Merck/deepbgc issues and pull requests

#101 - [Question] How can I use precomputed genes via GFF format with DeepBGC?

Issue - State: open - Opened by jolespin about 2 months ago

#100 - DeepBGC failed with ValueError: Grouper for 'sequence_id' not 1-dimensional

Issue - State: open - Opened by marlaux 4 months ago

#99 - installing deepbgc

Issue - State: open - Opened by kadesu 5 months ago - 1 comment

#98 - ValueError: End location (8780) must be greater than or equal to start location (9428)

Issue - State: open - Opened by PKU007 8 months ago

#97 - deepbgc info crash - same as Issue #39

Issue - State: open - Opened by jfoldi81 9 months ago

#95 - ImportError: Missing required dependencies ['numpy']

Issue - State: closed - Opened by chengyou96 11 months ago - 1 comment

#94 - Looking for individual genes

Issue - State: open - Opened by XT33KAKA about 1 year ago

#93 - Use https instead of ftp protocol for Pfam database download

Issue - State: closed - Opened by jasmezz about 1 year ago - 1 comment

#92 - Use https for pfam download

Pull Request - State: closed - Opened by prihoda about 1 year ago - 3 comments

#91 - running "deepbgc info" issue

Issue - State: open - Opened by AledHe over 1 year ago

#90 - Bugs for protein input

Issue - State: open - Opened by Xinpeng021001 over 1 year ago - 1 comment

#89 - Hmmer and Prodigal Package Access Problem

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

#88 - Could deepBGC be used for special gene clusters?

Issue - State: open - Opened by Xinpeng021001 over 1 year ago

#87 - what "inhibitor" means???

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

#86 - fit_generator

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

#85 - how to create negative samples?

Issue - State: open - Opened by wawpaopao almost 2 years ago - 1 comment

#84 - installation error

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

#83 - how to get a cluster?

Issue - State: open - Opened by wawpaopao about 2 years ago

#82 - WARNING: Tensor flow backened message when running deepbgc info into the CLI

Issue - State: open - Opened by zagonzalez about 2 years ago - 1 comment

#81 - run Deepbgc in fungal genomes

Issue - State: closed - Opened by Juliana-Soto24 about 2 years ago - 1 comment

#80 - Visualization

Issue - State: open - Opened by OwenNaicker about 2 years ago - 1 comment

#79 - fix get_proteins_by_id to avoid overwriting protein_id features

Pull Request - State: open - Opened by LuisFF about 2 years ago

#78 - bug in get_proteins_by_id affecting pfam annotator

Issue - State: open - Opened by LuisFF about 2 years ago - 4 comments

#77 - Update Pfam database

Pull Request - State: closed - Opened by jasmezz over 2 years ago - 1 comment

#76 - Where I can get the code of e-deepBGC?

Issue - State: closed - Opened by liangyong1991 over 2 years ago - 1 comment

#75 - Installation Failure

Issue - State: closed - Opened by NiklausChung over 2 years ago - 5 comments

#74 - Update setup.py

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

#73 - Error during detector training

Issue - State: open - Opened by esraagithub over 2 years ago - 5 comments

#72 - How to get antismash and deebgc cobined svg?

Issue - State: open - Opened by MenusGarg over 2 years ago

#71 - I am getting an issue regarding memory, how to solve this ?

Issue - State: open - Opened by devarajarun over 2 years ago

#70 - Bump numpy from 1.16.1 to 1.21.0

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#69 - Require hmmlearn < 0.2.7

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

#68 - Fix tests for geneborder HMM

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

#67 - DeepBGC failed with ValueError: missing molecule_type in annotations

Issue - State: open - Opened by chengyou96 almost 3 years ago - 3 comments

#66 - Missing required dependencies ['numpy'] with any version of deepbgc

Issue - State: closed - Opened by acelik almost 3 years ago - 1 comment

#65 - deepbgc pipeline does not seem to use more than 2 cores?

