# HG changeset patch
# User saketkc
# Date 1412721177 14400
# Node ID 473d1c2ca65df893da7d6a9060896ffbeafebb2b
# Parent  47ca5fb1b3f7b506a35ca5b35d6a9816f222adef
Uploaded

diff -r 47ca5fb1b3f7 -r 473d1c2ca65d chasm_webservice/chasm_webservice.xml
--- a/chasm_webservice/chasm_webservice.xml	Wed Jul 16 20:31:41 2014 -0400
+++ b/chasm_webservice/chasm_webservice.xml	Tue Oct 07 18:32:57 2014 -0400
@@ -1,7 +1,9 @@
 <tool id="chasm_webservice" name="CHASM Webservice" version="1.0.0" hidden="false">
     <requirements>
         <requirement type="package" version="2.2.1">requests</requirement>
+        <requirement type="package" version="0.9.3">xlrd</requirement>
         <requirement type="python-module">requests</requirement>
+        <requirement type="python-module">xlrd</requirement>
     </requirements>
     <description>CHASM score using CRAVAT webservice</description>
     <command interpreter="python">
diff -r 47ca5fb1b3f7 -r 473d1c2ca65d chasm_webservice/test-data/chasm_output_codons.tabular
--- a/chasm_webservice/test-data/chasm_output_codons.tabular	Wed Jul 16 20:31:41 2014 -0400
+++ b/chasm_webservice/test-data/chasm_output_codons.tabular	Tue Oct 07 18:32:57 2014 -0400
@@ -1,13 +1,14 @@
 #Amino Acid Level Analysis Report
-#2014-07-15 03:23:43.460539
+#2014-08-28 22:54:22.487446
+#CRAVAT version: 3.1
 #Analysis done at http://www.cravat.us.
-#Input file: dataset_346.dat
+#Input file: dataset_1.dat
 #This report shows analysis results at amino acid level.
 #Input coordinate was hg19 genomic.
 #For more information on CRAVAT, visit http://www.cravat.us.
 #
-Transcript	Amino acid position	Sequence Ontology	Reference amino acid(s)	Alternate amino acid(s)	HUGO symbol	Other transcripts	Occurrences in study [amino acid change]	Transcript in COSMIC	Protein sequence change in COSMIC	Occurrences in COSMIC [amino acid change]	Occurrences in COSMIC by primary sites [amino acid change]
+Transcript	Amino acid position	Sequence Ontology	Reference amino acid(s)	Protein sequence change	HUGO symbol	Other transcripts	Occurrences in study [amino acid change]	Transcript in COSMIC	Protein sequence change in COSMIC	Occurrences in COSMIC [amino acid change]	Occurrences in COSMIC by primary sites [amino acid change]
 NM_021090.3	1198	MS	N	I	MTMR3	NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I	1			0	
 NM_001206998.1	637	MS	H	R	ZNRF3	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R	2			0	
-NM_020831.3	648	MS	S	G	MKL1	ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G	1			0	
+NM_020831.3	648	MS	S	G	MKL1	ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G	1	ENST00000355630	p.S648G (stomach 1)	1	stomach(1)
 NM_020831.3	396	MS	A	T	MKL1	ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T	1			0	
diff -r 47ca5fb1b3f7 -r 473d1c2ca65d chasm_webservice/test-data/chasm_output_genes.tabular
--- a/chasm_webservice/test-data/chasm_output_genes.tabular	Wed Jul 16 20:31:41 2014 -0400
+++ b/chasm_webservice/test-data/chasm_output_genes.tabular	Tue Oct 07 18:32:57 2014 -0400
@@ -1,14 +1,15 @@
 #Gene Level Analysis Report
-#2014-07-15 03:23:43.461186
+#2014-08-28 22:54:22.487967
+#CRAVAT version: 3.1
 #Analysis done at http://www.cravat.us.
-#Input file: dataset_346.dat
+#Input file: dataset_1.dat
 #This report shows analysis results at gene level.
 #The composite p-value (Stouffer's combined p-value) and composite FDR of a gene show how probable it is to get the same p-value distribution for the gene as that obtained from the input variants by chance.
 #Input coordinate was hg19 genomic.
 #Tissue type for CHASM analysis: Other
 #For more information on CRAVAT, visit http://www.cravat.us.
