Ecosyste.ms: Issues

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GitHub / wilkelab/cinful issues and pull requests

#57 - Fix installation instructions

Pull Request - State: closed - Opened by AaronFeller 8 months ago

#56 - Fix best hits output for immunity proteins

Pull Request - State: closed - Opened by AaronFeller about 2 years ago

#55 - Fix setup_dbs.smk to produce corect pephash.csv files

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

#54 - Update microcins.verified.pep for input

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

#53 - Fixed two issues and cleaned up code in other places.

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

#52 - Update to codebase for publication

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

#51 - verified_directory

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

#50 - support gzipped assemblies

Issue - State: closed - Opened by tijeco about 3 years ago - 1 comment

#49 - Exact match to verified dataset

Issue - State: closed - Opened by tijeco about 3 years ago

#48 - add support for neubi

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

#47 - MFP submodule

Issue - State: closed - Opened by tijeco about 3 years ago

#46 - update for 0.1.0

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

#45 - Generate data for unit tests with updated routines

Issue - State: closed - Opened by tijeco about 3 years ago - 1 comment

#44 - Cinful

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

#43 - pass snakemake arguments to cinful

Issue - State: closed - Opened by tijeco about 3 years ago - 1 comment

#42 - cinful_id instead of Unnamed: 0

Issue - State: closed - Opened by tijeco about 3 years ago - 1 comment

#41 - too many files in python package

Issue - State: closed - Opened by tijeco about 3 years ago

#40 - rearrange merge (closes #39)

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

#39 - Rearrange merge with blast results and nr prodigal file

Issue - State: closed - Opened by tijeco about 3 years ago - 1 comment

#38 - Migrate cinful/notebooks to docs/notebooks

Issue - State: closed - Opened by tijeco about 3 years ago - 1 comment

#37 - output fasta files

Issue - State: closed - Opened by tijeco about 3 years ago

#36 - python wrapper / package

Issue - State: closed - Opened by tijeco about 3 years ago

#35 - signal match 3 orfs upstream and downstream of CvaB

Issue - State: open - Opened by tijeco about 3 years ago - 1 comment

#34 - use seqkit for nonredundant prodigal

Issue - State: open - Opened by tijeco about 3 years ago
Labels: enhancement

#33 - nonredundant_prodigal sample unit test

Issue - State: closed - Opened by tijeco about 3 years ago

#31 - allows for configuration closes #30

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

#30 - configuration

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

#29 - Run individual rules

Issue - State: closed - Opened by tijeco about 3 years ago

#28 - Add signalMatch start and stop to output

Issue - State: open - Opened by tijeco about 3 years ago - 1 comment

#27 - add signalSeq HMM to final output

Issue - State: closed - Opened by tijeco about 3 years ago

#26 - Signal search HMM needs to be put in different location

Issue - State: closed - Opened by tijeco about 3 years ago

#25 - input format and extention

Issue - State: closed - Opened by tijeco about 3 years ago - 1 comment

#24 - benchmark

Issue - State: closed - Opened by tijeco about 3 years ago

#23 - support for one thread with max_threads

Issue - State: closed - Opened by tijeco about 3 years ago

#22 - CvaB search with multithreaded diamond instead of blastp

Issue - State: closed - Opened by tijeco about 3 years ago

#21 - multithread blastp

Issue - State: closed - Opened by tijeco about 3 years ago

#20 - more strict CvaB pre-filter length

Issue - State: closed - Opened by tijeco about 3 years ago

#19 - component snakefiles

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

#18 - final output file with best hits for all three components

Issue - State: closed - Opened by tijeco over 3 years ago

#17 - pick best blast hit for cvab

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

#16 - catalytic triad of best cvab hit or maybe all hits using mafft add

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

#15 - pyhmmer microcin signal sequence search

Issue - State: closed - Opened by tijeco over 3 years ago

#14 - tmhmmPY for immunity protein

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

#12 - Make a single duomolog/blast/hmmer snakefile

Issue - State: closed - Opened by tijeco over 3 years ago

#11 - other Klebsiella refseq assemblies

Issue - State: closed - Opened by tijeco over 3 years ago

#10 - Klebsiella pneumoniae refseq assemblies

Issue - State: closed - Opened by tijeco over 3 years ago

#9 - Other Escherichia refseq assemblies

Issue - State: closed - Opened by tijeco over 3 years ago

#8 - E. coli refseq assemblies

Issue - State: closed - Opened by tijeco over 3 years ago

#7 - summarize refseq E. coli assemblies

Issue - State: closed - Opened by tijeco over 3 years ago

#4 - snakemake needs to be added to conda file

Issue - State: closed - Opened by tijeco over 3 years ago

#3 - 'InputFiles' object has no attribute 'verified_microcins'

Issue - State: closed - Opened by tijeco over 3 years ago

#2 - verified microcin file needs a specific flag

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

#1 - verified microcin

Issue - State: closed - Opened by tijeco over 3 years ago