def ali_needleFasta(fic1,fic2,outfile = "", gop = 10, gep = 0.5):
# par defaut, le fichier de sortie est place dans le repertoire du fichier 1
if outfile == "":
rep = files.get_filepath(fic1)
name = "%s-%s.needle" % (files.get_name(fic1).lower(),files.get_name(fic2).lower())
outfile = "%s/%s" % (rep, name)
cmd = "%s -asequence %s -bsequence %s -gapopen %s -gapextend %s -outfile %s -aformat3 fasta" % (System.NEEDLE,fic1,fic2,gop,gep,outfile)
os.system(cmd)
def lanceReverseComplementALaChaine():
for fqFile in glob.glob("/Volumes/BioSan/Users/friedrich/Reads/BGI/20130726/CleanData/CBS4104/*.fq"):
repOut = files.get_filepath(fqFile).replace("CleanData/", "CleanData/ReverseComplement/")
#repOut = rep
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmd = "chmod 777 %s" % repOut
os.system(cmd)
outfile = "%s/%s.fq" % (repOut, files.get_name(fqFile))
reverseComplement(fqFile, outfile)
def ali_water(fic1,fic2,outfile = "", gop = 10, gep = 0.5):
# par defaut, le fichier de sortie est place dans le repertoire du fichier 1
if outfile == "":
rep = files.get_filepath(fic1)
name = "%s-%s.water" % (files.get_name(fic1).lower(),files.get_name(fic2).lower())
outfile = "%s/%s" % (rep, name)
cmd = "%s -asequence %s -bsequence %s -gapopen %s -gapextend %s -outfile %s" % (System.WATER,fic1,fic2,gop,gep,outfile)
#print cmd
os.system(cmd)
def createSVConfFile(confFile, strain, bamFile, readLen, mapLen, mu, sigma):
outdir = files.get_filepath(confFile)
of = open(confFile, "w")
of.write(
"<general>\ninput_format = bam\nsv_type = all\nmates_orientation=FR\nread1_length=%s\nread2_length=%s\nmates_file=%s\ncmap_file=%s\noutput_dir=%s\n</general>\n\n" % (
readLen, readLen, bamFile, mapLen, outdir))
of.write("<detection>\nwindow_size=5000\nstep_length=2000\n</detection>\n\n")
of.write(
"<filtering>\nstrand_filtering=1\norder_filtering=1\ninsert_size_filtering=1\nnb_pairs_threshold=10\nnb_pairs_order_threshold=5\nindel_sigma_threshold=10\ndup_sigma_threshold=10\nsingleton_sigma_threshold=10\nfinal_score_threshold=0.9\nmu_length=%s\nsigma_length=%s\n</filtering>\n\n" % (
mu, sigma))
of.close()
def ali_stretcherFasta(fic1,fic2,outfile = ""):
# par defaut, le fichier de sortie est place dans le repertoire du fichier 1
if outfile == "":
rep = files.get_filepath(fic1)
name = "%s-%s.stretcher" % (files.get_name(fic1).lower(),files.get_name(fic2).lower())
outfile = "%s/%s" % (rep, name)
if not os.path.isfile(outfile):
cmd = "%s -asequence %s -bsequence %s -outfile %s -aformat3 fasta" % (System.STRETCHER,fic1,fic2,outfile)
#print cmd
os.system(cmd)
else:
print "%s already exists" % outfile
def client_delete_file(
sock, filename
): # the logic for when the client deletes a file and asks the host to delete it for everyone else too
try:
os.remove(files.get_filepath(filename)) # removes it locally
except Exception as e:
print("Error in client_delete_file: %s" % str(e))
message = DEL + filename + EOT
print("Sending: %s to %s" % (message, str(sock.getpeername())))
sock.send(message.encode(ENCODING))
time.sleep(0.01)
print("Sent Successfully!")
