-
Notifications
You must be signed in to change notification settings - Fork 11
/
eKLIPse_init.py
executable file
·353 lines (333 loc) · 25.3 KB
/
eKLIPse_init.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
import os
import shutil
import uuid
import time
import tabulate
import pybam
from Bio import SeqIO
from eKLIPse_fct import *
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def arg_manager(argv,pathRootDir,boolColor,boolQT,spinner):
struuid = str(uuid.uuid4())[:8] # analysis identifier
#***** Initialization Dictionnary *****#
dicoInit = {
'startTime':time.time(),\
'pathRootDir':os.path.dirname(os.path.realpath(__file__)),\
'pathDataDir':os.path.join(os.path.dirname(os.path.realpath(__file__)),"data"),\
'pathCircosTemplateDir':os.path.join(os.path.dirname(os.path.realpath(__file__)),"data","circos_template"),\
'pathInput':"",\
'pathOutputDir':os.path.join(os.getcwd(),"eKLIPse_"+struuid),\
'pathGbkRef':"",\
'pathTmpDir':os.path.join("/tmp","eKLIPse_"+struuid),\
'pathBlastN':"blastn",\
'pathMakeblastdb':"makeblastdb",\
'pathCircosBin':"circos",\
'pathSamtools':"samtools",\
'dicoBam':{},\
'dicoGbk':{},\
'windows':False,\
'lstTitleBam':[],\
'minQ':20, 'minlen':100, 'SCsize':25, 'MappedPart':20,\
'downCov':500000, 'delShift':5,\
'mitosize':1000, 'minblast':1, 'bilateral':True,\
'blastIdThreshold':80, 'blastCovThreshold':70,'blastGapOpen':0, 'blastGapExt':2,\
'nbThread':1, 'boolColor':boolColor,'boolQT':boolQT,\
}
#***** Check Required Arguments *****#
if len(argv)==1 or argv[1]=="-h" or argv[1]=="--help": manual_display([],dicoInit,spinner)
if not "-in" in argv and not "--test" in argv: manual_display(["Missing required \"-in\" argument"],dicoInit,spinner)
if not "-ref" in argv and not "--test" in argv: manual_display(["Missing required \"-ref\" argument"],dicoInit,spinner)
# Executables path (local for Windows / $PATH or arguments for linux)
path_exe_src = os.path.join(os.path.dirname(os.path.realpath(__file__)),"src")
if os.path.isdir(path_exe_src):
dicoInit['pathBlastN'] = os.path.join(path_exe_src,"blast-2.6.0+","blastn.exe")
dicoInit['pathMakeblastdb'] = os.path.join(path_exe_src,"blast-2.6.0+","makeblastdb.exe")
dicoInit['pathCircosBin'] = os.path.join(path_exe_src,"circos-0.69-6","bin","circos.exe")
dicoInit['pathSamtools'] = os.path.join(path_exe_src,"samtools.exe")
dicoInit['windows'] = True
else:
if not "-blastn" in argv and any(os.access(os.path.join(path, "blastn"), os.X_OK) for path in os.environ["PATH"].split(os.pathsep))==False: manual_display(["eKLIPse required \"blastn\" in PATH or \"-blastn\" defined"],dicoInit,spinner)
if not "-makeblastdb" in argv and any(os.access(os.path.join(path, "makeblastdb"), os.X_OK) for path in os.environ["PATH"].split(os.pathsep))==False: manual_display(["eKLIPse required \"makeblastdb\" in PATH or \"-makeblastdb\" defined"],dicoInit,spinner)
if not "-circos" in argv and any(os.access(os.path.join(path, "circos"), os.X_OK) for path in os.environ["PATH"].split(os.pathsep))==False: manual_display(["eKLIPse required \"circos\" in PATH or \"-circos\" defined"],dicoInit,spinner)
if not "-samtools" in argv and any(os.access(os.path.join(path, "samtools"), os.X_OK) for path in os.environ["PATH"].split(os.pathsep))==False: manual_display(["eKLIPse required \"samtools\" in PATH or \"-samtools\" defined"],dicoInit,spinner)
