AuReMe/mpwt issues and pull requests

#89 - I found a new modeling problem.

Issue - State: open - Opened by ChenCongZ 1 day ago

#88 - /mpwt/pwt_wrapper.py: ['Error', 'fatal error', 'No protein-coding genes with sequence data found.', 'Cannot continue.']

Issue - State: open - Opened by Alexander20mc 5 months ago - 3 comments

#87 - I have created dozens of genome files and this situation has occurred. How can I solve it.

Issue - State: open - Opened by ChenCongZ 7 months ago - 3 comments

#86 - When I use pathway tools to build models, this problem always appears: Fatal error: The search using the name of your rganism ("Caloramator Bacteria, Firmicutes, Clostridia, Clostridiales, Caloramator." strain=NIL) failed to find any Taxon class for your organism or returned ambiguous results.

Issue - State: closed - Opened by ChenCongZ about 1 year ago - 2 comments

#85 - Mpwt 0.8.2

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

#84 - Error when launching mpwt

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

#83 - Pathway Tools is not in the Path, mpwt can not work without it.

Issue - State: closed - Opened by ChenCongZ almost 2 years ago - 23 comments

#82 - Mpwt 0.8.0

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

#81 - Issue mpwt delete and ptools cache ?

Issue - State: closed - Opened by lcottret about 2 years ago - 3 comments

#80 - issue when there is an extra file in the input folder

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

#79 - bypass the genetic-elements.dat and organisms.dat creation

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

#78 - Mpwt 0.7.2

Pull Request - State: closed - Opened by ArnaudBelcour over 2 years ago

#77 - Pathway-tools 26.0 handles gbff and gff without input files.

Issue - State: open - Opened by ArnaudBelcour over 2 years ago
Labels: enhancement

#76 - Use -dump-flat-files-biopax to create flat files (Pathway-Tools 26.0).

Issue - State: closed - Opened by ArnaudBelcour over 2 years ago - 1 comment
Labels: enhancement

#75 - Add an option to use -complex-inference (Pathway-Tools 26.0).

Issue - State: closed - Opened by ArnaudBelcour over 2 years ago - 1 comment
Labels: enhancement

#74 - Mpwt 0.7.1

Pull Request - State: closed - Opened by ArnaudBelcour over 2 years ago

#73 - Issue mpwt with the --hf option

Issue - State: closed - Opened by Kisekya over 2 years ago - 1 comment

#72 - Mpwt 0.7.0

Pull Request - State: closed - Opened by ArnaudBelcour over 2 years ago

#71 - Issue with Pathway Tools 25.5 when checking log

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

#70 - String not Boolean and path incorrect

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

#69 - Add an option to give various Pathway Tools option to mpwt.

Issue - State: open - Opened by ArnaudBelcour almost 3 years ago - 1 comment
Labels: enhancement

#68 - Make each run of Pathway Tools independent.

Issue - State: closed - Opened by ArnaudBelcour about 3 years ago - 2 comments
Labels: enhancement

#67 - Issue with Pathway Tools 25.0 when checking log.

Issue - State: closed - Opened by ArnaudBelcour over 3 years ago - 1 comment
Labels: bug

#66 - Issue with encoding of flat_files_creation.log.

Issue - State: closed - Opened by ArnaudBelcour over 3 years ago - 1 comment
Labels: bug

#65 - mpwt 0.6.1

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

#64 - mpwt 0.6.0

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

#63 - mpwt move output files should be more flexible.

Issue - State: closed - Opened by ArnaudBelcour almost 4 years ago - 1 comment
Labels: enhancement

#62 - mpwt 0.5.9

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

#61 - Error when trying to create dat files without input folder.

Issue - State: closed - Opened by ArnaudBelcour almost 4 years ago - 2 comments
Labels: bug

#60 - Refactor how paths are handled.

Issue - State: closed - Opened by ArnaudBelcour almost 4 years ago - 1 comment
Labels: enhancement

#59 - Add version to mpwt.

Issue - State: closed - Opened by ArnaudBelcour almost 4 years ago - 1 comment
Labels: enhancement

#58 - mpwt 0.5.8

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

#57 - Pop-up showing after attribute-value files creations.

Issue - State: closed - Opened by ArnaudBelcour almost 4 years ago - 1 comment
Labels: bug

#56 - Encoding issues when creating terminal logs.

Issue - State: closed - Opened by ArnaudBelcour almost 4 years ago - 1 comment
Labels: bug

#55 - mpwt 0.5.7

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

#54 - PathoLogic error can occur after PGDB creation.

Issue - State: closed - Opened by ArnaudBelcour about 4 years ago - 1 comment
Labels: bug

#53 - Add an option to use Transporter Inference Parser with Pathologic.

Issue - State: closed - Opened by ArnaudBelcour about 4 years ago - 1 comment
Labels: enhancement

#52 - No join and close of Pool if an error occurred.

Issue - State: closed - Opened by ArnaudBelcour about 4 years ago - 1 comment
Labels: bug

#51 - Replace Pool map by starmap.

