GitLab

Formatting of SYNOPSIS code.

Passes unit tests.

Added external_db_id and hcoverage, for the 2 new columns in dna_align_feature and protein_align_feature.

fails, the feature is reconstructed from transforms of the unagpped
components of the feature
- Added some checks to Transcript/Exon transform that warns and skips
supporting features that do not transform successfully

to fetch ungapped_features from DNA-PEP transcript_supporting_features
(due tothe presence of Insertions that are non modulo-3 in length, which is
common for introns).

forward strand and "throw"ed on the reverse strand! Made them both
warnings.

now make sure to set up the group_id and level_id variables, but also the seqname is set without the need of having a slice associated. strands_reversed method set and returns 0 if variable undef

Added strands_reversed method that 0 or 1. 0 if the strand and hstrand are those originally obtained by the alignment program, 1 other wise

made sure seqname was maintained in alignfeatures and corrected an error message in SliceAdaptor

Added alignment_length method again for use in homologous gene pairing pipeline, to regenerate the original perc_id and perc_pos that blast gives. The blast Runnable returns the perc_id based on the query length without indels

database used for transform is _always_ taken from slice/contig (i.e. not feature or exon)
tidied up a bit in SeqFeature and BaseAlignFeature

_transform_to_RawSlice was not aware of reverse slices, but it is now thanks to Graham.  Cleaned up a few other things.

Exon - checks phase is defined before comparison
PredictionTranscript - checks phase is defined.  Commented out LOG print statements
TranscriptFactory - start_exon end_exon same old thang
ExonAdaptor - hmm.

bug fix to ensure supporting features are being passed properly

removed _transform_to_slice as should use one in SeqFeature and added a check so if features are split and second half has 0 length it is skipped

In _parse_features, making better use of strandedness information to make sure query and hit start and end coordinates are turned the right way around.

Removed deprecated Repeat, RepeatI modules
Added a few more PODs

These were causing infinite recursion due to new superclass implementation of entire_seq, attach_seq, and contig methods