Merge pull request #85 from woook/master

correct NGSEQ3 bed files and put in code to (try a) stop happening again
moka-guys · Dec 11, 2017 · 32d2a72 · 32d2a72
2 parents 8ac22d9 + 2fd03cd
commit 32d2a72
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Showing 12 changed files with 71 additions and 5 deletions.
diff --git a/LiveBedfiles/Pan1159_LogFile.txt b/LiveBedfiles/Pan1159_LogFile.txt
@@ -48,4 +48,11 @@ sort -k1,1V -k2,2n -o Pan1159dataSambamba.bed Pan1159dataSambamba.bed
 3. Pan1159dataRefSeqFormat.txt
 A line for each SNV was created in Pan1159_rsID_dataRefSeqFormat.bed
 
-These were copied and pasted in the same order as the above bed files
+These were copied and pasted in the same order as the above bed files
+
+# ============== Missing gene
+It was noticed that due to the missing header in the input file the first gene (ACVRL1) was missing from the output.
+The header line was added to the input file and mokabed re-run.
+The newly created bed files have the suffix _temporary (these were commited in commit https://github.com/woook/mokabed/pull/82/commits/3651f3210cc8e3c9e061cfff3b8b8f83d621260b).
+The lines for ACVRL1 were copied and pasted to the correct position in the bed file to avoid having to repeat the steps described above.
+The difference in https://github.com/woook/mokabed/pull/82/commits/c20b49cd93187411a6ab7411fd110d5cdfdf54c9 show that only lines relating to ACVRL1 were affected.
diff --git a/LiveBedfiles/Pan1159data.bed b/LiveBedfiles/Pan1159data.bed
@@ -501,6 +501,15 @@
 11	71155028	71155271	1717										DHCR7;NM_001360.2
 11	71155890	71156008	1717										DHCR7;NM_001360.2
 12	5153303	5155165	3741										KCNA5;NM_002234.3
+12	52306248	52306329	94										ACVRL1;NM_000020.2
+12	52306872	52307144	94										ACVRL1;NM_000020.2
+12	52307332	52307564	94										ACVRL1;NM_000020.2
+12	52307747	52307867	94										ACVRL1;NM_000020.2
+12	52308212	52308379	94										ACVRL1;NM_000020.2
+12	52308998	52309294	94										ACVRL1;NM_000020.2
+12	52309809	52310027	94										ACVRL1;NM_000020.2
+12	52312758	52312909	94										ACVRL1;NM_000020.2
+12	52314532	52314687	94										ACVRL1;NM_000020.2
 12	57944044	57944193	3798										KIF5A;NM_004984.3
 12	57957211	57957319	3798										KIF5A;NM_004984.3
 12	57957392	57957486	3798										KIF5A;NM_004984.3

diff --git a/LiveBedfiles/Pan1159dataRefSeqFormat.txt b/LiveBedfiles/Pan1159dataRefSeqFormat.txt
@@ -41,6 +41,7 @@ rs111033640	rs111033640	9	+	34646575	34646596	34646575	34646596	1	34646575	34646
 5091	PC;NM_001040716.1	11	-	66616359	66639640	66616359	66639640	20	66616359,66616690,66617071,66617397,66617680,66618134,66618500,66619250,66619899,66620207,66620699,66631234,66633647,66636306,66637762,66638235,66638512,66638775,66639147,66639484	66616628,66616851,66617340,66617597,66617945,66618404,66618761,66619427,66620141,66620317,66620864,66631437,66633830,66636445,66637934,66638373,66638678,66638961,66639352,66639640	nan	PC	nan	nan	0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 1717	DHCR7;NM_001360.2	11	-	71146410	71156008	71146410	71156008	7	71146410,71148847,71149914,71152262,71153298,71155028,71155890	71146895,71148999,71150139,71152496,71153409,71155271,71156008	nan	DHCR7	nan	nan	0,0,0,0,0,0,0
 3741	KCNA5;NM_002234.3	12	+	5153303	5155165	5153303	5155165	1	5153303	5155165	nan	KCNA5	nan	nan	0
+94	ACVRL1;NM_000020.2	12	+	52306248	52314687	52306248	52314687	9	52306248,52306872,52307332,52307747,52308212,52308998,52309809,52312758,52314532	52306329,52307144,52307564,52307867,52308379,52309294,52310027,52312909,52314687	nan	ACVRL1	nan	nan	0,0,0,0,0,0,0,0,0
 3798	KIF5A;NM_004984.3	12	+	57944044	57976972	57944044	57976972	28	57944044,57957211,57957392,57957880,57958232,57958690,57960898,57961266,57962735,57963028,57963307,57963759,57965093,57965833,57966352,57968856,57969412,57969859,57970041,57970533,57971485,57971781,57972010,57974728,57975187,57975642,57976374,57976873	57944193,57957319,57957486,57958005,57958301,57958766,57961006,57961411,57962860,57963197,57963476,57963955,57965182,57966060,57966519,57969065,57969550,57969944,57970171,57970655,57971566,57971873,57972135,57974965,57975361,57975745,57976422,57976972	nan	KIF5A	nan	nan	0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 29110	TBK1;NM_013254.3	12	+	64849640	64895171	64849640	64895171	20	64849640,64853958,64858103,64860670,64867999,64873781,64875611,64878072,64879224,64879695,64882256,64883810,64889252,64889468,64890136,64890718,64890932,64891417,64891737,64895099	64849747,64854119,64858253,64860872,64868180,64873912,64875811,64878289,64879303,64879807,64882378,64883909,64889394,64889565,64890196,64890840,64891049,64891544,64891829,64895171	nan	TBK1	nan	nan	0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 1610	DAO;NM_001917.4	12	+	109278772	109294321	109278772	109294321	10	109278772,109281215,109283234,109283973,109286747,109288028,109290771,109292444,109293142,109294169	109278986,109281350,109283331,109284059,109286822,109288153,109290874,109292582,109293261,109294321	nan	DAO	nan	nan	0,0,0,0,0,0,0,0,0,0

