added series of test scripts

scripts/CandidateSequences.py

@@ -6,7 +6,7 @@
 
 DB_ADDRESS = "hera.chem-eng.northwestern.edu"
 PORT=27017
-DB_NAME = "SeqGen_Database2"
+DB_NAME = "SeqGen_Database_v2"
 
 class CandidateSequences:
 
@@ -38,7 +38,7 @@ def add_entry(self, line):
     else:
       return False  
 
-  def calculate_senspec(self, motif_family, any_contains=True):
+  def calculate_senspec(self, motif_family, any_contains=True, get_nonoverlapping=True):
     """returns a score dict, which is a dict of dicts"""
     score_parent_dict = {}
     for key in self.sequence_dict:
@@ -56,13 +56,22 @@ def calculate_senspec(self, motif_family, any_contains=True):
       # to calculate the senspec score, multiply the sensitivity score with the
       # specificity score
       ontarget_list = self.get_ontarget_motifs(entry_list, motif_family,any_contains)
+      print(motif_family)
+      #print("ontarget list:")
       #print(list(ontarget_list))
-      nonoverlapping_ontarget_list = self.get_nonoverlapping_motifs(ontarget_list)
-
+      #for item in ontarget_list:
+      #  print(item['motif_name'])
+
+      if (get_nonoverlapping==True):
+        nonoverlapping_ontarget_list = self.get_nonoverlapping_motifs(ontarget_list)
+      else:
+        nonoverlapping_ontarget_list = ontarget_list
+        nonoverlapping_ontarget_list = list(nonoverlapping_ontarget_list)
+
       n_fam = len(nonoverlapping_ontarget_list)
       #calculate combined zscore
       z_fam = self.get_combined_zscore(nonoverlapping_ontarget_list)
-
+      print(z_fam)
       if n_fam == 0 :
         sensitivity_score = 0
         z_fam = 0
@@ -71,12 +80,16 @@ def calculate_senspec(self, motif_family, any_contains=True):
 
       offtarget_list = self.get_offtarget_motifs(entry_list,motif_family, any_contains)
       offtarget_list = list(offtarget_list)
-      n_other = len(offtarget_list)
+      print("offtarget list:")
+      for item in offtarget_list:
+        print(item['motif_name'])
 
-      if n_other == 0:
-        specificity_score = z_fam/1
+      #nonoverlapping_overall_list = self.get_nonoverlapping_motifs(entry_list)
+      z_other = self.get_combined_zscore(nonoverlapping_ontarget_list+offtarget_list)
+      if z_other == 0:
+        specificity_score = 0
       else:
-        specificity_score = z_fam/n_other #n_other contains motifs including overlapping
+        specificity_score = z_fam/z_other #n_other contains motifs including overlapping
 
       senspec_score = specificity_score * sensitivity_score
 
@@ -108,7 +121,7 @@ def insert_contents(self, collection_base_name, family_scores, individual_scores
     #sequence_dict is a dict with the key as the name and the entries as the
     #entries
     #for key in self.sequence_dict:
-      #entries_collection.insert(self.sequence_dict[key])
+    #  entries_collection.insert(self.sequence_dict[key])
 
     score_dict_list = []
     #insert scores
@@ -134,8 +147,8 @@ def insert_contents(self, collection_base_name, family_scores, individual_scores
     print(score_dict_list)
     #scores_collection_top.insert(score_dict_list[0:100])
     #scores_collection.insert(score_dict_list[100:])
-    scores_collection_top.insert(score_dict_list[0:1])
-    scores_collection.insert(score_dict_list[1:])
+    #scores_collection_top.insert(score_dict_list[0:1])
+    scores_collection.insert(score_dict_list[0:])
     mongo_client.close()
     return True  
 

scripts/FimoEvaluator.py

@@ -52,21 +52,35 @@
       #function parses line, and appends entry to the key
       result_list.append(line)
 