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

#50 - mpwt 0.5.6

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

#49 - Add a check to delete unfinished PathoLogic build.

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 1 comment
Labels: bug, enhancement

#48 - mpwt 0.5.5

Pull Request - State: closed - Opened by ArnaudBelcour over 4 years ago

#47 - Add support for .fsa extension.

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 1 comment
Labels: enhancement

#46 - --md should not be used without -o

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 1 comment
Labels: bug

#45 - Add a license to the project

Issue - State: closed - Opened by cfrioux over 4 years ago
Labels: enhancement

#44 - Add a --version option to mpwt

Issue - State: closed - Opened by cfrioux over 4 years ago - 1 comment
Labels: enhancement

#43 - Mpwt 0.5.4

Pull Request - State: closed - Opened by ArnaudBelcour over 4 years ago

#42 - Add an argument to select pathway prediction score.

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 2 comments
Labels: enhancement

#41 - mpwt --dat kills pathway-tools command if there is a non-fatal error

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 1 comment
Labels: bug

#40 - Add error message when there is multiple input files.

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 1 comment
Labels: bug

#39 - Add support to gbff.

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 1 comment
Labels: enhancement

#38 - No check of the presence of the taxon_id.tsv file.

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago - 1 comment
Labels: bug

#37 - Issue when checking input files.

Issue - State: closed - Opened by ArnaudBelcour over 4 years ago
Labels: bug

#36 - mpwt 0.5.3

Pull Request - State: closed - Opened by ArnaudBelcour over 4 years ago

#35 - Add an option to create taxon_id.tsv.

Issue - State: closed - Opened by ArnaudBelcour almost 5 years ago - 1 comment
Labels: enhancement

#34 - Manage issue with PubMed citations.

Issue - State: open - Opened by ArnaudBelcour almost 5 years ago - 4 comments
Labels: bug

#33 - Add an option to use Pathway Tools operon predictor.

Issue - State: closed - Opened by ArnaudBelcour almost 5 years ago - 1 comment
Labels: enhancement

#32 - mpwt 0.5.2

Pull Request - State: closed - Opened by ArnaudBelcour almost 5 years ago

#31 - Error when trying to run mpwt on Ubuntu with Python3.7

Issue - State: closed - Opened by mostueve about 5 years ago - 4 comments
Labels: bug

#30 - Add gbk2pf converter.

Issue - State: open - Opened by ArnaudBelcour about 5 years ago - 4 comments
Labels: enhancement

#29 - mpwt 0.5.1

Pull Request - State: closed - Opened by ArnaudBelcour about 5 years ago

#28 - Add more informations in taxon_id.tsv.

Issue - State: closed - Opened by ArnaudBelcour about 5 years ago - 1 comment
Labels: enhancement

#27 - mpwt 0.5

Pull Request - State: closed - Opened by ArnaudBelcour about 5 years ago

#26 - Reduce size argument could return compressed PGDB.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 2 comments
Labels: enhancement

#25 - Split multipwt.py into multiple scripts.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: enhancement

#24 - mpwt 0.4.2.3

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

#23 - Add argument to delete only PGDB redundant with input data.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 2 comments
Labels: enhancement

#22 - Handle error if PathoLogic build is aborted.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: bug

#21 - Add a better error if Pathway Tools failed.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 3 comments
Labels: bug, enhancement

#20 - Error with --clean when used with -v and --cpu.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: bug

#19 - Accept Pathologic file as input.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 6 comments
Labels: enhancement

#18 - mpwt 0.4.2.2

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

#17 - Error with dat creation if PGDB already there.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 2 comments
Labels: bug

#16 - mpwt 0.4.2.1

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

#15 - mpwt 0.4.2

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

#14 - Print error in pathologic.log in the terminal.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: enhancement

#13 - Run BioPAX/dat creation on PGDBs inside ptools-local but not in output folder.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: enhancement

#12 - Replace print with logging.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: enhancement

#11 - mpwt 0.4.1

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

#10 - Better error message if Pathway-Tools is not in PATH.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: enhancement

#9 - Add an option to use Pathway-Tools Hole-Filler.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: enhancement

#8 - Error with .DS_Store on Mac.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: bug

#7 - Fasta are required when using GFF file.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: bug, enhancement

#6 - mpwt 0.4

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

#5 - Accept GFF file as input file.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: enhancement

#4 - Error with Ubuntu OS.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 2 comments
Labels: bug

#3 - More flexible tool.

Issue - State: closed - Opened by ArnaudBelcour almost 6 years ago - 1 comment
Labels: enhancement

#2 - Add better error handling.

Issue - State: closed - Opened by ArnaudBelcour almost 6 years ago - 1 comment
Labels: enhancement

#1 - Multiprocess when moving file.

Issue - State: closed - Opened by ArnaudBelcour almost 6 years ago - 1 comment
Labels: enhancement

GitHub / AuReMe/mpwt issues and pull requests