diff --git a/LiveBedfiles/Pan1159dataSambamba.bed b/LiveBedfiles/Pan1159dataSambamba.bed
@@ -499,6 +499,15 @@
 11	71155028	71155271	11-71155028-71155271	0	+	DHCR7;NM_001360.2	1717
 11	71155890	71156008	11-71155890-71156008	0	+	DHCR7;NM_001360.2	1717
 12	5153303	5155165	12-5153303-5155165	0	+	KCNA5;NM_002234.3	3741
+12	52306248	52306329	12-52306248-52306329	0	+	ACVRL1;NM_000020.2	94
+12	52306872	52307144	12-52306872-52307144	0	+	ACVRL1;NM_000020.2	94
+12	52307332	52307564	12-52307332-52307564	0	+	ACVRL1;NM_000020.2	94
+12	52307747	52307867	12-52307747-52307867	0	+	ACVRL1;NM_000020.2	94
+12	52308212	52308379	12-52308212-52308379	0	+	ACVRL1;NM_000020.2	94
+12	52308998	52309294	12-52308998-52309294	0	+	ACVRL1;NM_000020.2	94
+12	52309809	52310027	12-52309809-52310027	0	+	ACVRL1;NM_000020.2	94
+12	52312758	52312909	12-52312758-52312909	0	+	ACVRL1;NM_000020.2	94
+12	52314532	52314687	12-52314532-52314687	0	+	ACVRL1;NM_000020.2	94
 12	57944044	57944193	12-57944044-57944193	0	+	KIF5A;NM_004984.3	3798
 12	57957211	57957319	12-57957211-57957319	0	+	KIF5A;NM_004984.3	3798
 12	57957392	57957486	12-57957392-57957486	0	+	KIF5A;NM_004984.3	3798

diff --git a/LiveBedfiles/Pan1457_LogFile.txt b/LiveBedfiles/Pan1457_LogFile.txt
@@ -1,4 +1,4 @@
-Time Stamp:2017-11-29 17:11:17.400293
+Time Stamp:2017-12-11 10:52:44.876015
 Command arguments executed:
 RefSeq table format version generated as /home/dnanexus/out/Output_files/Pan1457dataRefSeqFormat.txt
 /home/dnanexus/mokabed/LiveBedfiles/TestArea_for_bed_generation_script/OOBed7_uses_mirrored_database_.py --codingup 50 --codingdown 50 --useaccessions --transcripts /home/dnanexus/Pan1457.txt --minuschr --outputfile /home/dnanexus/out/Output_files/Pan1457data.bed --logfile /home/dnanexus/out/Output_files/Pan1457_LogFile.txt 
@@ -14,4 +14,4 @@ RefSeq table format version generated as /home/dnanexus/out/Output_files/Pan1457
 
  cruzdb module file path: /home/dnanexus/anaconda2/lib/python2.7/site-packages/cruzdb/__init__.py
 