-  print(result_list[0])
+  #print(result_list[0])
   seq_name=result_list[0].split()
   seq_name=seq_name[1]
   seq_name = seq_name.split("_")
-  motif_family = seq_name[0] + "_family.txt"
+  motif_family_file = seq_name[0] + "_family.txt"
+
+  with open(motif_family_file, 'r') as motif_file:
+    motif_family = [line.strip() for line in motif_file]
+
   collection_base_name = "_".join(seq_name[0:4])
   motif_name = "_".join(seq_name[0:-3])
   #after the results are aggregated, perform calculations
   #print("HELLOWORLD")
-  motif_family_scores = sequence_container.calculate_senspec(motif_family)
+  #print("CHECKING THE FAMILY")
+  motif_family_scores = sequence_container.calculate_senspec(motif_family,True,True)
   #print(motif_family_scores)
-  motif_indiv_scores = sequence_container.calculate_senspec([motif_name])
+  #print("CHECKING THE INDIVIDUAL")
+  #print(motif_name)
+  #print(seq_name)
+  #motif_name = "SMAD3_02"
+  #motif_name = "P53_01"
+  motif_indiv_scores = sequence_container.calculate_senspec([motif_name], True, True)
+  #get non-overlapping means only get motifs that don't overlap
+  #
+
   #print(motif_indiv_scores)
   #insert to model
   #sequence_container.insert_contents(Model)
+  #collection_base_name = "new_P53_seqs"
   sequence_container.insert_contents(collection_base_name, motif_family_scores, motif_indiv_scores)
 
   #big_dict = sequence_container.get_dict()

scripts/GATA1_01_1_7777.txt

@@ -0,0 +1,2 @@
+>GATA1_01_paper_control
+GATCAGAAGCTT CACTTGATAACAGAAAGTGATAACAGAAAGTGATAATCTGTCGACCGTCGT

scripts/GATA1_01_1_7778.txt

@@ -0,0 +1,8 @@
+>GATA1_01_3_10000000_s2045195
+GGCGATGGGTCGCGATGGTGCCTGATGGGG
+>GATA1_01_8_10000000_s4092571
+CCTGATGGTGCCTGATGCGGCTCCTGATGGGGC
+>GATA1_01_3_10000000_s8773906
+TGCTCCCGATAGGTCCTGATGGTGGCTGATGGGG
+>GATA1_01_8_10000000_s6344789
+CCTGATAGTGTGCTACGTGATGCCGGGCGATGGGG

scripts/GATA1_01_7777.txt

@@ -0,0 +1,2 @@
+>GATA1_01_paper_control
+GATCAGAAGCTT CACTTGATAACAGAAAGTGATAACAGAAAGTGATAATCTGTCGACCGTCGT

scripts/GATA1_top_seqs.txt

@@ -0,0 +1,6 @@
+>GATA1_01_10_1000000_s927177
+CGCGATGGGGCGTGATGGTGTCCAGCTGATGATGGCGATGGCG
+>GATA1_01_10_1000000_s786785
+CGTGATGGTTCAGGTGAGTCTTTAGGATAACCCAAGATGGTTCGGGTGATGGGG
+>GATA1_01_10_1000000_s340652
+CGCGATGGGGCGTGATGGTGTCCAGCTGATGATGGCGATGGCG

