# HG changeset patch # User saketkc # Date 1397581523 14400 # Node ID 7e8b135145d040a670cdd890b485d92b74ec1851 # Parent 4051693fb6908de48ea3fb6f0fb2c4909a2affd1 Uploaded diff -r 4051693fb690 -r 7e8b135145d0 transFIC_web/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transFIC_web/README.rst Tue Apr 15 13:05:23 2014 -0400 @@ -0,0 +1,35 @@ +Galaxy wrapper for the transFIC webservice +=================================================== + +This tool is copyright 2014 by Saket Choudhary, Indian Institute of Technology Bombay +All rights reserved. MIT licensed. + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + +Citations +=========== + + +If you use this Galaxy tool in work leading to a scientific publication please cite: + +Gonzalez-Perez A, Deu-Pons J and Lopez-Bigas N. Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation +Genome Medicine 2012. 4:89 doi:10.1186/gm390s diff -r 4051693fb690 -r 7e8b135145d0 transFIC_web/test-data/condel_input.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transFIC_web/test-data/condel_input.tsv Tue Apr 15 13:05:23 2014 -0400 @@ -0,0 +1,5 @@ +9 32473058 32473058 A +7 43918688 43918688 C +7 38471790 38471790 A +6 88372821 88372821 A +5 41934236 41934236 G diff -r 4051693fb690 -r 7e8b135145d0 transFIC_web/test-data/condel_input.txt --- a/transFIC_web/test-data/condel_input.txt Mon Apr 14 21:36:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -9 32473058 32473058 A -7 43918688 43918688 C -7 38471790 38471790 A -6 88372821 88372821 A -5 41934236 41934236 G diff -r 4051693fb690 -r 7e8b135145d0 transFIC_web/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transFIC_web/tool_dependencies.xml Tue Apr 15 13:05:23 2014 -0400 @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff -r 4051693fb690 -r 7e8b135145d0 transFIC_web/transFIC_web.xml --- a/transFIC_web/transFIC_web.xml Mon Apr 14 21:36:51 2014 -0400 +++ b/transFIC_web/transFIC_web.xml Tue Apr 15 13:05:23 2014 -0400 @@ -1,5 +1,13 @@ TransFIC web service + + requests + pycurl + beautifulsoup4 + requests + pycurl + bs4 + transFIC_web.py --input $input --output $output @@ -11,9 +19,70 @@ - + + + **What it does** + + This script calls TransFIC web api at http://bg.upf.edu/transfic/ + + TransFIC stands for TRANsformed Functional Impact for Cancer. + It is a method to transform Functional Impact Scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to + different functional classes. This transformation allows to use the scores provided by well-known tools (e.g. SIFT, Polyphen2, MutationAssessor) + to rank the functional impact of cancer somatic mutations. Mutations with greater transFIC are more likely to be cancer drivers. + + + **How does it work** + + + TransFIC takes as input the Functional Impact Score of a somatic mutation provided by one of the aforementioned tools. + It then compares that score to the distribution of scores of germline SNVs observed in genes with similar functional + annotations (for instance genes with the same molecular function as provided by the Gene Ontologies). + The score is thus transformed using the Zscore formula. + The result is that mutations in genes that are less tolerant to germline SNVs are amplified, + while the scores of mutations on relatively tolerant genes are decreased. + + **Input** + + There are two main formats allowed: + + + SNVs may be submitted for analysis both in chromosome and protein coordinates. + + + The chromosome coordinates (hg19) input must follow this format: + + + [CHROMOSOME] [START] [END] [MUTANT_NUCLEOTIDE] + + + + The END column is the same as the START for SNVs. + Those four columns must be separated by tabs. Also a fifth column can optionally be added with the Variant name + + + Ex: + + 9 32473058 32473058 A + + 7 43918688 43918688 C + + Additionally, the input could be composed by two columns the strand of the SNV and an identifier: + + [PROTEIN_ID][variant] + + Also tab separated. Currently only Uniprot, RefSeq_Peptide and Ensembl identifiers are recognized by the webserver. + + The variant column must contain the following information (in this order ): change_position, reference_aminoacid and changed_aminoacid + + **Citation** + + If you use this Galaxy tool in work leading to a scientific publication please cite: + + Gonzalez-Perez A, Deu-Pons J and Lopez-Bigas N. Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation + Genome Medicine 2012. 4:89 doi:10.1186/gm390s +