moshi4/FastDTLmapper issues and pull requests

#68 - FileNotFoundError

Issue - State: closed - Opened by wangchengww over 1 year ago - 1 comment

#67 - diamoand error

Issue - State: closed - Opened by suresh2014 about 2 years ago - 4 comments

#66 - FastDTLmapper error caused by python2.7 dependency

Issue - State: closed - Opened by moshi4 about 2 years ago - 12 comments

#65 - ANgst Folder is not created

Issue - State: closed - Opened by jaresoles about 2 years ago - 1 comment

#64 - Fix clean code

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#63 - Feat #62 add brn/dup/trn plot

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#62 - Add Brn/Dup/Trn plot in plot_gain_loss_map figure

Issue - State: closed - Opened by moshi4 almost 3 years ago - 1 comment
Labels: enhancement

#61 - Fix #60 change leaf node plot style

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#60 - Change gain/loss plot map style in leaf node (plot_gain_loss_map)

Issue - State: closed - Opened by moshi4 almost 3 years ago - 1 comment
Labels: enhancement

#59 - Add restart from option

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#58 - Feature #5 resolve multifurcation

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#57 - Feature #56 gain loss map plot

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#56 - Add publication-ready gain/loss map plot function

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#55 - #54 Replace invalid char to "_"(underscore)

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#54 - AnGST cannot handle "|" character in fasta annotation

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: bug

#53 - IQ-TREE parallel processing using Gnu Parallel cause an overload on CPU

Issue - State: closed - Opened by moshi4 almost 3 years ago - 1 comment
Labels: enhancement

#52 - Feature #51 use origin id in unique serial

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#51 - Use origin fasta annotation to unique serial id

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#50 - Addtest #49 goea test code

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#49 - Add GOEA test code

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#48 - Addtest #47 main integration test

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#47 - Add FastDTLmapper main integration test

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#46 - Feature #45 add filename dot char check

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#45 - Bug: Input filename cannot contain '.' (dot) character

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: bug

#44 - #38 Add PyPI deploy github actions code

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#43 - #39-#40 Add CI GitHub actions

Pull Request - State: closed - Opened by moshi4 almost 3 years ago - 1 comment

#42 - #39 #40 Add CI GitHub actions

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#41 - Feature #37 add test code

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#40 - Add python formatter linter github actions

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#39 - Add automated pytest coverage github actions

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#38 - Add PyPI automated deploy github actions

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#37 - Add test code

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#36 - #35 Refactor code with pylance type hints check

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#35 - Refactor: Strict type hints check

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: refactor

#34 - #33 update pyproject metadata

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#33 - Document: update pyproject.toml metadata

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: documentation

#32 - #31 Refactor: complex config.py

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#31 - Refactor: config.py is complex and has several responsibility

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: refactor

#30 - #29 Split UtilSeq class, UtilFasta and UtilGenbank

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#29 - Refactor: UtilSeq class should be split into two classes, UtilFasta and UtilGenbank.

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: refactor

#28 - #23 Change project structure 'fastdtlmapper' to 'src/fastdtlmapper'

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#27 - #24 Add project details in pyproject.toml

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#26 - #22 Change shebang line for python2

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#25 - Use GNU parallel log output function (--results option)

Issue - State: closed - Opened by moshi4 almost 3 years ago - 1 comment
Labels: enhancement

#24 - Add project details to pytproject.toml

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: documentation

#23 - Change project structure 'fastdtlmapper' to 'src/fastdtlmapper'

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: refactor

#22 - Bug: AnGST script shebang does not detect python2

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: bug

#21 - #20 change testable and packageable

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#20 - Change current direcotory strucuture to pytest testable & packageable

Issue - State: closed - Opened by moshi4 almost 3 years ago
Labels: enhancement

#19 - Feature #8 add goea summary report

Pull Request - State: closed - Opened by moshi4 almost 3 years ago

#18 - #11 Add transfer gene list providing function

Pull Request - State: closed - Opened by moshi4 about 3 years ago

#17 - #6 Add --plot_color option

Pull Request - State: closed - Opened by moshi4 about 3 years ago

#16 - #10 Add optional argument of max bootstrap number

Pull Request - State: closed - Opened by moshi4 about 3 years ago

#15 - #13 Plot only specified depth GOterm

Pull Request - State: closed - Opened by moshi4 about 3 years ago - 1 comment

#14 - Refactor: plot parameter

Pull Request - State: closed - Opened by moshi4 about 3 years ago

#13 - Plot only specified depth of GOterm in GOEA result

Issue - State: closed - Opened by moshi4 about 3 years ago
Labels: enhancement

#11 - Provide a list of predicted results for horizontal gene transfer for each gene

Issue - State: closed - Opened by moshi4 about 3 years ago
Labels: enhancement

#10 - Add optional argument of bootstrap tree number limitation in AnGST running

Issue - State: closed - Opened by moshi4 about 3 years ago
Labels: enhancement

#8 - GOEA result summary report is desirable

Issue - State: closed - Opened by moshi4 about 3 years ago - 1 comment
Labels: enhancement

#7 - Plot parameters in goea.py must be instance variable

Issue - State: closed - Opened by moshi4 about 3 years ago
Labels: refactor

#6 - Add GOEA plot user select color option

Issue - State: closed - Opened by moshi4 about 3 years ago - 1 comment
Labels: enhancement

#5 - IQ-TREE randomly resolved multifurcation is not appropriate for DTL reconciliation

Issue - State: closed - Opened by moshi4 about 3 years ago - 1 comment
Labels: enhancement

#4 - #3 feature go enrichmen analysis

Pull Request - State: closed - Opened by moshi4 about 3 years ago

#3 - Add: GO enrichment analysis function

Issue - State: closed - Opened by moshi4 about 3 years ago
Labels: enhancement

#2 - Add IQ-TREE & AnGST DTL reconciliation implementation

Pull Request - State: closed - Opened by moshi4 about 3 years ago

#1 - Develop

Pull Request - State: closed - Opened by moshi4 about 3 years ago

GitHub / moshi4/FastDTLmapper issues and pull requests