scripts/GATA1_top_seqs_fimo.txt

@@ -0,0 +1,108 @@
+#pattern name	sequence name	start	stop	strand	score	p-value	q-value	matched sequence
+V$SP1_01	GATA1_01_10_1000000_s927177	7	16	+	10.8349	7.78e-05		GGGGCGTGAT
+V$SP1_01	GATA1_01_10_1000000_s340652	7	16	+	10.8349	7.78e-05		GGGGCGTGAT
+V$YY1_02	GATA1_01_10_1000000_s786785	27	46	-	12.6055	1.88e-05		CCCGAACCATCTTGGGTTAT
+V$DELTAEF1_01	GATA1_01_10_1000000_s786785	9	19	-	13.8652	4.99e-07		ACTCACCTGAA
+V$GATA1_01	GATA1_01_10_1000000_s927177	1	10	+	10.561	5.03e-07		CGCGATGGGG
+V$GATA1_01	GATA1_01_10_1000000_s927177	11	20	+	9.80488	2.01e-05		CGTGATGGTG
+V$GATA1_01	GATA1_01_10_1000000_s927177	34	43	+	10.061	8.05e-06		GGCGATGGCG
+V$GATA1_01	GATA1_01_10_1000000_s786785	1	10	+	9.18293	9.89e-05		CGTGATGGTT
+V$GATA1_01	GATA1_01_10_1000000_s786785	45	54	+	10.3171	2.73e-06		GGTGATGGGG
+V$GATA1_01	GATA1_01_10_1000000_s340652	1	10	+	10.561	5.03e-07		CGCGATGGGG
+V$GATA1_01	GATA1_01_10_1000000_s340652	11	20	+	9.80488	2.01e-05		CGTGATGGTG
+V$GATA1_01	GATA1_01_10_1000000_s340652	34	43	+	10.061	8.05e-06		GGCGATGGCG
+V$GATA2_01	GATA1_01_10_1000000_s927177	34	43	+	9.46988	4.61e-05		GGCGATGGCG
+V$GATA2_01	GATA1_01_10_1000000_s340652	34	43	+	9.46988	4.61e-05		GGCGATGGCG
+V$HSF1_01	GATA1_01_10_1000000_s786785	35	44	+	10.3371	8.83e-05		AGATGGTTCG
+V$AP4_Q5	GATA1_01_10_1000000_s927177	21	30	-	11.9633	5.36e-05		ATCAGCTGGA
+V$AP4_Q5	GATA1_01_10_1000000_s340652	21	30	-	11.9633	5.36e-05		ATCAGCTGGA
+V$AP4_Q6	GATA1_01_10_1000000_s927177	21	30	-	12.6016	4.22e-05		ATCAGCTGGA
+V$AP4_Q6	GATA1_01_10_1000000_s340652	21	30	-	12.6016	4.22e-05		ATCAGCTGGA
+V$AREB6_01	GATA1_01_10_1000000_s786785	8	20	-	13.1376	2.5e-05		GACTCACCTGAAC
+V$AREB6_02	GATA1_01_10_1000000_s786785	8	19	-	14.6224	1.35e-06		ACTCACCTGAAC
+V$PPARA_02	GATA1_01_10_1000000_s786785	33	51	+	6.80612	6.25e-05		CAAGATGGTTCGGGTGATG
+V$LBP1_Q6	GATA1_01_10_1000000_s927177	22	28	-	11.9675	8.78e-05		CAGCTGG
+V$LBP1_Q6	GATA1_01_10_1000000_s340652	22	28	-	11.9675	8.78e-05		CAGCTGG
+V$HEB_Q6	GATA1_01_10_1000000_s927177	21	28	+	7.90244	8.21e-05		TCCAGCTG
+V$HEB_Q6	GATA1_01_10_1000000_s340652	21	28	+	7.90244	8.21e-05		TCCAGCTG
+V$SREBP_Q3	GATA1_01_10_1000000_s786785	42	53	-	13.6147	1.7e-05		CCCATCACCCGA
