parser = get_parser() # start command line argument parser
args = parser.parse_args() # parse command line arguments
globals().update(args.__dict__)
start_time = time.time()
# start timing function
get_input_variables()
database_v = int(database_v)
allowed_mismatches = int(allowed_mismatches)
directory = directory + '/'
# hash PSM_DATA and define variables
psm_hash = proBAM_input.get_PSM_hash(psm_file, decoy_annotation,
validated_only)
parse_results = proBAM_IDparser.parseID(psm_hash, species, database,
decoy_annotation, database_v,
three_frame_translation,
pre_picked_annotation)
annotation = parse_results[1]
psm_hash = parse_results[0]
transcript_hash = annotation[0]
exon_hash = annotation[1]
id_map = parse_results[2]
# convert to SAM
if conversion_mode != 'proBED':
file = open_sam_file(directory, name)
create_SAM_header(file, version, database, sorting_order,
database_v, species, command_line, psm_file,
comments)
PSM2SAM(psm_hash, transcript_hash, exon_hash, decoy_annotation,
allowed_mismatches, file, rm_duplicates,
def execute_proBAM(root):
"""
:param root: window root
:return:
"""
root.config(cursor="watch")
root.update()
start_time = time.time() # start timing function
Label(text="console:", pady=5, width=70, background="#f2f2f2").grid(row=12, columnspan=2)
std_text = ScrolledText.ScrolledText(root, height=20)
std_text.grid(row=15, columnspan=2)
sys.stdout = Std_redirector(std_text)
sys.stderr = Std_redirector(std_text)
sys.stdin = Std_redirector(std_text)
root.update()
# get and print arguments
try:
_print_arguments_()
command_line = (
"python proBAM.py --name "
+ str(name)
+ " --mismatches "
+ str(allowed_mismatches.get())
+ " --version "
+ str(database_v.get())
+ " --database "
+ str(database.get().upper())
+ " --species "
+ str(species.get())
+ " --file "
+ str(psm_file)
+ " --directory "
+ str(directory)
+ " --rm_duplicates "
+ str(rm_duplicates.get())
+ " --allow_decoys "
+ str(allow_decoys.get())
+ " --tri_frame_translation "
+ str(three_frame_translation.get() + " --pre_picked_annotation " + pre_picked_annotation)
)
print "\n"
# hash PSM_DATA and define variables
psm_hash = proBAM_input.get_PSM_hash(psm_file, decoy_annotation)
parse_results = proBAM_IDparser.parseID(
psm_hash,
species.get().replace(" ", "_"),
database.get().upper(),
decoy_annotation,
int(database_v.get()),
three_frame_translation.get(),
pre_picked_annotation,
)
annotation = parse_results[1]
psm_hash = parse_results[0]
transcript_hash = annotation[0]
exon_hash = annotation[1]
id_map = parse_results[2]
# convert to SAM
if probed == "N":
file = proBAM.open_sam_file(directory, name.get())
proBAM.create_SAM_header(
file,
version,
database.get().upper(),
sorting_order,
database_v.get(),
species.get(),
command_line,
psm_file,
comments,
)
proBAM.PSM2SAM(
psm_hash,
transcript_hash,
exon_hash,
decoy_annotation,
int(allowed_mismatches.get()),
file,
allow_decoys.get(),
rm_duplicates.get(),
three_frame_translation.get(),
psm_file,
id_map,
root,
)
proBAM.compute_NH_XL(directory, name.get())
proBAM.sam_2_bam(directory, name.get())
else:
file = proBAM_proBED.open_bed_file(directory, name.get())
proBAM_proBED.create_BED_header(
file,
version,
database.get().upper(),
sorting_order.get(),
database_v.get(),
species.get(),
command_line,
psm_file,
comments,
)
proBAM_proBED.PSM2BED(
psm_hash,
transcript_hash,
exon_hash,
decoy_annotation,
allowed_mismatches.get(),
file,
allow_decoys.get(),
rm_duplicates.get(),
three_frame_translation.get(),
psm_file,
id_map,
)
root.config(cursor="")
print ("proBAM conversion succesful")
print ("%f seconds" % (time.time() - start_time)) # output script run time
except Exception, e:
print "ERROR:" + str(
e
) + "\n" "Please check if all parameters were supplied correctly, if the error keeps occuring contact " 'the developers at "https://github.com/Biobix/proBAMconvert/issues" ' "and provide the file to be processed along with the following error message:"
print e
root.config(cursor="")
