EMBLmyGFF3-1.2.3

• UnicodeDecodeError fix (#12). Non ASCII characters from gff3 (e.g "α" (greek alpha)) are now handled properly.
• New warning to inform user when a CDS is partial. (This is something allowed, so it is not an error message !)
• Information about the feature ID in the error message when a stop codon is found in the translated CDS.
• option --organelle fixed
• activate the --de option to add a description. The description is usually overwritten by information filled through the web interface / xml - file according to if you do a programmatic or manual submission (This is something to check... have they change this behavior ?).
• Add option use_attribute_value_as_locus_tag as asked in issue #17

EMBLmyGFF3-1.2.2

Fix:
ambiguous DNA was not handled everywhere.
Augustus example data was containing stop codon in CDS (was run without the option --noInFrameStop=true). So, this test was not passing the last validator properly. We have updated the augustus.gff file.
embl-api-validator-1.1.180.jar was raising error on Prokka example due to metadata information missing for the source feature. Indeed: At least one of the following qualifiers "strain, environmental_sample, isolate" must exist when organism belongs to Bacteria. So we have added the corresponding options to pass them by the command line. We also added a checks where we prompt the user when something is missing.
Enhancement:

progress bar

no_wrap_qualifier option added to avoid line-wrapping for qualifiers.

expose_translations option added to access easily the json mapping files.

Update help and advanced help

EMBLmyGFF3-1.2.1

change log:

• add option "locus_numbering_start" to be able to start numbering the locus at a certain value.
  Useful when we plan to merge 2 EMBL files together (e.g mitochondria + nuclear genome).
• fix: The key instead of the item was saved into the legal_qualifiers list. It didn’t affect the result because this list was not really used. We now use it to check the correct start_codon of the CDS
• fix: when combining feature (only CDS currently) if a qualifier not already seen in the previous CDS chunck of the same CDS, it will be added.
• bug: start_codon optional qualifier of CDS feature on minus strand. We were using the phase of the last exon (the first in ascending order of their positions) instead of the first (the last in ascending order of their positions). (The bug was difficult to see because it is detected only by the flat-file-validator own by ENA and not the public one available in their repository (v1.1.180)).

EMBLmyGFF3-1.2

change log:

• Modify installation of the tool. Could be installed/uninstalled using pip
• fix issue #1 => sorting the features to be sure they are sorted in increasing order of their locations, no matter their strand.
• Add python scripts to test the examples
• Some logs are now compressed by default for a better reading + Add the parameter --uncompressed_log to be able to have the log in its whole.

EMBLmyGFF3-1.1

change log:

• add of the extra line "AC * _Contig"
• DE line is no more filled by the 1 row of the gff3. XXX instead
• Locus tag in sequential order for the whole genome (Before it was restarting to 1 for each sequence)
• Separate the locus_tag information from the accession information => New locus_tag parameter added.
• Use of taxid allowed in the species parameter (Will be translated to the species name).
• Fill automatically the classification parameter fetch from the NCBI taxonomy DB
• Add "email" parameter that will be use to fetch information from NCBI
• Ambiguous DNA handled now for translation
• Last character removed if stop (*) when "translation" parameter activated. Add a warning if premature codon stop.
• Value "UNKNOWN" replaced by "XXX"

EMBLmyGFF3-1

This release has been checked against Augustus, Prokka and Maker gff3 annotation files.
It has been designed to be able to handle the different GFF3 files that could be meet.
The imprecision found in the pre-release have been fixed (Text wrapping, skipping unknown features, use of regex within qualifier added, add of extended help... )

pre-release of GFF3_to_EMBL

This is the pre-release.