Commit ffa140f3 authored by Roman Sarrazin-Gendron's avatar Roman Sarrazin-Gendron
Browse files

added bayespairing2 development

parent 753baa66
......@@ -4,6 +4,7 @@
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......@@ -26,6 +27,7 @@
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......@@ -46,6 +48,7 @@
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......@@ -347,6 +350,7 @@
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......@@ -393,6 +397,7 @@
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......@@ -522,6 +527,7 @@
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......@@ -3223,6 +3229,7 @@
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......@@ -7801,6 +7808,7 @@
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......@@ -7853,6 +7861,7 @@
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......@@ -8901,13 +8910,7 @@
"137 8\n",
"39 Exterior Loop\n",
"40 Exterior Loop\n",
"41 Exterior Loop\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"41 Exterior Loop\n",
"42 Exterior Loop\n",
"102 Exterior Loop\n",
"103 Exterior Loop\n",
......@@ -10561,6 +10564,7 @@
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......@@ -10601,6 +10605,7 @@
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......@@ -10639,7 +10644,10 @@
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......@@ -10679,7 +10687,10 @@
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......@@ -10697,7 +10708,8 @@
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......@@ -10719,7 +10731,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.7"
"version": "3.6.0"
}
},
"nbformat": 4,
This diff is collapsed.
scanning @ 510ea632
Subproject commit 510ea632270109d5941f1e7c54b68c7fb8225b2b
......@@ -268,6 +268,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
#print(input[index:index + w])
bf = max(0, index)
maxs = run_BP(input[index:index + w], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
if interm:
print('PURE SEQUENCE RESULTS:',maxs)
for mod in modules_to_parse:
corrected_maxes = []
for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
......@@ -275,11 +277,13 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
corrected_maxes.append([i + bf for i in cand])
else:
corrected_maxes.append(cand)
all_maxes.append((mod, index, corrected_maxes))
all_maxes.append((mod, *corrected_maxes))
index = index + s
#print("Running Bayespairing on sequence part:", index, len(input))
#print(input[index:])
maxs = run_BP(input[index:], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
if interm:
print('PURE SEQUENCE RESULTS:',maxs)
for mod in modules_to_parse:
corrected_maxes = []
for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
......@@ -287,7 +291,9 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
corrected_maxes.append([i + index for i in cand])
else:
corrected_maxes.append(cand)
all_maxes.append((mod, index, corrected_maxes))
all_maxes.append((mod, *corrected_maxes))
#print("ALL MAXES FINAL:",all_maxes)
fOUTPUT=fOUTPUT+present_output(all_maxes, t)+"\n"
pickle.dump(all_maxes,open("../output/"+o+".pickle","wb"))
return fOUTPUT,sequences
......
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