Issue - State: open - Opened by bkm23644 almost 3 years ago - 2 comments

#64 - leave-class out validation

Issue - State: closed - Opened by pmobio almost 3 years ago - 1 comment

#63 - deepbgc output result tsv file

Issue - State: closed - Opened by APengs494 almost 3 years ago - 1 comment

#62 - deepbgc download error

Issue - State: closed - Opened by APengs494 almost 3 years ago

#61 - Deepbgc installation through conda

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

#60 - Cope without Bio.Alphabet for Biopython 1.78 onwards

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

#59 - Update util.py

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

#58 - Automatically re-annotate PFAM domains if they are incompatible

Issue - State: open - Opened by susheelbhanu over 3 years ago - 3 comments
Labels: bug

#57 - gbff GenBank file format is not recognised

Issue - State: closed - Opened by gkapatai over 3 years ago - 2 comments

#56 - Installing deepBGC

Issue - State: open - Opened by planctoqueen over 3 years ago - 8 comments

#55 - Fails with deepbgc. ImportError: cannot import name 'ChainMap'

Issue - State: closed - Opened by APengs494 over 3 years ago - 5 comments

#54 - Installing 0.1.26 with Anaconda

Issue - State: open - Opened by danudwary over 3 years ago - 2 comments

#53 - DeepBGC failed with Exception: Unexpected error detecting protein domains using HMMER hmmscan

Issue - State: closed - Opened by Bollie15 over 3 years ago - 2 comments

#52 - ERROR: Could not find a version that satisfies the requirement tensorflow<2.0.0,>=1.15.4 (from deepbgc)

Issue - State: closed - Opened by Bollie15 over 3 years ago - 3 comments

#51 - Bump tensorflow from 1.15.4 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 3 comments
Labels: dependencies

#50 - Fix cluster tsv output with mixed cluster types, freeze dependency versions

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

#49 - different number of elements in *.bgc.tsv rows

Issue - State: closed - Opened by artur-matysik over 3 years ago - 2 comments

#48 - Handle Pfam boundaries in incomplete CDS

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

#47 - DeepBGC failed with KeyError: pfam_id

Issue - State: closed - Opened by artur-matysik over 3 years ago - 6 comments

#46 - Problem for training DeepBGC from scratch

Issue - State: open - Opened by yangziyi1990 over 3 years ago - 6 comments

#45 - How to use DeepBGC's results to the antiSMASH

Issue - State: closed - Opened by yangziyi1990 almost 4 years ago - 14 comments

#44 - No module named 'sklearn.ensemble.forest'

Issue - State: closed - Opened by ghost almost 4 years ago - 1 comment

#43 - using deepBGC with metagenomes

Issue - State: open - Opened by drelo almost 4 years ago - 9 comments

#42 - MD5SUM is not match

Issue - State: closed - Opened by qb-lyu about 4 years ago - 3 comments

#41 - Is there other way to download data set?[speed restriction]

Issue - State: closed - Opened by Bollie15 about 4 years ago - 5 comments

#40 - Require Python 3.6 or 3.7

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

#39 - Test run not working

Issue - State: closed - Opened by ariverosw about 4 years ago - 3 comments

#38 - TensorFlow version problem

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

#37 - Retrain on MIBiG 2.0

Issue - State: open - Opened by prihoda over 4 years ago - 11 comments
Labels: enhancement

#36 - Replace hmmscan with hmmsearch?

Issue - State: closed - Opened by danudwary over 4 years ago - 5 comments
Labels: enhancement, help wanted

#35 - Fix protein IDs in --protein mode, add tests

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

#34 - Add --protein mode to readme.

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

#33 - Add experimental --protein mode

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

#32 - Protein mode

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

#31 - Does DeepBGC works with plants (Brassica spp) ?

Issue - State: closed - Opened by anani-a-missinou almost 5 years ago - 9 comments

#30 - hmmscan runs on only one core

Issue - State: closed - Opened by thinkgenome about 5 years ago - 4 comments

#29 - Add --prodigal-meta-mode option

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

#28 - Prodigal Error

Issue - State: closed - Opened by thinkgenome about 5 years ago - 2 comments

#27 - UserWarning: Reached maximum number of 50 sequences for plotting, some sequences will not be plotted.

Issue - State: closed - Opened by thinkgenome about 5 years ago - 2 comments

#26 - Fix rsplit error in python 2.7

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

#25 - DeepBGC failed with TypeError: rsplit() takes no keyword arguments

Issue - State: closed - Opened by thinkgenome about 5 years ago - 2 comments

#24 - Add support for gzipped input

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

#23 - allow for gzip genome fasta input

Issue - State: closed - Opened by nick-youngblut about 5 years ago - 1 comment

#22 - Fix tensorflow dependency specs

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

#21 - Remove debug printing of pfam descriptions

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

#20 - Improve download help annotation, add default values to help annotations

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

#19 - defaults in script docs

Issue - State: closed - Opened by nick-youngblut about 5 years ago - 1 comment

#18 - allow user-defined downloads directory

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

#17 - Enable using path to model instead of model name.

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