#**** Read Passed Arguments *****#
prev_arg = ""
lstErrorDisplay = []
for i in range(1,len(argv),2):
if prev_arg=="--": i-=1
prev_arg = ""
# Input file with BAMs path
if argv[i]=="-in":
if not os.path.isfile(argv[i+1]): lstErrorDisplay.append("Input file \""+argv[i+1]+"\" not found")
else:
dicoInit['pathInput'] = argv[i+1]
IN = open(argv[i+1],'r') ; lstLine = split(IN.read(),"\n") ; IN.close()
for j in range(len(lstLine)):
if lstLine[j]!="" and not lstLine[j][0]=="#":
try:
pathBam = split(lstLine[j],"\t")[0]
titleBam = split(lstLine[j],"\t")[1]
if not os.path.isfile(pathBam): lstErrorDisplay.append("Input file at line"+str(j+1)+": \""+pathBam+"\" not found")
if titleBam in dicoInit['lstTitleBam']: lstErrorDisplay.append("Input file at line "+str(j+1)+": \""+titleBam+"\" name already used")
dicoInit['lstTitleBam'].append(titleBam)
dicoInit["dicoBam"][titleBam] = {'path':pathBam, 'refName':"", 'nbReads':0, 'path_downsampling':""}
except: lstErrorDisplay.append("Input file at line "+str(j+1)+": bad syntax")
# Reference GBK file
elif argv[i]=="-ref":
if not os.path.isfile(argv[i+1]): lstErrorDisplay.append("Reference GBK file \""+argv[i+1]+"\" not found")
else:
dicoInit['pathGbkRef'] = argv[i+1]
for gb_record in SeqIO.parse(open(argv[i+1],"r"), "genbank") :
dicoInit["dicoGbk"]['refName'] = gb_record.name
dicoInit["dicoGbk"]['refDescr'] = gb_record.description
dicoInit["dicoGbk"]['refSeq'] = str(gb_record.seq)
dicoInit["dicoGbk"]['refLength'] = len(gb_record.seq)
dicoInit["dicoGbk"]['lstGene'] = []
for feature in gb_record.features:
if feature.type=="gene":
if feature.qualifiers['nomenclature'][0].lower().__contains__("trna"): geneType = "trna"
elif feature.qualifiers['nomenclature'][0].lower().__contains__("rna"): geneType = "rrna"
else: geneType = "protein"
try: name = split(split(feature.qualifiers['nomenclature'][0],"|")[0],":")[1].replace(" ","")
except: name = feature.qualifiers['gene'][0]
dicoInit["dicoGbk"]['lstGene'].append([name,int(feature.location.start)+1,int(feature.location.end),geneType])
if len(dicoInit["dicoGbk"])==0: lstErrorDisplay.append("Cannot Read Reference GBK file \""+argv[i+1]+"\"")
elif argv[i]=="--test":
prev_arg = "--"
dicoInit['lstTitleBam'] = ["test_Illumina","test_proton"]
dicoInit["dicoBam"] = {"test_Illumina":{'path':dicoInit["pathDataDir"]+"/test_illumina.bam", 'refName':"", 'nbReads':0, 'path_downsampling':""},"test_proton":{'path':dicoInit["pathDataDir"]+"/test_proton.bam", 'refName':"", 'nbReads':0, 'path_downsampling':""}}
dicoInit['pathGbkRef'] = dicoInit["pathDataDir"]+"/NC_012920.1.gb"
for gb_record in SeqIO.parse(open(dicoInit['pathGbkRef'],"r"), "genbank") :
dicoInit["dicoGbk"]['refName'] = gb_record.name
dicoInit["dicoGbk"]['refDescr'] = gb_record.description
dicoInit["dicoGbk"]['refSeq'] = str(gb_record.seq)
dicoInit["dicoGbk"]['refLength'] = len(gb_record.seq)
dicoInit["dicoGbk"]['lstGene'] = []
for feature in gb_record.features:
if feature.type=="gene":
if feature.qualifiers['nomenclature'][0].lower().__contains__("trna"): geneType = "trna"
elif feature.qualifiers['nomenclature'][0].lower().__contains__("rna"): geneType = "rrna"
else: geneType = "protein"
try: name = split(split(feature.qualifiers['nomenclature'][0],"|")[0],":")[1].replace(" ","")
except: name = feature.qualifiers['gene'][0]