+V$E2_Q6_01	GATA1_01_10_1000000_s786785	29	44	-	13.6327	1.37e-05		CGAACCATCTTGGGTT
+V$TAL1_Q6	GATA1_01_10_1000000_s927177	21	30	+	14.5447	1.07e-05		TCCAGCTGAT
+V$TAL1_Q6	GATA1_01_10_1000000_s340652	21	30	+	14.5447	1.07e-05		TCCAGCTGAT
+V$DEC_Q1	GATA1_01_10_1000000_s786785	7	19	-	11.3902	5.76e-05		ACTCACCTGAACC
+V$HELIOSA_02	GATA1_01_10_1000000_s786785	21	31	+	11.809	4.54e-05		TTTAGGATAAC
+V$SREBP1_Q5	GATA1_01_10_1000000_s786785	39	53	-	10.5854	8.44e-05		CCCATCACCCGAACC
+V$TBX15_02	GATA1_01_10_1000000_s927177	8	25	+	-7.48361	9.42e-05		GGGCGTGATGGTGTCCAG
+V$TBX15_02	GATA1_01_10_1000000_s340652	8	25	+	-7.48361	9.42e-05		GGGCGTGATGGTGTCCAG
+V$KLF15_Q2	GATA1_01_10_1000000_s927177	2	15	+	12.9083	2.22e-05		GCGATGGGGCGTGA
+V$KLF15_Q2	GATA1_01_10_1000000_s340652	2	15	+	12.9083	2.22e-05		GCGATGGGGCGTGA
+V$MATH1_Q2	GATA1_01_10_1000000_s927177	20	29	-	11.3443	8.74e-05		TCAGCTGGAC
+V$MATH1_Q2	GATA1_01_10_1000000_s340652	20	29	-	11.3443	8.74e-05		TCAGCTGGAC
+V$T3RALPHA_Q6	GATA1_01_10_1000000_s786785	8	18	+	11.0337	7.91e-05		GTTCAGGTGAG
+V$YY1_Q6_03	GATA1_01_10_1000000_s786785	34	40	-	10.3553	6.51e-05		CCATCTT
+V$SP4_03	GATA1_01_10_1000000_s927177	1	17	-	12.7152	1.83e-05		CATCACGCCCCATCGCG
+V$SP4_03	GATA1_01_10_1000000_s340652	1	17	-	12.7152	1.83e-05		CATCACGCCCCATCGCG
+V$TCFE2A_04	GATA1_01_10_1000000_s786785	29	45	+	10.753	7.39e-05		AACCCAAGATGGTTCGG
+V$SLUG_Q6	GATA1_01_10_1000000_s786785	10	17	-	12.945	4.87e-05		TCACCTGA
+V$CARRXR_Q2	GATA1_01_10_1000000_s786785	5	18	-	11.9326	4.38e-05		CTCACCTGAACCAT
+V$TAL1_Q6_01	GATA1_01_10_1000000_s927177	22	28	-	11.8807	9.74e-05		CAGCTGG
+V$TAL1_Q6_01	GATA1_01_10_1000000_s340652	22	28	-	11.8807	9.74e-05		CAGCTGG
+V$RXRPXR_Q2	GATA1_01_10_1000000_s786785	6	25	-	11.044	6.76e-05		CTAAAGACTCACCTGAACCA
+V$TFEA_Q6	GATA1_01_10_1000000_s786785	9	20	+	11.3853	6.66e-05		TTCAGGTGAGTC
+V$KLF14_01	GATA1_01_10_1000000_s927177	4	17	-	11.3212	4.4e-05		CATCACGCCCCATC
+V$KLF14_01	GATA1_01_10_1000000_s340652	4	17	-	11.3212	4.4e-05		CATCACGCCCCATC
+V$SP1_05	GATA1_01_10_1000000_s927177	6	16	-	10.7576	7.78e-05		ATCACGCCCCA
+V$SP1_05	GATA1_01_10_1000000_s340652	6	16	-	10.7576	7.78e-05		ATCACGCCCCA