-version as defined by git tag = v1.0-204-g5ab2be3
+version as defined by git tag = v1.0-248-g8ac22d9
diff --git a/LiveBedfiles/Pan1457_RPKM.bed b/LiveBedfiles/Pan1457_RPKM.bed
@@ -498,6 +498,15 @@
 11	71154988	71155311	1717
 11	71155850	71156048	1717
 12	5153263	5155205	3741
+12	52306208	52306369	94
+12	52306832	52307184	94
+12	52307292	52307604	94
+12	52307707	52307907	94
+12	52308172	52308419	94
+12	52308958	52309334	94
+12	52309769	52310067	94
+12	52312718	52312949	94
+12	52314492	52314727	94
 12	57944004	57944233	3798
 12	57957171	57957359	3798
 12	57957352	57957526	3798

diff --git a/LiveBedfiles/Pan1457data.bed b/LiveBedfiles/Pan1457data.bed
@@ -1,4 +1,4 @@
-#2017-11-29 17:11:37.853845
+#2017-12-11 10:53:06.106674
 #Chr	Start	Stop	EntrezID										Gene_Accession
 1	11073734	11074072	23435										TARDBP;NM_007375.3
 1	11076850	11077114	23435										TARDBP;NM_007375.3
@@ -500,6 +500,15 @@
 11	71154988	71155311	1717										DHCR7;NM_001360.2
 11	71155850	71156048	1717										DHCR7;NM_001360.2
 12	5153263	5155205	3741										KCNA5;NM_002234.3
+12	52306208	52306369	94										ACVRL1;NM_000020.2
+12	52306832	52307184	94										ACVRL1;NM_000020.2
+12	52307292	52307604	94										ACVRL1;NM_000020.2
+12	52307707	52307907	94										ACVRL1;NM_000020.2
+12	52308172	52308419	94										ACVRL1;NM_000020.2
+12	52308958	52309334	94										ACVRL1;NM_000020.2
+12	52309769	52310067	94										ACVRL1;NM_000020.2
+12	52312718	52312949	94										ACVRL1;NM_000020.2
+12	52314492	52314727	94										ACVRL1;NM_000020.2
 12	57944004	57944233	3798										KIF5A;NM_004984.3
 12	57957171	57957359	3798										KIF5A;NM_004984.3
 12	57957352	57957526	3798										KIF5A;NM_004984.3

diff --git a/LiveBedfiles/Pan1457dataRefSeqFormat.txt b/LiveBedfiles/Pan1457dataRefSeqFormat.txt
@@ -40,6 +40,7 @@
 5091	PC;NM_001040716.1	11	-	66616319	66639680	66616319	66639680	20	66616319,66616650,66617031,66617357,66617640,66618094,66618460,66619210,66619859,66620167,66620659,66631194,66633607,66636266,66637722,66638195,66638472,66638735,66639107,66639444	66616668,66616891,66617380,66617637,66617985,66618444,66618801,66619467,66620181,66620357,66620904,66631477,66633870,66636485,66637974,66638413,66638718,66639001,66639392,66639680	nan	PC	nan	nan	0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 1717	DHCR7;NM_001360.2	11	-	71146370	71156048	71146370	71156048	7	71146370,71148807,71149874,71152222,71153258,71154988,71155850	71146935,71149039,71150179,71152536,71153449,71155311,71156048	nan	DHCR7	nan	nan	0,0,0,0,0,0,0
 3741	KCNA5;NM_002234.3	12	+	5153263	5155205	5153263	5155205	1	5153263	5155205	nan	KCNA5	nan	nan	0
+94	ACVRL1;NM_000020.2	12	+	52306208	52314727	52306208	52314727	9	52306208,52306832,52307292,52307707,52308172,52308958,52309769,52312718,52314492	52306369,52307184,52307604,52307907,52308419,52309334,52310067,52312949,52314727	nan	ACVRL1	nan	nan	0,0,0,0,0,0,0,0,0
 3798	KIF5A;NM_004984.3	12	+	57944004	57977012	57944004	57977012	28	57944004,57957171,57957352,57957840,57958192,57958650,57960858,57961226,57962695,57962988,57963267,57963719,57965053,57965793,57966312,57968816,57969372,57969819,57970001,57970493,57971445,57971741,57971970,57974688,57975147,57975602,57976334,57976833	57944233,57957359,57957526,57958045,57958341,57958806,57961046,57961451,57962900,57963237,57963516,57963995,57965222,57966100,57966559,57969105,57969590,57969984,57970211,57970695,57971606,57971913,57972175,57975005,57975401,57975785,57976462,57977012	nan	KIF5A	nan	nan	0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 29110	TBK1;NM_013254.3	12	+	64849600	64895211	64849600	64895211	20	64849600,64853918,64858063,64860630,64867959,64873741,64875571,64878032,64879184,64879655,64882216,64883770,64889212,64889428,64890096,64890678,64890892,64891377,64891697,64895059	64849787,64854159,64858293,64860912,64868220,64873952,64875851,64878329,64879343,64879847,64882418,64883949,64889434,64889605,64890236,64890880,64891089,64891584,64891869,64895211	nan	TBK1	nan	nan	0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 1610	DAO;NM_001917.4	12	+	109278732	109294361	109278732	109294361	10	109278732,109281175,109283194,109283933,109286707,109287988,109290731,109292404,109293102,109294129	109279026,109281390,109283371,109284099,109286862,109288193,109290914,109292622,109293301,109294361	nan	DAO	nan	nan	0,0,0,0,0,0,0,0,0,0