 #
-HUGO symbol	Best driver score from representative transcripts	Composite p value	Composite FDR	Occurrences in study [gene mutated]	Occurrences in COSMIC [gene mutated]	Occurrences in COSMIC by primary sites [gene mutated]	MuPIT link
-MTMR3	0.6	0.3364	0.55	1	102	upper_aerodigestive_tract(2);large_intestine(24);haematopoietic_and_lymphoid_tissue(5);endometrium(12);urinary_tract(4);oesophagus(1);liver(3);skin(17);lung(17);ovary(5);prostate(2);kidney(4);breast(6
)	 
-ZNRF3	0.514	0.171	0.55	2	73	upper_aerodigestive_tract(2);large_intestine(19);autonomic_ganglia(1);haematopoietic_and_lymphoid_tissue(2);endometrium(12);urinary_tract(2);lung(16);liver(5);skin(1);oesophagus(3);ovary(2);NS(1);prostate(2);kidney(3);breast(2
)	 
-MKL1	0.728	0.793956248886469	1	2	68	large_intestine(15);stomach(2);central_nervous_system(1);haematopoietic_and_lymphoid_tissue(3);endometrium(13);urinary_tract(1);lung(19);breast(3);skin(1);ovary(5);kidney(4);liver(1
)	 
+HUGO symbol	Driver Genes	TARGET	Best driver score from representative transcripts	Occurrences in study [gene mutated]	Occurrences in COSMIC [gene mutated]	Occurrences in COSMIC by primary sites [gene mutated]	MuPIT link
+MTMR3			0.582	1	103	upper_aerodigestive_tract(2);large_intestine(24);haematopoietic_and_lymphoid_tissue(5);endometrium(12);urinary_tract(4);oesophagus(1);breast(6);skin(17);lung(17);ovary(5);NS(1);prostate(2);kidney(4);liver(3)	 
+ZNRF3			0.524	2	73	upper_aerodigestive_tract(2);large_intestine(19);autonomic_ganglia(1);haematopoietic_and_lymphoid_tissue(2);endometrium(12);urinary_tract(2);lung(16);liver(5);skin(1);oesophagus(3);ovary(2);NS(1);prostate(2);kidney(3);breast(2)	 
+MKL1			0.668	2	68	large_intestine(15);stomach(2);central_nervous_system(1);haematopoietic_and_lymphoid_tissue(3);endometrium(13);urinary_tract(1);lung(19);breast(3);skin(1);ovary(5);kidney(4);liver(1)	 
diff -r 47ca5fb1b3f7 -r 473d1c2ca65d chasm_webservice/test-data/chasm_output_variants.tabular
--- a/chasm_webservice/test-data/chasm_output_variants.tabular	Wed Jul 16 20:31:41 2014 -0400
+++ b/chasm_webservice/test-data/chasm_output_variants.tabular	Tue Oct 07 18:32:57 2014 -0400
@@ -1,15 +1,16 @@
 #Variant Level Analysis Report
-#2014-07-15 03:23:43.461879
+#2014-08-28 22:54:22.488508
+#CRAVAT version: 3.1
 #Analysis done at http://www.cravat.us.
-#Input file: dataset_346.dat
+#Input file: dataset_1.dat
 #This report shows analysis results at variant level.
 #Input coordinate was hg19 genomic.
 #Tissue type for CHASM analysis: Other
 #For more information on CRAVAT, visit http://www.cravat.us.
 #
-ID	Chromosome	Position	Strand	Reference base	Alternate base	Sample ID	HUGO symbol	Transcript	Transcript strand	Codon change	Amino acid position	Sequence Ontology	Reference amino acid(s)	Alternate amino acid(s)	Other transcripts	Mappability Warning	Driver score of representative transcript (driver mutations close to 0)	Empirical p-value	FDR (Benjamini-Hochberg) (not available with less than 10 unique mutations)	Best driver score and transcript	All transcripts and driver scores	dbSNP	1000 Genomes allele frequency	ESP6500 allele frequency (European American)	ESP6500 allele frequency (African American)	Occurrences in study [exact nucleotide change]	Transcript in COSMIC	Protein sequence change in COSMIC	Occurrences in COSMIC [exact nucleotide change]	Occurrences in COSMIC by primary sites [exact nucleotide change]	MuPIT Link
-TR1	chr22	30421786	+	A	T	No_sample_ID	MTMR3	NM_021090.3	+	aAc>aTc	1198	MS	N	I	NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I		0.6(NM_021090.3:N1198I)	0.3364	0.60	0.572(ENST00000323630:N1062I)	ENST00000323630:N1062I(0.572),ENST00000406629:N1170I(0.602),ENST00000401950:N1198I(0.6),ENST00000351488:N1161I(0.572),NM_153050.2:N1170I(0.572),ENST00000333027:N1170I(0.572),NM_021090.3:N1198I(0.6),NM_153051.2:N1161I(0.572)	rs75623810	0.00778388278388	0	0.0226963	1					 
-TR2	chr22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R		0.514(NM_001206998.1:H637R)	0.1710	0.60	0.442(ENST00000544604:H637R)	ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514)	rs62641746	0	0.00598145	0.00104004	2					 
-TR3	chr22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R		0.514(NM_001206998.1:H637R)	0.1710	0.60	0.442(ENST00000544604:H637R)	ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514)	rs62641746	0	0.00598145	0.00104004	2					 