+V$TFAP4_02	GATA1_01_10_1000000_s927177	21	30	+	11.0121	5.83e-05		TCCAGCTGAT
+V$TFAP4_02	GATA1_01_10_1000000_s340652	21	30	+	11.0121	5.83e-05		TCCAGCTGAT
+V$FOXG1_04	GATA1_01_10_1000000_s927177	14	25	-	15.303	2.55e-06		CTGGACACCATC
+V$FOXG1_04	GATA1_01_10_1000000_s340652	14	25	-	15.303	2.55e-06		CTGGACACCATC
+V$FOXK1_06	GATA1_01_10_1000000_s927177	14	24	-	10.7394	4.96e-05		TGGACACCATC
+V$FOXK1_06	GATA1_01_10_1000000_s340652	14	24	-	10.7394	4.96e-05		TGGACACCATC
+V$TBX20_02	GATA1_01_10_1000000_s927177	8	23	+	11.3576	2.47e-05		GGGCGTGATGGTGTCC
+V$TBX20_02	GATA1_01_10_1000000_s340652	8	23	+	11.3576	2.47e-05		GGGCGTGATGGTGTCC
+M3678_0.90$ZEB1	GATA1_01_10_1000000_s786785	11	18	+	13.503	1.21e-05		CAGGTGAG
+M3688_0.90$YY1	GATA1_01_10_1000000_s927177	29	43	+	11.8	3.19e-05		ATGATGGCGATGGCG
+M3688_0.90$YY1	GATA1_01_10_1000000_s340652	29	43	+	11.8	3.19e-05		ATGATGGCGATGGCG
+M3798_0.90$YY1	GATA1_01_10_1000000_s927177	28	42	+	10.4182	6.85e-05		GATGATGGCGATGGC
+M3798_0.90$YY1	GATA1_01_10_1000000_s340652	28	42	+	10.4182	6.85e-05		GATGATGGCGATGGC
+M3626_0.90$CTCF	GATA1_01_10_1000000_s927177	22	36	+	10.3818	7.85e-05		CCAGCTGATGATGGC
+M3626_0.90$CTCF	GATA1_01_10_1000000_s340652	22	36	+	10.3818	7.85e-05		CCAGCTGATGATGGC
+M3713_0.90$CTCF	GATA1_01_10_1000000_s927177	19	36	+	9.77576	9.57e-05		TGTCCAGCTGATGATGGC
+M3713_0.90$CTCF	GATA1_01_10_1000000_s340652	19	36	+	9.77576	9.57e-05		TGTCCAGCTGATGATGGC
+M3718_0.90$CTCF	GATA1_01_10_1000000_s927177	19	36	+	9.70303	9.16e-05		TGTCCAGCTGATGATGGC
+M3718_0.90$CTCF	GATA1_01_10_1000000_s340652	19	36	+	9.70303	9.16e-05		TGTCCAGCTGATGATGGC
+M3775_0.90$CTCF	GATA1_01_10_1000000_s927177	19	38	+	10.4639	6.76e-05		TGTCCAGCTGATGATGGCGA
+M3775_0.90$CTCF	GATA1_01_10_1000000_s340652	19	38	+	10.4639	6.76e-05		TGTCCAGCTGATGATGGCGA
+M3842_0.90$CTCF	GATA1_01_10_1000000_s927177	17	37	+	9.99398	9.02e-05		GGTGTCCAGCTGATGATGGCG
+M3842_0.90$CTCF	GATA1_01_10_1000000_s340652	17	37	+	9.99398	9.02e-05		GGTGTCCAGCTGATGATGGCG
+M3849_0.90$CTCF	GATA1_01_10_1000000_s927177	19	36	+	10.1758	8.2e-05		TGTCCAGCTGATGATGGC
+M3849_0.90$CTCF	GATA1_01_10_1000000_s340652	19	36	+	10.1758	8.2e-05		TGTCCAGCTGATGATGGC
+M4736_0.90$KLF14	GATA1_01_10_1000000_s927177	4	17	-	11.3212	4.4e-05		CATCACGCCCCATC
