
exp_file = root_dir + '/ExpressionInput/' + file
elif 'exp.' in file and 'steady-state' in file:
steady_state_exp_file = root_dir + '/ExpressionInput/' + file
global sample_group_db
sample_group_db = ExpressionBuilder.simplerGroupImport(exp_file)
#outputdir=findParentDir(PSIFilename)+"sashimiplots"
outputdir = root_dir + '/ExonPlots'
outputdir = root_dir + '/SashimiPlots'
try:
os.mkdir(unique.filepath(outputdir))
except Exception:
pass
if show:
s = open(outputdir + '/show.txt', 'w')
s.write('TRUE')
s.close()
else:
s = open(outputdir + '/show.txt', 'w')
s.write('FALSE')
s.close()
geneSymbol_db = Sashimiplottting(bamdir,
countinp,
PSIFilename,
eventsToVisualizeFilename,
events=events)
for filename in os.listdir(outputdir):
if '.pdf' in filename or '.png' in filename:
fn = string.replace(filename, '.pdf', '')
fn = string.replace(fn, '.png', '')
newname = string.split(fn, '__')
if newname[0] in geneSymbol_db:
new_filename = str(filename)
if '__' in filename:
new_filename = string.split(filename, '__')[1]
elif '\\' in filename:
new_filename = string.split(filename, '\\')[1]
elif '/' in filename:
new_filename = string.split(filename, '/')[1]
nnname = geneSymbol_db[
newname[0]][0] + '-SashimiPlot_' + new_filename
try:
os.rename(os.path.join(outputdir, filename),
os.path.join(outputdir, nnname))
except Exception:
if 'already exists' in traceback.format_exc():
### File already exists, delete the new one
try:
os.remove(os.path.join(outputdir, nnname))
except Exception:
pass
### Now right the new one
try:
os.rename(os.path.join(outputdir, filename),
os.path.join(outputdir, nnname))
except Exception:
pass
pass
else:
continue
print ''
def sashmi_plot_list(bamdir,
eventsToVisualizeFilename,
PSIFilename,
events=None):
try:
import gene_associations
gene_to_symbol = gene_associations.getGeneToUid(
species, ('hide', 'Ensembl-Symbol'))
from import_scripts import OBO_import
symbol_to_gene = OBO_import.swapKeyValues(gene_to_symbol)
except Exception:
symbol_to_gene = {}
if events == None:
splicing_events, expandedSearch = importSplicingEventsToVisualize(
eventsToVisualizeFilename)
else:
### Replace any ":" from the input events
#for i in range(len(events)): events[i] = string.replace(events[i],':','__')
expandedSearch = True
for i in range(len(events)):
gene = string.split(events[i], '__')[0]
if gene in gene_to_symbol:
symbol = gene_to_symbol[gene][0]
elif 'ENS' not in gene or 'G0000' in gene:
if gene in symbol_to_gene:
ensID = symbol_to_gene[gene][0]
symbol = gene
events[
i] = ensID ### translate this ID to an Ensembl gene ID for propper SashimiPlot lookup
splicing_events = events ### optionally get from supplied variable
if len(splicing_events) == 0:
print eventsToVisualizeFilename
forceNoCompatibleEventsInFile
print 'Exporting plots',
### Determine Groups for Coloring
groups_file = 'None'
dir_list = unique.read_directory(root_dir + '/ExpressionInput')
for file in dir_list:
if 'groups.' in file:
groups_file = root_dir + '/ExpressionInput/' + file
if groups_file != None:
try:
import ExpressionBuilder
sample_group_db = ExpressionBuilder.simplerGroupImport(groups_file)
groups = []
for sample in sample_group_db:
if sample_group_db[sample] not in groups:
groups.append(sample_group_db[sample]
) ### create an ordered list of unique group
except Exception:
groups = ['None']
#print traceback.format_exc()
pass
processed_events = formatAndSubmitSplicingEventsToSashimiPlot(
PSIFilename, bamdir, splicing_events, sample_group_db, groups, False)
mopup_events = getMopUpEvents(splicing_events, processed_events)
### Do the same for supplied gene queries or junctions that didn't map above using the gene expression values as a guide
#print len(splicing_events),len(processed_events),len(mopup_events)
processed_events = formatAndSubmitSplicingEventsToSashimiPlot(
steady_state_exp_file, bamdir, mopup_events, sample_group_db, groups,
expandedSearch)
if len(processed_events) > 0:
mopup_events = getMopUpEvents(mopup_events, processed_events)
processed_events = formatAndSubmitSplicingEventsToSashimiPlot(
PSIFilename, bamdir, mopup_events, sample_group_db, groups, True)
return gene_to_symbol
def remoteSashimiPlot(Species, fl, bamdir, eventsToVisualizeFilename, events=None, show=False):
