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- Aug 02, 2016
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James Allen authored
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James Allen authored
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
Add get_Gene() method to CDS, ExtonTranscript and UTR objects to match Transcript method, for consistency in accessing.
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- Jul 27, 2016
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Thomas Maurel authored
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Thomas Maurel authored
Added source_dir and target_dir parameters allowing copy of databases outside the MySQL default internal directory on Sanger machines /mysql/data_3306/databases/. When target_dir is specified, the script will automatically create a symlink from target_dir to /mysql/data_3306/databases/. This change will allow us to copy databases from and to the new ens-staging3 MySQL server
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- Jul 25, 2016
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Magali Ruffier authored
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Magali Ruffier authored
This reverts commit cbd14e9f.
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Matthew Laird authored
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Matthew Laird authored
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Kieron Taylor authored
Compara test db for Slice methods
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Matthew Laird authored
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Matthew Laird authored
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Magali Ruffier authored
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- Jul 21, 2016
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Matthew Laird authored
Changing all ens-staging1/2 to ens-staging3, as we'll be using this new host for pipelines until the EBI shift over
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Matthieu Muffato authored
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Matthieu Muffato authored
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Matthieu Muffato authored
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Matthieu Muffato authored
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Matthieu Muffato authored
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Matthieu Muffato authored
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- Jul 20, 2016
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Matthew Laird authored
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Matthew Laird authored
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Matthew Laird authored
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- Jul 08, 2016
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Matthew Laird authored
It should be seq_region_start and seq_region_end for UTRs, since start/end now are relative to the feature, as with other feature types
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- Jul 07, 2016
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Matthew Laird authored
Because of a fix of a very old bug in the mapper, some Exon features if they're made via a Slice have start() and end() relative to the feature. So in genomic2cdna calls we were using $self->start() and $self->end(), this means we were sometimes using incorrect coordinates. Change to seq_reion_start and seq_region_end
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Matthew Laird authored
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- Jul 05, 2016
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Magali Ruffier authored
bugfix: get_all_DBAdaptors() should return an empty list if the species name (alias) does not exist
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- Jul 01, 2016
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Daniel Zerbino authored
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- Jun 28, 2016
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Matthew Laird authored
Tweak to gene description filters
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Kevin Howe authored
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- Jun 24, 2016
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Matthieu Muffato authored
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- Jun 23, 2016
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Alessandro Vullo authored
Support for multi letter patches
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Michael Nuhn authored
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Michael Nuhn authored
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Michael Nuhn authored
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- Jun 17, 2016
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Magali Ruffier authored
- Fix how UTRs are created, they should be created with start/end rel…
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Matthew Laird authored
- Fix how UTRs are created, they should be created with start/end relative to the feature, not in genomic coordinates - Update tests to check UTRs are created correctly when transcripts are fetched from a Slice - UTR test cases for forward and reverse strand transcripts
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- Jun 16, 2016
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Kieron Taylor authored
Changes to gtf serializer to deal with offset in codon and utr reginos
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