+M4736_0.90$KLF14	GATA1_01_10_1000000_s340652	4	17	-	11.3212	4.4e-05		CATCACGCCCCATC
+M1798_0.90$SP1	GATA1_01_10_1000000_s927177	7	16	+	10.6	7.08e-05		GGGGCGTGAT
+M1798_0.90$SP1	GATA1_01_10_1000000_s340652	7	16	+	10.6	7.08e-05		GGGGCGTGAT
+M5099_0.90$YY2	GATA1_01_10_1000000_s927177	30	40	+	11.097	6e-05		TGATGGCGATG
+M5099_0.90$YY2	GATA1_01_10_1000000_s340652	30	40	+	11.097	6e-05		TGATGGCGATG
+M0555_0.90$MLL	GATA1_01_10_1000000_s927177	6	15	+	6.82738	9.29e-05		TGGGGCGTGA
+M0555_0.90$MLL	GATA1_01_10_1000000_s340652	6	15	+	6.82738	9.29e-05		TGGGGCGTGA
+M5027_0.90$TBX20	GATA1_01_10_1000000_s927177	8	23	+	10.4242	4.74e-05		GGGCGTGATGGTGTCC
+M5027_0.90$TBX20	GATA1_01_10_1000000_s340652	8	23	+	10.4242	4.74e-05		GGGCGTGATGGTGTCC
+M0174_0.90$Tcfap4	GATA1_01_10_1000000_s927177	22	30	+	10.6303	3.31e-06		CCAGCTGAT
+M0174_0.90$Tcfap4	GATA1_01_10_1000000_s340652	22	30	+	10.6303	3.31e-06		CCAGCTGAT
+M0186_0.90$Srebf1	GATA1_01_10_1000000_s786785	42	50	+	9.98844	1.34e-05		TCGGGTGAT
+M0188_0.90$Srebf2	GATA1_01_10_1000000_s786785	42	49	+	10.9758	6.55e-05		TCGGGTGA
+M0370_0.90$Sp1	GATA1_01_10_1000000_s927177	6	14	+	11.5091	5.53e-05		TGGGGCGTG
+M0370_0.90$Sp1	GATA1_01_10_1000000_s340652	6	14	+	11.5091	5.53e-05		TGGGGCGTG
+M0379_0.90$Sp4	GATA1_01_10_1000000_s927177	6	14	+	10.6364	9.57e-05		TGGGGCGTG
+M0379_0.90$Sp4	GATA1_01_10_1000000_s340652	6	14	+	10.6364	9.57e-05		TGGGGCGTG
+M0380_0.90$Sp4	GATA1_01_10_1000000_s927177	5	14	+	11.097	4.32e-05		ATGGGGCGTG
+M0380_0.90$Sp4	GATA1_01_10_1000000_s340652	5	14	+	11.097	4.32e-05		ATGGGGCGTG
+M0383_0.90$Klf7	GATA1_01_10_1000000_s927177	7	16	+	10.6848	5.75e-05		GGGGCGTGAT
+M0383_0.90$Klf7	GATA1_01_10_1000000_s340652	7	16	+	10.6848	5.75e-05		GGGGCGTGAT
+M0399_0.90$Klf8	GATA1_01_10_1000000_s927177	7	16	+	9.64458	6.95e-05		GGGGCGTGAT
+M0399_0.90$Klf8	GATA1_01_10_1000000_s340652	7	16	+	9.64458	6.95e-05		GGGGCGTGAT
+M0405_0.90$Dnajc21	GATA1_01_10_1000000_s786785	43	52	+	5	4.88e-05		CGGGTGATGG
+M0421_0.90$Klf12	GATA1_01_10_1000000_s927177	7	16	+	10.4485	7.39e-05		GGGGCGTGAT
+M0421_0.90$Klf12	GATA1_01_10_1000000_s340652	7	16	+	10.4485	7.39e-05		GGGGCGTGAT
+M0974_0.90$Pbx1	GATA1_01_10_1000000_s786785	45	53	+	5.56122	3.28e-05		GGTGATGGG