dicoInit["dicoGbk"]['lstGene'].append([name,int(feature.location.start)+1,int(feature.location.end),geneType])
# Results Directory
elif argv[i]=="-out":
if boolQT==True: dicoInit['pathOutputDir'] = argv[i+1] # uuid already done
else: dicoInit['pathOutputDir'] = os.path.join(argv[i+1],"eKLIPse_"+struuid)
# Temporary Directory
elif argv[i]=="-tmp": # Temporary folder
if boolQT==True: dicoInit['pathTmpDir'] = argv[i+1] # uuid already done
else: dicoInit['pathTmpDir'] = os.path.join(argv[i+1],"eKLIPse_"+struuid)
# Min Read quality
elif argv[i]=="-minq": # The minimum read quality to consider
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-minQ\" integer expected")
else: dicoInit["minQ"] = int(argv[i+1])
# Min Read length
elif argv[i]=="-minlen":
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-minlen\" integer expected")
else: dicoInit["minlen"] = int(argv[i+1])
# SoftClipping analysis threshold
elif argv[i]=="-scsize": # The minimum length of softclip to keep
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-SC_size\" integer expected")
else: dicoInit["SCsize"] = int(argv[i+1])
# SoftClipping analysis threshold
elif argv[i]=="-mapsize": # The size of mapped read sequence send to blast
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-MappedPart\" integer expected")
else: dicoInit["MappedPart"] = int(argv[i+1])
# Maximum reads coverage
elif argv[i]=="-downcov": #
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-downCov\" integer expected")
else: dicoInit["downCov"] = int(argv[i+1])
# Deletion position shift
elif argv[i]=="-shift": #
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-shift\" integer expected")
else: dicoInit["delShift"] = int(argv[i+1])
# Minimal length for deleted mito
elif argv[i]=="-mitosize": #
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-mitosize\" integer expected")
else: dicoInit["mitosize"] = int(argv[i+1])
# Minimal number of BLAST per breakpoint
elif argv[i]=="-minblast": #
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-minblast\" integer expected")
else: dicoInit["minblast"] = int(argv[i+1])
# Filter non-bilateral BLAST deletions
elif argv[i]=="-bilateral": #
if argv[i+1].lower()!="true" and argv[i+1].lower()!="false": lstErrorDisplay.append("\"-bilateral\" boolean expected")
else:
if argv[i+1].lower()=="true": dicoInit["bilateral"] = True
else: dicoInit["bilateral"] = False
# BlastN analysis threshold
elif argv[i]=="-id": # The minimum identity to keep a blast
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-blast_id\" integer expected")
else: dicoInit["blastIdThreshold"] = int(argv[i+1])
elif argv[i]=="-cov": # The minimum depth between the query and the subject in the blast
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-blast_cov\" integer expected")
else: dicoInit["blastCovThreshold"] = int(argv[i+1])
elif argv[i]=="-gapopen": # Cost to open a gap
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-blast_gapopen\" integer expected")
else: dicoInit["blastGapOpen"] = int(argv[i+1])
elif argv[i]=="-gapext": # Cost to extend a gap
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-blast_gapext\" integer expected")
else: dicoInit["blastGapExt"] = int(argv[i+1])
# Number of threads
elif argv[i]=="-thread":
if string_to_num(argv[i+1])!="int": lstErrorDisplay.append("\"-nb_threads\" integer expected")