def lancePregCont(strain, config, K):
if string.atoi(K) < 32:
soap = csys.SOAPDENOVO31
elif string.atoi(K) < 64:
soap = csys.SOAPDENOVO63
else:
soap = csys.SOAPDENOVO127
outfile = "%s/ace%s_%s" % (files.get_filepath(config), strain, K)
cmdPG = "%s pregraph -s %s -K %s -d -R -o %s" % (soap, config, K, outfile)
os.system(cmdPG)
cmdC = "%s contig -R -g %s" % (soap, outfile)
os.system(cmdC)
def lanceMapScaf(strain, config, K):
if string.atoi(K) < 31:
soap = csys.SOAPDENOVO31
elif string.atoi(K) < 63:
soap = csys.SOAPDENOVO63
else:
soap = csys.SOAPDENOVO127
outfile = "%s/ace%s_%sPrep" % (files.get_filepath(config), strain, K)
cmdM = "%s map -s %s -g %s" % (soap, config, outfile)
os.system(cmdM)
cmdS = "%s scaff -F -g %s" % (soap, outfile)
os.system(cmdS)
def client_delete_file_from_host(
s, n, data
): # the logic for deleting a file that the host wants the client to delete
fname = data[CCLEN:data.find(EOT)]
print("Request to delete %s" % fname)
currfiles = n.get_file_list()
if fname not in currfiles: # if they dont have the file, for some reason. never ran into this tho
print("do nothing pretty much")
else:
time.sleep(0.1)
print("Deleting file named: %s " % (fname))
try:
os.remove(files.get_filepath(fname))
except Exception as e:
print("Error in client_delete_file_from_host: %s" % str(e))
def traiteFicBug(ficBug):
lgBug = open(ficBug, "r").read().split("\n")
ficBugPrio = "%s/bugPrio2.txt" % files.get_filepath(ficBug)
f = open(ficBugPrio, "w")
for lg in lgBug:
if lg[0:6] == "Reading":
print lg
f.write("\n")
f.write("%s\n" % lg)
elif "n'est pas align" in lg:
print lg
elif "taille inferieur" in lg:
print lg
else:
f.write("%s\n" % lg)
f.close
def client_update_file(
sock, name): # logic for client updating a file and sending it out
truepath = files.get_filepath(name)
fsize = os.path.getsize(truepath)
message = UPD + name + ETX + str(fsize) + EOT
print("Sending: %s to %s" % (message, str(sock.getpeername())))
sock.send(message.encode(ENCODING))
time.sleep(0.01)
with open(truepath, 'rb') as k:
bytessent = 0
while bytessent < fsize:
data = k.read(BUFFER_SIZE)
sock.send(data)
bytessent += len(data)
k.close()
print("Sent Successfully!")
def host_delete_file(filename):
try:
os.remove(files.get_filepath(filename)) # removes it locally
for file in masterlist:
if file.name == filename:
masterlist.remove(
file
) # Add to the master list of all files that are supposed to be synchronized
print("File removed")
except Exception as e:
print("Error in host_delete_file: %s" % str(e))
# Send out command to all current connections to delete that file as well
for sock in sock_list:
message = DEL + filename + EOT
print("Sending: %s to %s" % (message, str(sock.getpeername())))
sock.send(message.encode(ENCODING))
time.sleep(0.01)
print("Sent Successfully!")
def host_delete_file_from_client(sock, n, data):
fname = data[CCLEN:data.find(
EOT)] # Pull the file name from the command sent to us
try:
os.remove(files.get_filepath(fname)) # removes it locally
for file in masterlist:
if file.name == fname:
masterlist.remove(file)
print("File removed")
except Exception as e:
print("Error in host_delete_file_from_client: %s" % str(e))
# Send delete command to all other nodes
for conn in sock_list:
message = DEL + fname + EOT
print("Sending %s to %s" % (message, str(conn.getpeername())))
conn.send(message.encode(ENCODING))
time.sleep(0.01)
print("Sent Successfully!")
def filter_pe_in_fastq(PE_ids, input_fastq):
""" Remove the Pair End sequences detected (the file is strainName-PEseq.sam)
from the fastq files
"""
#output_rep = files.get_filepath(input_fastq).replace("friedrich/Reads/BGI/20130726/CleanData/","dpflieger/NEW/Reads/clean_MP")
output_rep = files.get_filepath(input_fastq).replace("GB-3G/Reads/RawMatePair/", "NEW/Reads/clean_MP/")
print output_rep
if not os.path.isdir(output_rep):
os.mkdir(output_rep)
cmd = "chmod 777 %s" % output_rep
os.system(cmd)
MP_ids = [rec for rec in SeqIO.parse(input_fastq, "fastq") if rec.id[:-2] not in PE_ids] #rm PE entries from fastq
#print "Found %i sequences" % len(MP_ids)
outfile = "%s/%s.fq" % (output_rep, files.get_name(input_fastq))
output_handle = open(outfile, "w")
SeqIO.write(MP_ids, output_handle, "fastq")
output_handle.close()
print "%s created" % outfile
def lanceALaChaine():