scripts/P53_01_1_7777.txt

@@ -0,0 +1,6 @@
+>P53_01_1_1000000_s767476
+GGACATGCCCGGGCATGTCGGAACATGCCCGGGCATGTCTTCCGGACATGCCCGGGCATGTCATTTGAACATGCCCGGGCATGTCC
+>P53_01_1_1000000_s754784
+GGACATGCCCGGGCATGTCCAGGCATGCCCGGGCATGTCGCATTGAACATGCCCGGGCATGTCTCAGAACATGCCCGGGCATGTCC
+>P53_01_1_1000000_s873835
+GAACATGCCCGGGCATGTCTGAACATGCCCGGGCATGTCTGTAGAACATGCCCGGGCATGTCGCGAGGACATGCCCGGGCATGTCC

scripts/P53_01_1_7778.txt

@@ -0,0 +1,4 @@
+>P53_addgene_control
+CCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGG
+>P53_strategene_control
+TGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGG

scripts/P53_01_1_7779.txt

@@ -0,0 +1,8 @@
+>P53_01_1_10000000_s3135594
+GGGGCATGTCCGGACATGTCTGGACATGCCCGGGCATGTCTGGACATGTCCGGACATGTCT
+>P53_01_9_10000000_s1977093
+TGAAGACATGTCCGGGCATGTCCGGACATGTCCGGACATGTCCGGACATGTCCGGGCATGCTGGAATAG
+>P53_01_5_10000000_s3849070
+GGACATGTCCGGACATGTCCGGACATGTCCGGGCATGTCCGGACATGCCCGAGCATGTCCAACA
+>P53_01_5_10000000_s6267301
+CCGGACATGTCCGGGCATGTCTGGACATGTCCGGACATGTCTGGACATGTCCGGACATGTTGG

scripts/P53_01_1_7780.txt

@@ -0,0 +1,8 @@
+>P53_01_best_seq_0
+GGACATGCCCGGGCATGTCCAGGCATGCCAGGGCATGTCGCATTGAACATGCCCGGGCATGTCTCAGAACATGCCCGGGCATGTCC
+>P53_01_best_seq_1
+GGACATGCCCGGGCATGTCCAGGCATGCCTGGGCATGTCGCATTGAACATGCCCGGGCATGTCTCAGAACATGCCCGGGCATGTCC
+>P53_01_best_seq_3
+GGACATGCCCGGGCATGTCCAGGCATGCCGGGGCATGTCGCATTGAACATGCCCGGGCATGTCTCAGAACATGCCCGGGCATGTCC
+>P53_01_best_seq_2
+GGACATGCCCGGGCATGTCCAGGCATGCCTGGGCTGTCGCATTGAACATGCCCGGGCATGTCTCAGAACATGCCCGGGCATGTCC

scripts/P53_01_control_seqs.txt

@@ -0,0 +1,4 @@
+>P53_addgene_control
+CCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGG
+>P53_strategene_control
+TGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGG

scripts/P53_01_top_seqs.txt

@@ -0,0 +1,6 @@
+>P53_01_1_1000000_s767476
+GGACATGCCCGGGCATGTCGGAACATGCCCGGGCATGTCTTCCGGACATGCCCGGGCATGTCATTTGAACATGCCCGGGCATGTCC
+>P53_01_1_1000000_s754784
+GGACATGCCCGGGCATGTCCAGGCATGCCCGGGCATGTCGCATTGAACATGCCCGGGCATGTCTCAGAACATGCCCGGGCATGTCC
+>P53_01_1_1000000_s873835
+GAACATGCCCGGGCATGTCTGAACATGCCCGGGCATGTCTGTAGAACATGCCCGGGCATGTCGCGAGGACATGCCCGGGCATGTCC

scripts/P53_control_seqs.txt

@@ -0,0 +1,4 @@
+>P53_addgene_control
+CCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGGCCAGGCAAGTCCAGGCAGG
+>P53_strategene_control
+TGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGGTGCCTGGACTTGCCTGG

scripts/P53_family.txt

@@ -2,3 +2,8 @@ P53
 TP53
 P73
 TP73
+P63
+Trp73
+TRP73
+TRP53
+Trp53

scripts/P53_top_seqs.txt

@@ -0,0 +1,6 @@
+>P53_01_1_1000000_s767476
+GGACATGCCCGGGCATGTCGGAACATGCCCGGGCATGTCTTCCGGACATGCCCGGGCATGTCATTTGAACATGCCCGGGCATGTCC
+>P53_01_1_1000000_s754784
+GGACATGCCCGGGCATGTCCAGGCATGCCCGGGCATGTCGCATTGAACATGCCCGGGCATGTCTCAGAACATGCCCGGGCATGTCC
+>P53_01_1_1000000_s873835
+GAACATGCCCGGGCATGTCTGAACATGCCCGGGCATGTCTGTAGAACATGCCCGGGCATGTCGCGAGGACATGCCCGGGCATGTCC