Recent Releases of voseq
voseq - v2.2.2
- fixed usage of django-suit for admin interface.
- allow partial match to voucher code, genus, species, accession numbers, gene_codes when searching for Vouchers or Sequences in the admin interface. Eg. searching for "Meli" will return matches to Melitaea, Melinaea, etc.
- References to vouchers from Sequence objects will show voucher code, genus and species.
- dropped support for python 3.5
- added config.json for initial deployment.
- Python
Published by carlosp420 almost 6 years ago
voseq - version 2.1.4
- Fixed bug when generating datasets with certain codon positions.
- Python
Published by carlosp420 over 8 years ago
voseq -
- Create log for django in tmp directory.
- Install ncbi-blast+ when provisioning in vagrant.
- Python
Published by carlosp420 almost 9 years ago
voseq - version 2.1.1
- Avoid error 500 when doing BLAST and there are no sequences in database to create the BLAST database.
- Python
Published by carlosp420 almost 9 years ago
voseq - Version 2.1.0
- Datasets now include taxon names if required.
- Dropped using Haystack for advanced search results, but autosuggestion still using haystack.
- Added indexes to speed up queries.
- Python
Published by carlosp420 about 9 years ago
voseq - Version 2.0.4
Fixed bug when validating coordinates during import. Fixes #357
- Python
Published by carlosp420 over 9 years ago
voseq - Version 2.0.3
- Upgraded dependency Django to version 1.10.2
- Python
Published by carlosp420 over 9 years ago
voseq - Version 2.0.1
Fix for django-import-export that issued errors for the function self.save_instance when importing vouchers.
- Python
Published by carlosp420 over 9 years ago
voseq - Version 2.0
Version 2.0 (2016-09-26)
Fixed bugs
- Createdataset tool will produce gene partitions sorted regardless of letter case. The same for Phylip charsetblock.
- Creating Phylip datasets for charsetblock partitioned by codon position and 1st2nd3rd. The same for Phylip charset_block.
- Fixed bugs for creation of Nexus files using partitions. The same for Phylip charset_block.
- Characters not in IUPAC (except '?-') will not be accepted when importing or saving sequences.
- Added tool for batch import of sequences in admin interface.
- Added tool to add genes in admin interface.
- In dataset creation, moved warnings to bottom of page. There will be only a big warning message on top.
- Dataset creation tool will issue error messages when users wants datasets containing only codons 1,3 and 2,3.
- Dataset creation tool, genes will be sorted alphabetically, regardless of case.
- Fixed version on footer.
- MEGA datasets.
- Refactoring of
create_datasetmodule. - Editing vouchers in Admin interface: adding photos is optional not mandatory.
- Error message will be shown when attempting to translate bad codon such as "N--".
- Shown error message if sequence is longer than specified nchar value.
- Show message that FASTA datasets have all the sequences concatenated.
- Sorted list of gene codes in voucher page.
- Corrected path for media files in nginx so uploaded images will be shown in voucher pages.
- Convert symbols and white spaces of code and taxon names to underscore to avoid choking Biopython when creating datasets.
- Fixed method to import flickr images.
- Fixed template to show thumbnail of flickr images.
Features
- date collection is flexible. Added a start and end collection dates which can be complete (YYYY-mm-dd) or incomplete (only year, or only year and month).
- added alert message when user attempts to generate voucher table without specifying the gene codes or taxon sets.
- added optional deployment for test installations.
- Python
Published by carlosp420 over 9 years ago
voseq - Pre-release version 2.0.0-beta
- Interactive overview table to browse taxa and the genes sequenced for them.
- Easy instalation and deployment using Vagrant virtual machines. Install
and configure VoSeq and all its dependencies with the command
vagrant up. - Fixed search unnecessary spelling suggestions in search results due to capital and lower cases of the same word.
- Added interactive overview table for vouchers and genes using
dataTables. - Added taxonset creation by adding lists of taxon codes.
- Importing voucher images to Flickr (optional, by default it keeps all the image files in the local server).
- Added batch upload of voucher data. It will show a diff between fields that could be updated and will also show a confirmation page before execution of changes.