else: dicoInit["nbThread"] = int(argv[i+1])
# Programs
elif argv[i]=="-blastn":
if not os.path.isfile(argv[i+1]): lstErrorDisplay.append("\"-blastn\" binary not found")
else: dicoInit['pathBlastN'] = argv[i+1]
elif argv[i]=="-makeblastdb":
if not os.path.isfile(argv[i+1]): lstErrorDisplay.append("\"-makeblastdb\" binary not found")
else: dicoInit['pathMakeblastdb'] = argv[i+1]
elif argv[i]=="-circos":
if not os.path.isfile(argv[i+1]): lstErrorDisplay.append("\"-circos\" binary not found")
else: dicoInit['pathCircosBin'] = argv[i+1]
elif argv[i]=="-samtools":
if not os.path.isfile(argv[i+1]): lstErrorDisplay.append("\"-samtools\" binary not found")
else: dicoInit['pathSamtools'] = argv[i+1]
elif argv[i]=="--qtgui" or argv[i]=="--nocolor": prev_arg = "--"
else: lstErrorDisplay.append("\""+argv[i]+"\" unrecognized parameters")
#***** CHECK GAP OPEN & EXTEND *****#
boolGap = False
if dicoInit["blastGapOpen"]>=2 and dicoInit["blastGapExt"]>=2: boolGap = True
if dicoInit["blastGapOpen"]==1 and dicoInit["blastGapExt"]==2: boolGap = True
if dicoInit["blastGapOpen"]==0 and dicoInit["blastGapExt"]==2: boolGap = True
if dicoInit["blastGapOpen"]==2 and dicoInit["blastGapExt"]==1: boolGap = True
if dicoInit["blastGapOpen"]==1 and dicoInit["blastGapExt"]==1: boolGap = True
if boolGap==False: lstErrorDisplay.append("Gap existence and extension "+str(dicoInit["blastGapOpen"])+" and "+str(dicoInit["blastGapExt"])+" are not supported. Please use (>=2 and >=2) or (1 and 2) or (0 and 2) or (2 and 1) or (1 and 1)")
#***** CREATE DIRECTORIES *****#
if not os.path.isdir(dicoInit['pathOutputDir']):
try: os.makedirs(dicoInit['pathOutputDir'])
except: lstErrorDisplay.append("Unable to create output folder \""+dicoInit['pathOutputDir']+"\"")
if not os.path.isdir(dicoInit['pathTmpDir']):
try: os.makedirs(dicoInit['pathTmpDir'])
except: lstErrorDisplay.append("Unable to create temporary folder \""+dicoInit['pathTmpDir']+"\"")
#***** CHECK errors & BAMs *****#
# Return error(s) if found
if len(lstErrorDisplay)!=0: manual_display(lstErrorDisplay,dicoInit,spinner)
# Else check BAMs
else:
# Copy circos conf files
headerBool = False
for titleBam in dicoInit["dicoBam"].keys():
# Test bai
if not os.path.isfile(dicoInit['dicoBam'][titleBam]['path']+".bai"):
cmd_index = dicoInit['pathSamtools']+" index "+dicoInit['dicoBam'][titleBam]['path']
os.system(cmd_index)
# Retrieve header
path_idxstats = os.path.join(dicoInit['pathTmpDir'],"idxstats.txt")
if dicoInit['windows']==False: cmd_idxstats = dicoInit['pathSamtools']+" idxstats "+dicoInit['dicoBam'][titleBam]['path']+" 1>"+path_idxstats+" 2>/dev/null"
else: cmd_idxstats = dicoInit['pathSamtools']+" idxstats "+dicoInit['dicoBam'][titleBam]['path']+" 1>"+path_idxstats+" 2> nul"
os.system(cmd_idxstats)
IN = open(path_idxstats,'r') ; lst_lines = split(IN.read(),"\n") ; IN.close()
for line in lst_lines:
split_line = split(line,"\t")
if len(split_line)>1:
refName = split_line[0]
refSize = int(split_line[1])
nb_reads = int(split_line[2])
if refSize==dicoInit["dicoGbk"]['refLength']:
headerBool = True
dicoInit["dicoBam"][titleBam]['refName'] = refName
dicoInit["dicoBam"][titleBam]['nbReads'] = nb_reads
break
if not headerBool: lstErrorDisplay.append("Any mitochondrial header found in file \""+dicoInit["dicoBam"][titleBam]['path']+"\"")