global PSIFilename
global outputdir
global root_dir
global steady_state_exp_file
global species
species = Species
try:
countinp = fl.CountsFile()
root_dir = fl.RootDir()
except Exception:
root_dir = fl
search_dir = root_dir + "/ExpressionInput"
files = unique.read_directory(search_dir)
for file in files:
if "counts." in file and "steady-state.txt" not in file:
countinp = search_dir + "/" + file
PSIFilename = root_dir + "/AltResults/AlternativeOutput/" + species + "_RNASeq_top_alt_junctions-PSI.txt"
import ExpressionBuilder
dir_list = unique.read_directory(root_dir + "/ExpressionInput")
for file in dir_list:
if "exp." in file and "steady-state" not in file:
exp_file = root_dir + "/ExpressionInput/" + file
elif "exp." in file and "steady-state" in file:
steady_state_exp_file = root_dir + "/ExpressionInput/" + file
global sample_group_db
sample_group_db = ExpressionBuilder.simplerGroupImport(exp_file)
# outputdir=findParentDir(PSIFilename)+"sashimiplots"
outputdir = root_dir + "/ExonPlots"
outputdir = root_dir + "/SashimiPlots"
try:
os.mkdir(unique.filepath(outputdir))
except Exception:
pass
if show:
s = open(outputdir + "/show.txt", "w")
s.write("TRUE")
s.close()
else:
s = open(outputdir + "/show.txt", "w")
s.write("FALSE")
s.close()
geneSymbol_db = Sashimiplottting(bamdir, countinp, PSIFilename, eventsToVisualizeFilename, events=events)
for filename in os.listdir(outputdir):
if ".pdf" in filename or ".png" in filename:
fn = string.replace(filename, ".pdf", "")
fn = string.replace(fn, ".png", "")
newname = string.split(fn, "__")
if newname[0] in geneSymbol_db:
new_filename = str(filename)
if "__" in filename:
new_filename = string.split(filename, "__")[1]
elif "\\" in filename:
new_filename = string.split(filename, "\\")[1]
elif "/" in filename:
new_filename = string.split(filename, "/")[1]
nnname = geneSymbol_db[newname[0]][0] + "-SashimiPlot_" + new_filename
try:
os.rename(os.path.join(outputdir, filename), os.path.join(outputdir, nnname))
except Exception:
if "already exists" in traceback.format_exc():
### File already exists, delete the new one
try:
os.remove(os.path.join(outputdir, nnname))
except Exception:
pass
### Now right the new one
try:
os.rename(os.path.join(outputdir, filename), os.path.join(outputdir, nnname))
except Exception:
pass
pass
else:
continue
print ""
def remoteSashimiPlot(Species,fl,bamdir,eventsToVisualizeFilename,events=None,show=False):
global PSIFilename
global outputdir
global root_dir
global steady_state_exp_file
global species
species = Species
try:
countinp = fl.CountsFile()
root_dir = fl.RootDir()
except Exception:
root_dir = fl
search_dir = root_dir+'/ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'counts.' in file and 'steady-state.txt' not in file:
countinp = search_dir+'/'+file
PSIFilename = root_dir+'/AltResults/AlternativeOutput/'+species+'_RNASeq_top_alt_junctions-PSI.txt'
import ExpressionBuilder
dir_list = unique.read_directory(root_dir+'/ExpressionInput')
for file in dir_list:
if 'exp.' in file and 'steady-state' not in file:
exp_file = root_dir+'/ExpressionInput/'+file
elif 'exp.' in file and 'steady-state' in file:
steady_state_exp_file = root_dir+'/ExpressionInput/'+file
global sample_group_db
sample_group_db = ExpressionBuilder.simplerGroupImport(exp_file)
#outputdir=findParentDir(PSIFilename)+"sashimiplots"
outputdir = root_dir+'/ExonPlots'
outputdir = root_dir+'/SashimiPlots'
try: os.mkdir(unique.filepath(outputdir))
except Exception: pass
if show:
s = open(outputdir+'/show.txt','w')
s.write('TRUE'); s.close()
else:
s = open(outputdir+'/show.txt','w')
s.write('FALSE'); s.close()
geneSymbol_db=Sashimiplottting(bamdir,countinp,PSIFilename,eventsToVisualizeFilename,events=events)
for filename in os.listdir(outputdir):
if '.pdf' in filename or '.png' in filename:
fn = string.replace(filename,'.pdf','')
fn = string.replace(fn,'.png','')
newname=string.split(fn,'__')
if newname[0] in geneSymbol_db:
new_filename = str(filename)
if '__' in filename:
new_filename = string.split(filename,'__')[1]
elif '\\' in filename:
new_filename = string.split(filename,'\\')[1]
elif '/' in filename:
new_filename = string.split(filename,'/')[1]
nnname=geneSymbol_db[newname[0]][0]+'-SashimiPlot_'+new_filename
