ensembl-io merge requestshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests2020-08-18T08:19:01Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/108add carp to cpan - e1022020-08-18T08:19:01ZMarek Szubaadd carp to cpan - e102*Created by: ima23*
modules/Bio/EnsEMBL/IO/Parser.pm uses Carp*Created by: ima23*
modules/Bio/EnsEMBL/IO/Parser.pm uses Carphttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/107add carp to cpan2020-08-18T08:18:46ZMarek Szubaadd carp to cpan*Created by: ima23*
modules/Bio/EnsEMBL/IO/Parser.pm uses Carp*Created by: ima23*
modules/Bio/EnsEMBL/IO/Parser.pm uses Carphttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/109add carp lib to cpan - master2020-08-18T08:18:10ZMarek Szubaadd carp lib to cpan - master*Created by: ima23*
modules/Bio/EnsEMBL/IO/Parser.pm uses Carp*Created by: ima23*
modules/Bio/EnsEMBL/IO/Parser.pm uses Carphttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/78Don't use Try::Tiny as it doesn't work with BigFile code on web2019-02-25T09:46:57ZMarek SzubaDon't use Try::Tiny as it doesn't work with BigFile code on web*Created by: ens-ap5*
As discussed with Tiago, this is a blocker for release 96 - reverting to old version that used eval.*Created by: ens-ap5*
As discussed with Tiago, this is a blocker for release 96 - reverting to old version that used eval.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/78Don't use Try::Tiny as it doesn't work with BigFile code on web2019-02-25T09:46:57ZMarek SzubaDon't use Try::Tiny as it doesn't work with BigFile code on web*Created by: ens-ap5*
As discussed with Tiago, this is a blocker for release 96 - reverting to old version that used eval.*Created by: ens-ap5*
As discussed with Tiago, this is a blocker for release 96 - reverting to old version that used eval.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/69Extra Genbank parser methods to aid RefSeqGPFFParser2018-11-20T15:38:18ZMarek SzubaExtra Genbank parser methods to aid RefSeqGPFFParser*Created by: tgrego*
Xref RefSeqGPFFParser does the parsing of Genbank files.
Refactoring this Xref parser as part of the xref sprint efforts led to the decision of using an existing genbank parser rather than implementing it again wit...*Created by: tgrego*
Xref RefSeqGPFFParser does the parsing of Genbank files.
Refactoring this Xref parser as part of the xref sprint efforts led to the decision of using an existing genbank parser rather than implementing it again within the RefSeqGPFFParser.
This will obviously be better in terms of future maintainability, and if development efforts are concentrated in one place it will be more efficient.
Some required data was however not very easy to access using the Genbank parser, so this brings new methods that extract that data in an easy way.
No existing functionality has been modified, only new one added.
Tests are included for the new methods.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/69Extra Genbank parser methods to aid RefSeqGPFFParser2018-11-20T15:38:18ZMarek SzubaExtra Genbank parser methods to aid RefSeqGPFFParser*Created by: tgrego*
Xref RefSeqGPFFParser does the parsing of Genbank files.
Refactoring this Xref parser as part of the xref sprint efforts led to the decision of using an existing genbank parser rather than implementing it again wit...*Created by: tgrego*
Xref RefSeqGPFFParser does the parsing of Genbank files.
Refactoring this Xref parser as part of the xref sprint efforts led to the decision of using an existing genbank parser rather than implementing it again within the RefSeqGPFFParser.
This will obviously be better in terms of future maintainability, and if development efforts are concentrated in one place it will be more efficient.
Some required data was however not very easy to access using the Genbank parser, so this brings new methods that extract that data in an easy way.
No existing functionality has been modified, only new one added.
Tests are included for the new methods.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/59Unification merge conflict2018-11-19T16:03:51ZMarek SzubaUnification merge conflict*Created by: tgrego*
Do not merge!
This branch is a merge of master and feature/unified-design branches, that have diverged...
Apparently both branches are used in different places, so the merge has to be correct for master to becom...*Created by: tgrego*
Do not merge!
This branch is a merge of master and feature/unified-design branches, that have diverged...
Apparently both branches are used in different places, so the merge has to be correct for master to become the only branch used.
Some minor fixes added. https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/59Unification merge conflict2018-11-19T16:03:51ZMarek SzubaUnification merge conflict*Created by: tgrego*
Do not merge!
This branch is a merge of master and feature/unified-design branches, that have diverged...
Apparently both branches are used in different places, so the merge has to be correct for master to becom...*Created by: tgrego*
Do not merge!
This branch is a merge of master and feature/unified-design branches, that have diverged...
Apparently both branches are used in different places, so the merge has to be correct for master to become the only branch used.
Some minor fixes added. https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/60Master2018-07-27T08:57:08ZMarek SzubaMaster*Created by: ens-ap5*
## Description
Minor improvements to error reporting when attaching remote files.
## Use case
Mainly for user feedback when attaching and parsing trackhubs. See JIRA ticket ENSWEB-2052
## Benefits
Us...*Created by: ens-ap5*
## Description
Minor improvements to error reporting when attaching remote files.
## Use case
Mainly for user feedback when attaching and parsing trackhubs. See JIRA ticket ENSWEB-2052
## Benefits
Usability improvements
## Possible Drawbacks
None.