diff --git a/LiveBedfiles/Pan1457dataSambamba.bed b/LiveBedfiles/Pan1457dataSambamba.bed
@@ -498,6 +498,15 @@
 11	71154988	71155311	11-71154988-71155311	0	+	DHCR7;NM_001360.2	1717
 11	71155850	71156048	11-71155850-71156048	0	+	DHCR7;NM_001360.2	1717
 12	5153263	5155205	12-5153263-5155205	0	+	KCNA5;NM_002234.3	3741
+12	52306208	52306369	12-52306208-52306369	0	+	ACVRL1;NM_000020.2	94
+12	52306832	52307184	12-52306832-52307184	0	+	ACVRL1;NM_000020.2	94
+12	52307292	52307604	12-52307292-52307604	0	+	ACVRL1;NM_000020.2	94
+12	52307707	52307907	12-52307707-52307907	0	+	ACVRL1;NM_000020.2	94
+12	52308172	52308419	12-52308172-52308419	0	+	ACVRL1;NM_000020.2	94
+12	52308958	52309334	12-52308958-52309334	0	+	ACVRL1;NM_000020.2	94
+12	52309769	52310067	12-52309769-52310067	0	+	ACVRL1;NM_000020.2	94
+12	52312718	52312949	12-52312718-52312949	0	+	ACVRL1;NM_000020.2	94
+12	52314492	52314727	12-52314492-52314727	0	+	ACVRL1;NM_000020.2	94
 12	57944004	57944233	12-57944004-57944233	0	+	KIF5A;NM_004984.3	3798
 12	57957171	57957359	12-57957171-57957359	0	+	KIF5A;NM_004984.3	3798
 12	57957352	57957526	12-57957352-57957526	0	+	KIF5A;NM_004984.3	3798

diff --git a/LiveBedfiles/TestArea_for_bed_generation_script/OOBed7_uses_mirrored_database_.py b/LiveBedfiles/TestArea_for_bed_generation_script/OOBed7_uses_mirrored_database_.py
@@ -213,7 +213,17 @@ def filereader(self):
 		if self.genes:
 			self.bed = pd.read_table(self.genes, header= 0)
 		if self.transcripts:
-			self.bed = pd.read_table(self.transcripts, header= 0)
+			# check the transcript file has a header line
+			with open(self.transcripts, 'r') as f:
+				# read the first line only
+    				first_line = f.readline()
+    			# check the first line doesn't contain "NM_" and the header contains a string that should be present in at least one of the column headers (header is GuysAccession	approvedsymbol	GuysAccessionVersion)
+    			if "Accession" in first_line and "NM_" not in first_line:
+    				# read the file into a pandas table
+				self.bed = pd.read_table(self.transcripts, header= 0)
+			else:
+				# if no header report the missing header and exit
+				sys.exit("missing header in transcript file")
 
 	def coordfile(self):
 		#Set up bed file using a bed file where the start positions for each exon are base 0

diff --git a/LiveBedfiles/Transcripts/Pantranscriptfiles/Pan1159.txt b/LiveBedfiles/Transcripts/Pantranscriptfiles/Pan1159.txt
@@ -1,3 +1,4 @@
+Accession	ApprovedSymbol	GuysAccessionVersion
 NM_000020	ACVRL1	0
 NM_020919	ALS2	0
 NM_001145	ANG	0

diff --git a/LiveBedfiles/Transcripts/Pantranscriptfiles/Pan1457.txt b/LiveBedfiles/Transcripts/Pantranscriptfiles/Pan1457.txt
@@ -1,3 +1,4 @@
+GuysAccession	Symbol	GuysAccessionVersion
 NM_000020	ACVRL1	0
 NM_020919	ALS2	0
 NM_001145	ANG	0