Mercurial > repos > saketkc > mutation_assessor

changeset 7:f1dab7df4f16 draft

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Uploaded
author saketkc
date Mon, 14 Apr 2014 15:34:36 -0400
parents 69f164052a59
children d5489187fc88
files mutationassesor_web/mutation_assesor.xml mutationassesor_web/test-data/ma_empty.csv mutationassesor_web/test-data/ma_nucleotide_output.csv mutationassesor_web/test-data/ma_proper_nucleotide.csv mutationassesor_web/test-data/ma_proper_protein.csv mutationassesor_web/test-data/ma_proper_protein.tsv mutationassesor_web/test-data/ma_protein_output.csv
diffstat 6 files changed, 26 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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>
 
--- /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","","","","",""
--- /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
--- /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
--- /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 
--- /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","",""