if dicoInit["dicoBam"][titleBam]['refName']=="": lstErrorDisplay.append("Unable to find correspunding reference size in header \""+dicoInit["dicoBam"][titleBam]['path']+"\"")
# Return BAM error(s) if found
if len(lstErrorDisplay)!=0: manual_display(lstErrorDisplay,dicoInit,spinner)
#***** WRITE REFERENCE Fasta and blastdb *****#
path_fasta_out = os.path.join(dicoInit['pathTmpDir'],"ref.fa")
OUT = open(path_fasta_out,'w')
OUT.write(">"+dicoInit["dicoGbk"]['refName']+"\n"+dicoInit["dicoGbk"]['refSeq']+"\n")
OUT.close()
if dicoInit['windows']==False: os.system(dicoInit['pathMakeblastdb']+" -dbtype nucl -in "+path_fasta_out+" > /dev/null 2>&1")
else: os.system(dicoInit['pathMakeblastdb']+" -dbtype nucl -in "+path_fasta_out+" > nul 2>&1")
# Return dicoInit
return dicoInit
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def manual_display(lst_error,dicoInit,spinner):
if dicoInit['boolQT']==False: spinner.stop()
printcolor("\n\n USAGE: python eKLIPse -in <FILE with Alignment paths> -ref <GBK reference> [OPTIONS]\n\n","bold yellow",dicoInit['boolColor'])
printcolor(" OPTIONS:\n","bold white",dicoInit['boolColor'])
printcolor(" -out <str> : Output directory path [current]\n","white",dicoInit['boolColor'])
printcolor(" -tmp <str> : Temporary directory path [/tmp]\n","white",dicoInit['boolColor'])
printcolor(" -scsize <int> : Soft-clipping minimal length [25]\n","white",dicoInit['boolColor'])
printcolor(" -mapsize <int> : Upstream mapping length [20]\n","white",dicoInit['boolColor'])
printcolor(" -downcov <int> : Downsampling reads number [500000] (0=disable)\n","white",dicoInit['boolColor'])
printcolor(" -minq <int> : Read quality threshold [20]\n","white",dicoInit['boolColor'])
printcolor(" -minlen <int> : Read length threshold [100]\n","white",dicoInit['boolColor'])
printcolor(" -shift <int> : Breakpoint BLAST shift length [5]\n","white",dicoInit['boolColor'])
printcolor(" -minblast <int> : Minimal number of BLAST per breakpoint [1]\n","white",dicoInit['boolColor'])
printcolor(" -bilateral <bool> : Filter non-bilateral BLAST deletions [True]\n","white",dicoInit['boolColor'])
printcolor(" -mitosize <int> : Minimal resulting mitochondria size [1000]\n","white",dicoInit['boolColor'])
printcolor(" -id <int> : BLAST %identity threshold [80]\n","white",dicoInit['boolColor'])
printcolor(" -cov <int> : BLAST %coverage threshold [70]\n","white",dicoInit['boolColor'])
printcolor(" -gapopen <int> : BLAST cost to open a gap [0:proton, 5:illumina]\n","white",dicoInit['boolColor'])
printcolor(" -gapext <int> : BLAST cost to extend a gap [2]\n","white",dicoInit['boolColor'])
printcolor(" -thread <int> : Number of thread to use [2]\n","white",dicoInit['boolColor'])
printcolor(" -samtools <str> : samtools bin path [$PATH]\n","white",dicoInit['boolColor'])
printcolor(" -blastn <str> : BLASTn bin path [$PATH]\n","white",dicoInit['boolColor'])
printcolor(" -makeblastdb <str> : makeblastdb bin path [$PATH]\n","white",dicoInit['boolColor'])
printcolor(" -circos <str> : circos bin path [$PATH]\n","white",dicoInit['boolColor'])
printcolor(" --test : eKLIPse test\n","white",dicoInit['boolColor'])
printcolor(" --nocolor : Disable output colors\n\n","white",dicoInit['boolColor'])
printerror(lst_error)
try: shutil.rmtree(dicoInit['pathOutputDir']) ; shutil.rmtree(dicoInit['pathTmpDir'])
except: pass
