deprekate/PHANOTATE issues and pull requests

#40 - "parallel edges are forbidden" error in v1.6.4 but not in v1.5.1

Issue - State: closed - Opened by mtisza1 4 months ago - 2 comments

#39 - fastpathz cannot traverse the network: TypeError: no path to target

Issue - State: open - Opened by jmeppley 5 months ago - 2 comments

#38 - Inquiry on upload

Issue - State: open - Opened by songmj86 7 months ago - 1 comment

#37 - Different outputs between 1.5.1 and 1.6.1. Also, odd hash symbols.

Issue - State: open - Opened by raw937 7 months ago - 2 comments

#36 - Update

Pull Request - State: closed - Opened by deprekate 9 months ago

#35 - Update

Pull Request - State: closed - Opened by deprekate 9 months ago

#34 - Protein Fasta format output (.faa)?

Issue - State: open - Opened by raw937 9 months ago - 20 comments

#33 - Fixed bug with missing chevrons for genes that extend off of genome

Pull Request - State: closed - Opened by deprekate over 1 year ago

#32 - Truncated proteins at genome end

Issue - State: open - Opened by ilyavs over 1 year ago - 1 comment

#31 - Added support for aragorn

Pull Request - State: closed - Opened by deprekate over 1 year ago

#30 - Include Aragorn for tRNA masking in addition to tRNAscan-SE

Issue - State: open - Opened by ilyavs over 1 year ago - 5 comments

#29 - multithreading

Issue - State: closed - Opened by b-tierney almost 2 years ago - 3 comments

#28 - Adding a requirements.txt file to ease development

Pull Request - State: closed - Opened by linsalrob almost 2 years ago

#27 - redirecting output of the gap regions.

Pull Request - State: closed - Opened by linsalrob almost 2 years ago

#26 - Develop: incorrect output

Issue - State: open - Opened by linsalrob almost 2 years ago

#25 - Warning: tRNAscan not found, proceding without tRNA masking.

Issue - State: closed - Opened by noutin2020 almost 2 years ago - 9 comments

#24 - Add a zenodo id

Issue - State: open - Opened by linsalrob almost 3 years ago

#23 - Adding a requirements.txt file

Pull Request - State: closed - Opened by linsalrob almost 3 years ago - 1 comment

#22 - missing phanotate_lastal_alignments.tgz

Issue - State: closed - Opened by tsp-kucbd over 3 years ago - 1 comment

#21 - Continuously increasing RAM demand

Issue - State: open - Opened by thackl over 3 years ago - 14 comments

#20 - Adding hotfixes from the master branch to the develop branch

Pull Request - State: closed - Opened by deprekate over 3 years ago

#19 - Update README.md : dependencies

Pull Request - State: closed - Opened by vloux almost 4 years ago

#18 - pip install failed

Issue - State: closed - Opened by liyangjie about 4 years ago - 1 comment

#17 - Adding a new version option (-v)

Pull Request - State: closed - Opened by linsalrob about 4 years ago
Labels: enhancement

#16 - Can you create a release with the current version?

Issue - State: closed - Opened by telatin about 4 years ago - 2 comments

#15 - Develop

Pull Request - State: closed - Opened by deprekate about 4 years ago

#14 - Develop

Pull Request - State: closed - Opened by deprekate about 4 years ago

#13 - Develop

Pull Request - State: closed - Opened by deprekate about 4 years ago

#12 - Cutoff for phanotate score

Issue - State: closed - Opened by aponsero over 4 years ago - 2 comments

#11 - TypeError: a bytes-like object is required, not 'str'

Issue - State: closed - Opened by pck0 almost 5 years ago - 4 comments

#10 - Makefile error

Issue - State: closed - Opened by kshingler almost 5 years ago - 1 comment

#9 - AttributeError: 'int' object has no attribute 'position'

Issue - State: closed - Opened by snayfach about 5 years ago - 3 comments

#8 - No ORFs for 38kb phage with 33 Prodigal genes

Issue - State: closed - Opened by snayfach about 5 years ago - 17 comments

#7 - Protein sequence from gene call

Issue - State: closed - Opened by snayfach about 5 years ago - 11 comments

#6 - suitable for metagenomic assemblies?

Issue - State: open - Opened by guille0387 about 5 years ago - 1 comment

#5 - How to use the output file .gb to assign functions to ORFs.

Issue - State: open - Opened by manuss11 about 5 years ago - 3 comments

#4 - Updating the validation code

Pull Request - State: closed - Opened by linsalrob over 5 years ago

#3 - Release Changes

Pull Request - State: closed - Opened by linsalrob over 5 years ago

#2 - Interpretation of results

Issue - State: open - Opened by Handymanalan over 5 years ago - 1 comment

#1 - Working

Pull Request - State: closed - Opened by deprekate about 6 years ago

GitHub / deprekate/PHANOTATE issues and pull requests