-TR4	chr22	40814500	-	A	G	No_sample_ID	MKL1	NM_020831.3	-	Agc>Ggc	648	MS	S	G	ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G		0.728(NM_020831.3:S648G)	0.6890	0.80	0.708(ENST00000402042:S598G)	ENST00000407029:S648G(0.728),NM_020831.3:S648G(0.728),ENST00000396617:S648G(0.728),ENST00000355630:S648G(0.728),ENST00000402042:S598G(0.708)	rs878756	0.419871794872	0.396977	0.860645	1					 
-TR5	chr22	40815256	+	C	T	No_sample_ID	MKL1	NM_020831.3	-	Gcc>Acc	396	MS	A	T	ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T		0.748(NM_020831.3:A396T)	0.7476	0.80	0.748(ENST00000407029:A396T)	ENST00000407029:A396T(0.748),NM_020831.3:A396T(0.748),ENST00000396617:A396T(0.748),ENST00000355630:A396T(0.748),ENST00000402042:A346T(0.754)	rs34736200	0.0201465201465	0.00127937	0.0834091	1					 
+ID	Chromosome	Position	Strand	Reference base	Alternate base	Sample ID	HUGO symbol	Transcript	Transcript strand	Codon change	Amino acid position	Sequence Ontology	Reference amino acid(s)	Protein sequence change	Other transcripts	Mappability Warning	Driver Genes	TARGET	Driver score of representative transcript (driver mutations close to 0)	Empirical p-value	FDR (Benjamini-Hochberg) (not available with less than 10 unique mutations)	Best driver score and transcript	All transcripts and driver scores	dbSNP	1000 Genomes allele frequency	ESP6500 allele frequency (European American)	ESP6500 allele frequency (African American)	Occurrences in study [exact nucleotide change]	Transcript in COSMIC	Protein sequence change in COSMIC	Occurrences in COSMIC [exact nucleotide change]	Occurrences in COSMIC by primary sites [exact nucleotide change]	MuPIT Link
+TR1	chr22	30421786	+	A	T	No_sample_ID	MTMR3	NM_021090.3	+	aAc>aTc	1198	MS	N	I	NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I				0.582(NM_021090.3:N1198I:&)	0.2972	 	0.572(ENST00000351488:N1161I:=)	ENST00000323630:N1062I:=(0.594),ENST00000406629:N1170I:=(0.602),ENST00000401950:N1198I:=(0.592),ENST00000351488:N1161I:=(0.572),NM_153050.2:N1170I:=(0.582),ENST00000333027:N1170I:=(0.582),NM_021090.3:N1198I:&(0.582),NM_153051.2:N1161I:=(0.582)	rs75623810	0.00778388278388	0	0.0226963	1					 
+TR2	chr22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R				0.524(NM_001206998.1:H637R:&)	0.1872	 	0.442(ENST00000544604:H637R:=)	ENST00000544604:H637R:=(0.442),NM_032173.3:H537R:=(0.524),ENST00000402174:H537R:=(0.524),ENST00000406323:H537R:=(0.514),NM_001206998.1:H637R:&(0.524),ENST00000332811:H537R:=(0.524)	rs62641746	0	0.00598145	0.00104004	2					 
+TR3	chr22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R				0.524(NM_001206998.1:H637R:&)	0.1872	 	0.442(ENST00000544604:H637R:=)	ENST00000544604:H637R:=(0.442),NM_032173.3:H537R:=(0.524),ENST00000402174:H537R:=(0.524),ENST00000406323:H537R:=(0.514),NM_001206998.1:H637R:&(0.524),ENST00000332811:H537R:=(0.524)	rs62641746	0	0.00598145	0.00104004	2					 
+TR4	chr22	40814500	-	A	G	No_sample_ID	MKL1	NM_020831.3	-	Agc>Ggc	648	MS	S	G	ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G				0.728(NM_020831.3:S648G:&)	0.6890	 	0.704(ENST00000402042:S598G:=)	ENST00000407029:S648G:=(0.728),NM_020831.3:S648G:&(0.728),ENST00000396617:S648G:=(0.728),ENST00000355630:S648G:=(0.728),ENST00000402042:S598G:=(0.704)	rs878756	0.419871794872	0.396977	0.860645	1	ENST00000355630	p.S648G (stomach 1)	1	stomach(1)	 
+TR5	chr22	40815256	+	C	T	No_sample_ID	MKL1	NM_020831.3	-	Gcc>Acc	396	MS	A	T	ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T				0.668(NM_020831.3:A396T:&)	0.5102	 	0.668(ENST00000407029:A396T:=)	ENST00000407029:A396T:=(0.668),NM_020831.3:A396T:&(0.668),ENST00000396617:A396T:=(0.668),ENST00000355630:A396T:=(0.668),ENST00000402042:A346T:=(0.67)	rs34736200	0.0201465201465	0.00127937	0.0834091	1					 
diff -r 47ca5fb1b3f7 -r 473d1c2ca65d chasm_webservice/tool_dependencies.xml
--- a/chasm_webservice/tool_dependencies.xml	Wed Jul 16 20:31:41 2014 -0400
+++ b/chasm_webservice/tool_dependencies.xml	Tue Oct 07 18:32:57 2014 -0400
@@ -2,5 +2,6 @@
 <tool_dependency>
     <package name="requests" version="2.2.1">
         <repository changeset_revision="570c2648d96d" name="package_requests_2_2_1" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0045f1732185" name="package_xlrd_0_9_3" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>