Mercurial > repos > saketkc > condel
changeset 6:699ab41c6d76 draft
Uploaded
author | saketkc |
---|---|
date | Tue, 15 Apr 2014 13:00:06 -0400 |
parents | 84247b644a7d |
children | 67212f958e5a |
files | condel_web/condel_web.xml condel_web/test-data/condel_input.tsv condel_web/test-data/condel_input.txt condel_web/tool_dependencies.xml |
diffstat | 4 files changed, 60 insertions(+), 8 deletions(-) [+] |
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--- a/condel_web/condel_web.xml Mon Apr 14 21:37:22 2014 -0400 +++ b/condel_web/condel_web.xml Tue Apr 15 13:00:06 2014 -0400 @@ -2,7 +2,9 @@ <description>Condel web service</description> <requirements> <requirement type="package" version="2.2.1">requests</requirement> + <requirement type="package" version="7.19.3.1">pycurl</requirement> <requirement type="python-module">requests</requirement> + <requirement type="python-package">pycurl</requirement> </requirements> <command interpreter="python"> condel_web.py --input $input --output $output @@ -15,7 +17,7 @@ </outputs> <tests> <test> - <param name="input" value="condel_input.txt"/> + <param name="input" value="condel_input.tsv"/> <output name="output" file="condel_output.csv"/> </test> </tests> @@ -36,6 +38,53 @@ dataset of approximately 20000 missense SNPs, both deleterious and neutral. The probability that a predicted deleterious mutation is not a false positive of the method and the probability that a predicted neutral mutation is not a false negative are employed as weights. + **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 + + Ex: + + EGFR_HUMAN R521K + + EGFR_HUMAN R98Q + + .. class:: warningmark + + Note + + Please, note that the Variant Effect Predictor assumes that the allele submitted is coded in the forward strand. + + If you are assessing the effect of variants coded in the reverse strand, please introduce the complementary nucleotide instead. + **Citation**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/condel_web/test-data/condel_input.tsv Tue Apr 15 13:00:06 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
--- a/condel_web/test-data/condel_input.txt Mon Apr 14 21:37:22 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
--- a/condel_web/tool_dependencies.xml Mon Apr 14 21:37:22 2014 -0400 +++ b/condel_web/tool_dependencies.xml Tue Apr 15 13:00:06 2014 -0400 @@ -1,6 +1,9 @@ <?xml version="1.0"?> <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" /> + <package name="beautifulsoup4" version="4.1.0"> + <repository changeset_revision="df0beb7ea718" name="package_beautifulsoup4_4_1_0" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="pycurl" version="7.19.3.1"> + <repository changeset_revision="9b02e8e36eff" name="package_pycurl_7_19_3_1" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>