- Added Zwick et al. method to degenerate DNA sequences for create_dataset tool.
- Implemented
get_updated_fieldfor haystack so it would be quicker to update our database index as the optionage=number of hourscan be used.
- Python
Published by carlosp420 almost 11 years ago
voseq - Pre-relase VoSeq v2.0.0-alpha-3
- Getting correct VoSeq version number from
HISTORY.rst. - Importing voucher image files to database and new VoSeq package.
- Python
Published by carlosp420 almost 11 years ago
voseq - Pre-relase VoSeq v2.0.0-alpha-2
- Note that it still needs the ability to generate datasets using the degenerated translations by Zwick et al, 2012.
New features
- Create dataset in MEGA format.
- Search results show a text box with the full list of vouchers so that they can be copied in order to create new taxonsets.
- Python
Published by carlosp420 about 11 years ago
voseq - Pre-relase VoSeq v2.0.0-alpha-1
VoSeq is being rewritten
I arrived to the conclusion that it will be quicker and more efficient a complete redesign of the inner workings of VoSeq, rather than trying to improve and fix the old code in PHP and MySQL.
We are rewriting everything in the language Python using the framework Django. The advantage of Python is that we can use the tools from BioPython for handling molecular data.
The advantage of Django is that the application can be build really modular with isolated components. It also makes it easy to write new plugins to extend functionality that can be incorporated into Voseq without any effort.
I have also moved the database to PostgreSQL which seems to have nicer features than MySQL. I am also trying to include a indexing back-end so that the database can be used in an efficient way, and be very quick.
Features
Most of all features in the last release of VoSeq 1.7.4 are ready in this pre-release version:
Re-written features
- Browse page for vouchers recently modified/added to the database.
- Blast new sequence tool for blasting any sequence against all or a subset of sequences kept in VoSeq.
- View genes tool to quickly see what genes are currently in the database. New: there is a badge for each gene showing the number of voucher records that have sequences for that particular gene.
- Create dataset tool to generate ready-to-run datasets in commonly used phylogenetic software such as TNT, PAUP, MrBayes, BEAST, RaXML. Note that it still needs the ability to generate datasets using the degenerated translations by Zwick et al, 2012.
- Create voucher table tool that generates a ready for publication CSV table (importable in MS Excel) with information for each voucher record, such as: Code, Genus, Species, Locality, Sequences present or not for each gene, etc.
- Create gene table tool that generates a CSV table with statistics about particular DNA alignments (constructed with the vouchers and gene codes that you can select) such as gene type, sequences length, dataset completion, percentage of variable sites, parsimony informative, conserved sites, and frequency of each nucleotide in your alignment.
- Create GenBank FASTA file tool that generates FASTA file with most of the required info ready for submission to GenBank using their Sequin software.
- Share data with GBIF tool that creates a data dump of the information from all vouchers into a CSV table (that can be imported in MS Excel) ready for being used with GBIF's tool IPT.
- Advanced search tool for searching voucher or sequences using combination of data fields.
- Batch modification of voucher data tool in the Administration interface.
New features
- Faster generation of datasets due to the use of more efficient algorithms.
- Faster advanced searches due to the indexing of the database using the backend elasticsearch.
- General search tool in the navegation bar that accepts taxonomic keywords to search for voucher records.
- Keyword suggestions tool for the general search. If users misspell a taxonomic name when they use this tool, they will be shown the possible correct spelling of the query with the message "Did you mean:".
- Pagination tool for searches, so that up to 20 results are shown per page along with links to next and previous pages.
- Fine grained permissions to upload and look at the sequences.
- Login accounts. Only users with a working account will be able to look/retrieve any DNA sequence. They will not be able to create datasets. However, they will still be able to look at voucher information, search for vouchers and sequences and perform BLASTs.
- Superuser account. Only the Superuser/Administrator will be able to create login accounts, change passwords, add user email. Also users can be given specific permission to most of components in VoSeq such as: adding genes, gene sets, members, vouchers, primers, sequences, etc.
- Users can be grouped for better management of permissions.
- Batch deletion tools for vouchers and sequences.
- Python
Published by carlosp420 about 11 years ago