def execute_proBAM(root):
'''
:param root: window root
:return:
'''
root.config(cursor="watch")
root.update()
start_time = time.time() # start timing function
Label(text='console:', pady=5, width=70,
background="#f2f2f2").grid(row=12, columnspan=2)
std_text = ScrolledText.ScrolledText(root, height=20)
std_text.grid(row=15, columnspan=2)
sys.stdout = Std_redirector(std_text)
sys.stderr = Std_redirector(std_text)
sys.stdin = Std_redirector(std_text)
root.update()
# get and print arguments
try:
_print_arguments_()
command_line = "python proBAM.py --name " + str(name.get()) + " --mismatches " + str(
allowed_mismatches.get()) + " --version " + str(database_v.get()) \
+ " --database " + str(database.get().upper()) + " --species " + str(species.get().replace(' ','_')) + " --file " + str(psm_file) + \
" --directory " + str(directory) + " --rm_duplicates " + str(rm_duplicates.get()) + \
" --tri_frame_translation " + \
str(three_frame_translation+" --pre_picked_annotation "+pre_picked_annotation) +\
" --include_unmapped "+str(include_unmapped)
print '\n'
# hash PSM_DATA and define variables
psm_hash = proBAM_input.get_PSM_hash(psm_file, decoy_annotation)
parse_results = proBAM_IDparser.parseID(
psm_hash,
species.get().replace(' ', '_'),
database.get().upper(), decoy_annotation, int(database_v.get()),
three_frame_translation, pre_picked_annotation)
annotation = parse_results[1]
psm_hash = parse_results[0]
transcript_hash = annotation[0]
exon_hash = annotation[1]
id_map = parse_results[2]
# convert to SAM
if conversion_mode.get() != 'proBED':
file = proBAM.open_sam_file(directory, name.get())
proBAM.create_SAM_header(file, version,
database.get().upper(), sorting_order,
database_v.get(),
species.get().replace(' ', '_'),
command_line, psm_file, comments)
proBAM.PSM2SAM(psm_hash, transcript_hash,
exon_hash, decoy_annotation,
int(allowed_mismatches.get()), file,
rm_duplicates.get(), three_frame_translation,
psm_file, id_map, root)
proBAM.compute_NH_XL(directory, name.get(), include_unmapped,
conversion_mode)
proBAM.sam_2_bam(directory, name.get())
else:
file = proBAM_proBED.open_bed_file(directory, name.get())
proBAM_proBED.create_BED_header(file,
database.get().upper(),
database_v.get(), command_line,
psm_file, comments)
proBAM_proBED.PSM2BED(psm_hash, transcript_hash, exon_hash,
decoy_annotation,
int(allowed_mismatches.get()), file,
rm_duplicates.get(), three_frame_translation,
id_map, root, database_v.get(),
species.get().replace(' ', '_'))
root.config(cursor="")
print("proBAM conversion succesful")
print("%f seconds" % (time.time() - start_time)
) # output script run time
except Exception, e:
print "ERROR:"+str(e)+"\n" \
"Please check if all parameters were supplied correctly, if the error keeps occuring contact " \
"the developers at \"https://github.com/Biobix/proBAMconvert/issues\" " \
"and provide the file to be processed along with the following error message:"
print e
root.config(cursor="")
line=line.split("\t")
key=line[19]+"_"+line[0]
return key
####################
### MAIN PROGRAM ###
####################
if __name__=='__main__':
#get_input_variables()
start_time = time.time()
# start timing function
# hash PSM_DATA and define variables
psm_hash=proBAM_input.get_PSM_hash(psm_file,decoy_annotation)
parse_results=proBAM_IDparser.parseID(psm_hash,species,database,decoy_annotation,database_v,three_frame_translation
,pre_picked_annotation)
annotation=parse_results[1]
psm_hash=parse_results[0]
transcript_hash=annotation[0]
exon_hash=annotation[1]
id_map=parse_results[2]
# convert to SAM
if probed=='N':
file = open_sam_file(directory, name)
create_SAM_header(file, version, database, sorting_order, database_v, species, command_line, psm_file, comments)
PSM2SAM(psm_hash,transcript_hash,exon_hash,decoy_annotation,allowed_mismatches,file,allow_decoys,rm_duplicates,
three_frame_translation,psm_file,id_map,None)
compute_NH_XL(directory, name)
sam_2_bam(directory, name)
