Merge in upstream (mainly MSA resume)#5
Merged
Conversation
Merge in upstream changes
Previously, observing lines in Fasta files prior to the initial ">" was previously seen as comments. This behaviour was depricated from BioPython release 1.85. This causes an ValueError in reading prokka GFFs, as the fasta is passed with '##FASTA'. *Solution*: Try and except statement excepts the ValueError thrown by BioPython >=1.85 and makes use of format='fasta-pearson' to allow inital Fasta lines, before ">"
Merge in upstream changes
…python Handling bad fasta parsing
Resume Multiple Sequence Alignments
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Need to merge in upstream changes, particularly the MSA resume mode, but also other minor changes.