# rep = "/Volumes/BioSan/Users/friedrich/GB-3G/SOAPdenovo/CleanReads/Complete/SofConfig/scafmap/scafToFasta"
# #rep = "/Volumes/BioSan/Users/jhou/Documents/Incompatibility/SOAPdenovo/AceRef/ScaffChimere2610"
# liStrains = ['55-86_1','62-196','62-1041','67-588','77-1003','CBS2861','CBS4104','CBS4568','CBS5828','CBS6545','CBS6547','CBS6626','CBS10367','CBS10368','dd281a','DBVPG3108','DBVPG4002','NCYC543',"CBS3082b","CBS3082a","NRBC1892","NRBC1811","NRBC10955","NRBC10572","NRBC101999","DBVPG3452","CBS6546","CBS10369","68917-2"]
# liStrains = ['55-86_1','62-196','62-1041','67-588','77-1003','CBS2861','CBS4104','CBS4568','CBS5828','CBS6545']
# liStrains = ['CBS6547','CBS6626','CBS10367','CBS10368','dd281a','DBVPG3108','DBVPG4002','NCYC543',"CBS3082b","CBS3082a"]
# liStrains = ["NRBC1892","NRBC1811","NRBC10955","NRBC10572","NRBC101999","DBVPG3452","CBS6546","CBS10369","68917-2"]
# #liStrains = ['CECT10266_1b','TL229S2.2','Y6_b','YJM428_1b','YJM454_1b']
# #liStrains = ['Y6_b']
# for strain in liStrains:
# for infile in glob.glob("/Volumes/BioSan/Users/friedrich/GB-3G/SOAPdenovo/CleanReads/Complete/SofConfig/scafmap/scafToFasta/lakl/*fasta"):
## infile = "%s/ace%s.fasta" % (rep, strain)
# rep = files.get_filepath(infile)
# print infile
# identifyScaffChimere("lakl",infile,rep)
#identifyScaffChimere("sace",infile,rep)
for infile in glob.glob("/Volumes/BioSan/Users/friedrich/GB-3G/SOAPdenovo/CleanReads/Complete/SofConfig/scafmap/scafToFasta/lakl/ace10955_2j28_63Prep.fasta"):
# infile = "%s/ace%s.fasta" % (rep, strain)
rep = files.get_filepath(infile)
print infile
identifyScaffChimere("lakl",infile,rep)
def client_console(s, n): # the main driver for client actions
sg.theme('Default1')
layout = [[sg.Listbox(files.get_file_names(), size=(60, 10), key='list')],
[
sg.Button('Add File'),
sg.Button('Update File'),
sg.Button('Delete File'),
sg.Button('Open File'),
sg.Button('Disconnect')
]]
hel = sg.Window('DoggyDoor', layout, icon=logo)
while True:
event, values = hel.read(timeout=3000)
hel['list'].update(files.get_file_names())
if event is None:
break
if event == 'Add File': # logic for adding a file
filepath = sg.popup_get_file('File to add')
print(filepath)
if filepath:
try:
head, filename = os.path.split(filepath)
client_add_file(s, filepath, filename)
hel['list'].update(files.get_file_names())
except socket.error as e:
if e.errno == errno.WSAECONNRESET:
s.close()
break
if event == 'Update File': # logic for updating a file
filename = ''
try:
filename = values['list'][
0] # Throws an exception when nothing is selected, catch it here
except:
print("Make sure you have selected a file to update")
if filename:
try:
client_update_file(s, filename)
hel['list'].update(files.get_file_names())
except socket.error as e:
if e.errno == errno.WSAECONNRESET:
s.close()
break
if event == 'Delete File': # logic for deleting a file
filename = ''
try:
filename = values['list'][
0] # Throws an exception when nothing is selected, catch it here
except:
print("Make sure you have selected a file to delete")
if filename:
try:
client_delete_file(s, filename)
hel['list'].update(files.get_file_names())
except socket.error as e:
if e.errno == errno.WSAECONNRESET:
s.close()
break
if event == 'Open File': # logic for opening a file
filename = ''
try:
filename = values['list'][
0] # Throws an exception when nothing is selected, catch it here
except:
print("Make sure you have selected a file to open")
os.startfile(files.get_filepath(filename))
if event == 'Disconnect': # logic for disconnecting from the host
# delete connection
message = DIS + EOT
try:
s.send(message.encode(
ENCODING)) # sends a message that its disconnecting
except Exception as e:
print("Error in client_console: %s" % str(e))
finally:
s.close()
hel.close()
break
hel['list'].update(files.get_file_names())
def host_console(name, n):
sg.theme('Default1')
layout = [[sg.Listbox(files.get_file_names(), size=(60, 10), key='list')],
[
sg.Button('Add File'),
sg.Button('Update File'),
sg.Button('Delete File'),
sg.Button('Open File'),
sg.Button('Disconnect')
]]
hel = sg.Window('Doggy Door', layout, icon=logo)
while True:
event, values = hel.read(timeout=3000)
hel['list'].update(files.get_file_names())
if event is None:
break
if event == 'Add File':
filepath = sg.popup_get_file('File to add')
print(filepath)
if filepath:
host_add_file(filepath, os.path.basename(filepath))
hel['list'].update(files.get_file_names())
if event == 'Update File':
filename = ''
try:
filename = values['list'][
0] # Throws an exception when nothing is selected, catch it here
except:
print("Make sure you have selected a file to update")
if filename:
host_update_file(filename)
hel['list'].update(files.get_file_names())
if event == 'Delete File':
filename = ''
try:
filename = values['list'][
0] # Throws an exception when nothing is selected, catch it here
except:
print("Make sure you have selected a file to delete")
if filename:
host_delete_file(filename)
hel['list'].update(files.get_file_names())
if event == 'Open File':
filename = ''
try:
filename = values['list'][
0] # Throws an exception when nothing is selected, catch it here
except:
print("Make sure you have selected a file to open")
os.startfile(files.get_filepath(filename))
if event == 'Disconnect':
# delete connection
host_close_connection()
n.nodeOpen = False
hel.close()
break