## Testing
Tested in the browser - there are no applicable unit tests.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/60Master2018-07-27T08:57:08ZMarek SzubaMaster*Created by: ens-ap5*
## Description
Minor improvements to error reporting when attaching remote files.
## Use case
Mainly for user feedback when attaching and parsing trackhubs. See JIRA ticket ENSWEB-2052
## Benefits
Us...*Created by: ens-ap5*
## Description
Minor improvements to error reporting when attaching remote files.
## Use case
Mainly for user feedback when attaching and parsing trackhubs. See JIRA ticket ENSWEB-2052
## Benefits
Usability improvements
## Possible Drawbacks
None.
## Testing
Tested in the browser - there are no applicable unit tests.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/50Experimental/rishi genbank2017-12-15T09:53:00ZMarek SzubaExperimental/rishi genbank*Created by: rishidev*
First genbank attempt submitted.
At submission time modules/t/bigbed.t is causing a fail with a file on TravisCI - if this has been fixed in another commit that can be bought in.
*Created by: rishidev*
First genbank attempt submitted.
At submission time modules/t/bigbed.t is causing a fail with a file on TravisCI - if this has been fixed in another commit that can be bought in.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/46Support for a single fasta sequence from a slice using the unified de…2017-12-15T09:53:00ZMarek SzubaSupport for a single fasta sequence from a slice using the unified de…*Created by: mn1*
…sign
Run like this:
```
perl scripts/fasta_serializer.pl
```
The main aim of this was to see, if I can get the writer/translator pattern to work correctly.
Let me know what you think.
*Created by: mn1*
…sign
Run like this:
```
perl scripts/fasta_serializer.pl
```
The main aim of this was to see, if I can get the writer/translator pattern to work correctly.
Let me know what you think.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/46Support for a single fasta sequence from a slice using the unified de…2017-12-15T09:53:00ZMarek SzubaSupport for a single fasta sequence from a slice using the unified de…*Created by: mn1*
…sign
Run like this:
```
perl scripts/fasta_serializer.pl
```
The main aim of this was to see, if I can get the writer/translator pattern to work correctly.
Let me know what you think.
*Created by: mn1*
…sign
Run like this:
```
perl scripts/fasta_serializer.pl
```
The main aim of this was to see, if I can get the writer/translator pattern to work correctly.
Let me know what you think.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/50Experimental/rishi genbank2017-12-15T09:53:00ZMarek SzubaExperimental/rishi genbank*Created by: rishidev*
First genbank attempt submitted.
At submission time modules/t/bigbed.t is causing a fail with a file on TravisCI - if this has been fixed in another commit that can be bought in.
*Created by: rishidev*
First genbank attempt submitted.
At submission time modules/t/bigbed.t is causing a fail with a file on TravisCI - if this has been fixed in another commit that can be bought in.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/53Experimental/unified design2017-06-21T09:49:08ZMarek SzubaExperimental/unified design*Created by: avullo*
This is introducing RDF writers for features (non ensembl) and corresponding xrefs.*Created by: avullo*
This is introducing RDF writers for features (non ensembl) and corresponding xrefs.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/53Experimental/unified design2017-06-21T09:49:08ZMarek SzubaExperimental/unified design*Created by: avullo*
This is introducing RDF writers for features (non ensembl) and corresponding xrefs.*Created by: avullo*
This is introducing RDF writers for features (non ensembl) and corresponding xrefs.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/44specify only start when seeking a region2017-04-20T08:35:33ZMarek Szubaspecify only start when seeking a region*Created by: at7*
I would like to be able to seek the whole content of a VCF file using the TabixParser. Can we support chr:start next to chr:start-end? It is supported by Bio/DB/HTS/Tabix.pm. The code change is a suggestion. We can do ...*Created by: at7*
I would like to be able to seek the whole content of a VCF file using the TabixParser. Can we support chr:start next to chr:start-end? It is supported by Bio/DB/HTS/Tabix.pm. The code change is a suggestion. We can do this in a different way if preferred.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/44specify only start when seeking a region2017-04-20T08:35:33ZMarek Szubaspecify only start when seeking a region*Created by: at7*
I would like to be able to seek the whole content of a VCF file using the TabixParser. Can we support chr:start next to chr:start-end? It is supported by Bio/DB/HTS/Tabix.pm. The code change is a suggestion. We can do ...*Created by: at7*
I would like to be able to seek the whole content of a VCF file using the TabixParser. Can we support chr:start next to chr:start-end? It is supported by Bio/DB/HTS/Tabix.pm. The code change is a suggestion. We can do this in a different way if preferred.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/33Fixing the test suite and bits of io2017-04-19T13:48:59ZMarek SzubaFixing the test suite and bits of io*Created by: andrewyatz*
There's a few changes coming in here. Short summary
- Tests will skip if you don't have Htslib/Kent XS bindings and core API. Tests always run on Travis no matter what
- Expanding the cpanfile and install depend...*Created by: andrewyatz*
There's a few changes coming in here. Short summary
- Tests will skip if you don't have Htslib/Kent XS bindings and core API. Tests always run on Travis no matter what
- Expanding the cpanfile and install dependencies
- Rejigged the big file parser
- Removed the VEP_output parser. Will said it wasn't right to keep in
- `Writer.pm` and the `writer.t` test now work. There's some awful delimiter initialisation problem that means I have to _fake open a file_