sys.exit()
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def config_display(dicoInit):
print "\n"
format_time = time.strftime('%d/%m/%y %H:%M:%S',time.localtime(dicoInit['startTime']))
printcolor(" Start time : ","bold white",dicoInit['boolColor'])
printcolor(format_time+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Input file path : ","bold white",dicoInit['boolColor'])
printcolor(dicoInit['pathInput']+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Reference : ","bold white",dicoInit['boolColor'])
printcolor(dicoInit['pathGbkRef']+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Output folder : ","bold white",dicoInit['boolColor'])
printcolor(dicoInit['pathOutputDir']+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Temporary folder : ","bold white",dicoInit['boolColor'])
printcolor(dicoInit['pathTmpDir']+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Read threshold : ","bold white",dicoInit['boolColor'])
printcolor("minQ="+str(dicoInit['minQ'])+" | minlen="+str(dicoInit['minlen'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" SC threshold : ","bold white",dicoInit['boolColor'])
printcolor("SCsize="+str(dicoInit['SCsize'])+" | MappedPart="+str(dicoInit["MappedPart"])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Deletion shift : ","bold white",dicoInit['boolColor'])
printcolor(str(dicoInit['delShift'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Min mito size : ","bold white",dicoInit['boolColor'])
printcolor(str(dicoInit['mitosize'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Min breakpoint BLAST : ","bold white",dicoInit['boolColor'])
printcolor(str(dicoInit['minblast'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Filter non-bilateral : ","bold white",dicoInit['boolColor'])
printcolor(str(dicoInit['bilateral'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" BLAST thresholds : ","bold white",dicoInit['boolColor'])
printcolor("id="+str(dicoInit['blastIdThreshold'])+" | cov="+str(dicoInit['blastCovThreshold'])+" | gapopen="+str(dicoInit['blastGapOpen'])+" | gapext="+str(dicoInit['blastGapExt'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Downsampling : ","bold white",dicoInit['boolColor'])
if dicoInit['downCov']==0 : printcolor("none\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
else : printcolor(str(dicoInit['downCov'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
printcolor(" Threads number : ","bold white",dicoInit['boolColor'])
printcolor(str(dicoInit['nbThread'])+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
bamTable = tabulate_bam(dicoInit['dicoBam'],dicoInit['lstTitleBam'],).replace("\n","\n ")
printcolor(" Input alignments : ","bold white",dicoInit['boolColor'])
printcolor(str(len(dicoInit['dicoBam']))+"\n","white",dicoInit['boolColor'])
printcolor(" "+bamTable+"\n","white",dicoInit['boolColor']) ; time.sleep(0.1)
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def tabulate_bam(dicoBam,lstTitleBam):
bamContent = [] ; bamHeader = ["Name","BAM header","Nb Reads"]
for titleBam in lstTitleBam:
bamContent.append([titleBam,dicoBam[titleBam]['refName'],dicoBam[titleBam]['nbReads']])
return str(tabulate.tabulate(bamContent,bamHeader,tablefmt="psql",stralign="center",numalign="center").encode('utf-8'))
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#