# HG changeset patch
# User saketkc
# Date 1397504076 14400
# Node ID f1dab7df4f1605678aabe27b4f9f81df53385568
# Parent  69f164052a59d8b6afc4d49a3931078d634a5f0d
Uploaded

diff -r 69f164052a59 -r f1dab7df4f16 mutationassesor_web/mutation_assesor.xml
--- a/mutationassesor_web/mutation_assesor.xml	Mon Apr 14 14:52:57 2014 -0400
+++ b/mutationassesor_web/mutation_assesor.xml	Mon Apr 14 15:34:36 2014 -0400
@@ -41,8 +41,6 @@
             <param name="protein" value="yes"/>
             <output name="output" value="ma_protein_output.csv"/>
         </test>
-
-
     </tests>
     <help>
 
diff -r 69f164052a59 -r f1dab7df4f16 mutationassesor_web/test-data/ma_empty.csv
diff -r 69f164052a59 -r f1dab7df4f16 mutationassesor_web/test-data/ma_nucleotide_output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutationassesor_web/test-data/ma_nucleotide_output.csv	Mon Apr 14 15:34:36 2014 -0400
@@ -0,0 +1,4 @@
+"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site"
+"1","hg19,13,32912555,G,T","D1355Y","BRCA2","http://getma.org/?cm=msa&ty=f&p=BRCA2_HUMAN&rb=1247&re=1420&var=D1355Y","","low","1.24","BRCA2_HUMAN","NP_000050","14","chr13:32912555","","","",""
+"2","hg19,7,55178574,G,A","","","","","","","","","0","","","","",""
+"3","hg19,7,55178574,G,A","","","","","","","","","0","","","","",""
diff -r 69f164052a59 -r f1dab7df4f16 mutationassesor_web/test-data/ma_proper_nucleotide.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutationassesor_web/test-data/ma_proper_nucleotide.csv	Mon Apr 14 15:34:36 2014 -0400
@@ -0,0 +1,3 @@
+13,32912555,G,T   BRCA2
+7,55178574,G,A   GBM
+7,55178574,G,A   GBM
diff -r 69f164052a59 -r f1dab7df4f16 mutationassesor_web/test-data/ma_proper_protein.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutationassesor_web/test-data/ma_proper_protein.csv	Mon Apr 14 15:34:36 2014 -0400
@@ -0,0 +1,6 @@
+EGFR_HUMAN,R521K
+EGFR_HUMAN,R98Q,Polymorphism
+EGFR_HUMAN,G719D,disease
+NP_000537,G356A
+NP_000537,G360A,dbSNP:rs35993958
+NP_000537,S46A,Abolishes,phosphorylation
diff -r 69f164052a59 -r f1dab7df4f16 mutationassesor_web/test-data/ma_proper_protein.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutationassesor_web/test-data/ma_proper_protein.tsv	Mon Apr 14 15:34:36 2014 -0400
@@ -0,0 +1,6 @@
+EGFR_HUMAN R521K 
+EGFR_HUMAN R98Q Polymorphism 
+EGFR_HUMAN G719D disease 
+NP_000537 G356A 
+NP_000537 G360A dbSNP:rs35993958 
+NP_000537 S46A Abolishes phosphorylation 
diff -r 69f164052a59 -r f1dab7df4f16 mutationassesor_web/test-data/ma_protein_output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutationassesor_web/test-data/ma_protein_output.csv	Mon Apr 14 15:34:36 2014 -0400
@@ -0,0 +1,7 @@
+"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site"
+"1","EGFR_HUMAN R521K","R521K","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=482&re=681&var=R521K","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=482&to=681&var=R521K","neutral","0.405","EGFR_HUMAN","NP_005219","399","chr7:55196748","1","1","",""
+"2","EGFR_HUMAN R98Q","R98Q","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=57&re=168&var=R98Q","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=57&to=168&var=R98Q","neutral","0.6","EGFR_HUMAN","NP_005219","181","chr7:55178543","","","",""
+"3","EGFR_HUMAN G719D","G719D","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719D","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719D","medium","3.115","EGFR_HUMAN","NP_005219","700","chr7:55209201","1","1","","0UN IRE FMM ANP CY7 HYZ 03P ITI DKI 685 T95 T74 ZZY M97 6XP 0K0 KRW 0JJ 0K1 P17 112 1N1 JIN STI P5C 585 S19 P16 VX6 P3Y SX7 ACK B90 AMP ZD6 STU 7PY BI9 BII ATP ADP 4ST VG8 YAM P1E 7X4 7X5 7X6 7X8 349 3JZ"
+"4","NP_000537 G356A","G356A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=318&re=359&var=G356A","http://getma.org/pdb.php?prot=P53_HUMAN&from=318&to=359&var=G356A","neutral","-0.895","P53_HUMAN","NP_000537","45","chr17:7514684","","1","",""
+"5","NP_000537 G360A","G360A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=360&re=393&var=G360A","","medium","2.25","P53_HUMAN","NP_000537","15","chr17:7514672","","","",""
+"6","NP_000537 S46A","S46A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=30&re=94&var=S46A","http://getma.org/pdb.php?prot=P53_HUMAN&from=30&to=94&var=S46A","neutral","0.55","P53_HUMAN","NP_000537","5","chr17:7520274","1","1","",""