try: os.rename(os.path.join(outputdir, filename), os.path.join(outputdir,nnname))
except Exception:
if 'already exists' in traceback.format_exc():
### File already exists, delete the new one
try: os.remove(os.path.join(outputdir,nnname))
except Exception: pass
### Now right the new one
try: os.rename(os.path.join(outputdir, filename), os.path.join(outputdir,nnname))
except Exception: pass
pass
else:
continue
print ''
def matrixImport(filename):
matrix={}
compared_groups={} ### track which values correspond to which groups for pairwise group comparisons
original_data={}
headerRow=True
for line in open(filename,'rU').xreadlines():
original_line = line
data = line.rstrip()
values = string.split(data,'\t')
#print len(values)
if headerRow:
group_db={}
groups=[]
if ':' in data:
group_sample_list = map(lambda x: string.split(x,':'),values[1:])
index=1
for (g,s) in group_sample_list:
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
index+=1
if g not in groups: groups.append(g)
else:
import ExpressionBuilder
search_dir = string.split(filename,'AltResults')[0]+'ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'groups.' in file and '.txt' in file:
#print file
sample_group_db = ExpressionBuilder.simplerGroupImport(search_dir+'/'+file)
index=0; count=0
for s in values[1:]:
if s in sample_group_db:
g = sample_group_db[s]
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
count+=1
if g not in groups: groups.append(g)
#else: print [s]
index+=1
#print count
headerRow = False
grouped_values=[]
original_data['header'] = original_line
else:
key = values[0]
values=values[1:]
grouped_floats=[]
float_values = []
associated_groups=[]
for g in groups: ### string values
gvalues_list=[]
for i in group_db[g]:
try:
if values[i] != '0':
try:
gvalues_list.append(float(values[i]))
except Exception: pass
else:
#try: gvalues_list.append('') ### Thus are missing values
#except Exception: pass
pass
except Exception:
#try: gvalues_list.append('') ### Thus are missing values
#except Exception: pass
pass
grouped_floats.append(gvalues_list)
if len(gvalues_list)>1:
associated_groups.append(g)
matrix[key] = grouped_floats
compared_groups[key] = associated_groups
if '\n' not in original_line:
original_line+='\n'
original_data[key] = original_line
last_line = line
return matrix,compared_groups,original_data
def matrixImport(filename):
matrix={}
compared_groups={} ### track which values correspond to which groups for pairwise group comparisons
original_data={}
headerRow=True
for line in open(filename,'rU').xreadlines():
original_line = line
data = line.rstrip()
values = string.split(data,'\t')
#print len(values)
if headerRow:
group_db={}
groups=[]
if ':' in data:
group_sample_list = map(lambda x: string.split(x,':'),values[1:])
index=1
for (g,s) in group_sample_list:
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
index+=1
if g not in groups: groups.append(g)
else:
import ExpressionBuilder
search_dir = string.split(filename,'AltResults')[0]+'ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'groups.' in file and '.txt' in file:
#print file
sample_group_db = ExpressionBuilder.simplerGroupImport(search_dir+'/'+file)
index=0; count=0
for s in values[1:]:
if s in sample_group_db:
g = sample_group_db[s]
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
count+=1
if g not in groups: groups.append(g)
#else: print [s]
index+=1
#print count
headerRow = False
grouped_values=[]
original_data['header'] = original_line
else:
key = values[0]
values=values[1:]
grouped_floats=[]
float_values = []
associated_groups=[]
for g in groups: ### string values
gvalues_list=[]
for i in group_db[g]:
try:
if values[i] != '0':
try:
gvalues_list.append(float(values[i]))
except Exception: pass
else:
#try: gvalues_list.append('') ### Thus are missing values
#except Exception: pass
pass
except Exception:
#try: gvalues_list.append('') ### Thus are missing values
#except Exception: pass
pass
grouped_floats.append(gvalues_list)
if len(gvalues_list)>1:
associated_groups.append(g)
matrix[key] = grouped_floats
compared_groups[key] = associated_groups
if '\n' not in original_line:
original_line+='\n'
original_data[key] = original_line
last_line = line
return matrix,compared_groups,original_data
