# HG changeset patch # User vipints # Date 1429825391 14400 # Node ID ee541c1852da1b74cbbe10ced7308edb8f8215f8 # Parent 154887a3d92fdb90cb43eaefef40ad61720f35b3 Uploaded version 2.1.0 diff -r 154887a3d92f -r ee541c1852da GFFtools-GX --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GFFtools-GX Thu Apr 23 17:43:11 2015 -0400 @@ -0,0 +1,959 @@ + + + + + + + + + + + + vipints/GFFtools-GX · GitHub + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
+ + + + + + + + + + +
+
+
+ +
+
+
+ + + +

+ + /GFFtools-GX + + + + + +

+
+
+ +
+
+
+ + + +
+ +
+

HTTPS clone URL

+
+ + + + +
+
+ + +
+

Subversion checkout URL

+
+ + + + +
+
+ + + +

You can clone with + HTTPS or Subversion. + + + +

+ + + + + + + Download ZIP + +
+
+ +
+ + + +
+
+ gfftools - Galaxy toolshed repository +
+ + + +
+ +
+ +
+
+ + +
+
    +
  1. + + + Python + 100% + +
    2. +
+
+
+
+ +
+ +
+ Python +
+ + + +
+ + + + + + + + +
+ + + branch: + master + + + +
+ + + +
GFFtools-GX/ + + + +
+
+ + + + +
+

+ fixed + +

+
+ + latest commit 0ea921f8d7 + +
+ @vipints + + authored + +
+
+
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Failed to load latest commit information.
+ + + + test-data + + + functional test perfomed after the change + + + +
+ + + + .gitignore + + + ignored pyc and swap files + + + +
+ + + + GFFParser.py + + + added a new field to carryover the isoform level score from the GFF f… + + + +
+ + + + README.md + + + fixed + + + +
+ + + + bed_to_gff.py + + + removing print statement from the code + + + +
+ + + + bed_to_gff.xml + + + updated the gbk_to_gff wrapper and fixed typo + + + +
+ + + + gbk_to_gff.py + + + gbk parsing and correctly assigning feature type + + + +
+ + + + gbk_to_gff.xml + + + updated the gbk_to_gff wrapper and fixed typo + + + +
+ + + + gff_to_bed.py + + + changing the float behaviour to int + + + +
+ + + + gff_to_bed.xml + + + updated the wrapper version + + + +
+ + + + gff_to_gtf.py + + + functional test performed and changed version to 0.6 + + + +
+ + + + gff_to_gtf.xml + + + functional test performed and changed version to 0.6 + + + +
+ + + + gtf_to_gff.py + + + updated the version 0.6 gtftogff + + + +
+ + + + gtf_to_gff.xml + + + updated the version 0.6 gtftogff + + + +
+ + + + helper.py + + + added a new field to carryover the isoform level score from the GFF f… + + + +
+ + + + tool_conf.xml.sample + + + updated the toolpanel list + + + +
+ + + + tool_dependencies.xml + + + biopython required + + + +
+ +
+ + +
+

+ + README.md +

+ +

+GFFtools-GX

+ +

A collection of tools for converting genome annotation between GTF, BED, GenBank and GFF.

+ +
+INTRODUCTION
+ +

Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. These programs can be easily integrated into your galaxy instance.

+ +
+CONTENTS
+ +

Included utilities are:

+ +
BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
+GBK-to-GFF: convert data from genbank format to GFF
+GFF-to-BED: convert data from GFF to 12 column BED format
+GFF-to-GTF: convert data from GFF to GTF 
+GTF-to-GFF: convert data from GTF to valid GFF
+
+ +

test-data: Test data set. (move to your galaxy-root-folder/test-data/)

+ +
You may need to move the test files into your test-data directory so galaxy can find them. 
+If you want to run the functional tests eg as: 
+
+exmaple: 
+sh run_functional_tests.sh -id fml_gtf2gff
+
+ +
+REQUIREMENTS
+ +
python2.6 or 2.7 and biopython  
+
+Galaxy should be able to automatically install biopython via Galaxy toolshed.
+
+ +
+COMMENTS/QUESTIONS
+ +

I can be reached at vipin [at] cbio.mskcc.org

+ +
+LICENSE
+ +

Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society

+ +
          2013-2015, Memorial Sloan Kettering Cancer Center
+          Vipin T Sreedharan <vipin@cbio.mskcc.org>  
+
+ +

All rights reserved.

+ +

Licensed under the BSD 2-Clause License: http://opensource.org/licenses/BSD-2-Clause

+ +
Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright notice,
+      this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+ +
+COURTESY
+ +

To the Galaxy Team.

+
+
+ + +
+ +
+
+
+
+ + +
+ +
+ +
+ + +
+
+
+ +
+
+
+
+
+
+ + + + + + +
+
+ + + + + + +
+ + + Something went wrong with that request. Please try again. +
+ + + + + + + + + + +