biocore microprot issues

biocore / microprot

structural annotation pipeline for microbial genomes and metagenomes

BSD 3-Clause "New" or "Revised" License

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issues

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DB clustering

#77 PawelSzczerbiak closed 4 years ago
0
refactor the Snakemake pipeline

#76 tkosciol opened 4 years ago
0
BUG: `MSA_ripe` rule fails on some non-standard amino acids

#75 tkosciol opened 6 years ago
0
added ability to filter matching hits for min sequence identity

#74 sjanssen2 closed 4 years ago
3
Fix split

#73 sjanssen2 closed 6 years ago
5
feature request: `split_search` by % identities

#72 tkosciol closed 4 years ago
3
BUG: `split_search` does not split correctly in some cases

#71 tkosciol closed 6 years ago
4
some records do not get propagated from log to `microprot_db`

#70 tkosciol opened 7 years ago
0
refactor setup.py and repo structure

#69 tkosciol opened 7 years ago
0
unit tests for `snakemake_helpers`

#68 tkosciol opened 7 years ago
0
merge snakemake rules and add msa_size info to index

#67 tkosciol closed 7 years ago
3
addressing issue #65: add match identifier to `match` files

#66 sjanssen2 closed 7 years ago
1
add match identifier to `match` files

#65 tkosciol closed 7 years ago
3
Explanations to naming conventions

#64 tkosciol closed 7 years ago
4
auto build and update microprot_db and HH-suite compatible DB

#63 tkosciol opened 7 years ago
0
keep output files in ffindex format

#62 tkosciol opened 7 years ago
2
pipeline: use DHM to keep databases in memory

#61 tkosciol opened 7 years ago
1
Snakemake: secondary predictions

#60 tkosciol closed 4 years ago
1
Snakefile: create outdirs if do not exist

#59 tkosciol closed 7 years ago
5
Snakemake: code outside of rules executed multiple times

#58 tkosciol opened 7 years ago
0
Snakemake: auto-generate benchmarking and reporting info

#57 tkosciol opened 7 years ago
0
replicating bug in issue #55

#56 sjanssen2 closed 7 years ago
2
BUG: split_sequence error, possible HHsearch issue

#55 tkosciol closed 7 years ago
2
adding a test with an alignment that contains seqs with duplicate IDs.

#54 sjanssen2 closed 7 years ago
2
BUG: calculate_Neff crashes if duplicate entries in DissimilarityMatrix

#53 tkosciol closed 7 years ago
4
Snakemake: reorganize output structure

#52 tkosciol closed 7 years ago
0
BUG: split_search.mask_sequence does not pick optimal fragments

#51 tkosciol opened 7 years ago
3
Fixed bug reported in issue #9

#50 qiyunzhu closed 7 years ago
4
BUG: calculate_Neff fails if 1 sequence in output

#49 tkosciol closed 7 years ago
1
Read MSA size & data source for `append_db` function in Snakemake

#48 tkosciol closed 7 years ago
1
added calculate Neff script

#47 qiyunzhu closed 7 years ago
5
Snakemake scaffold

#46 tkosciol closed 7 years ago
19
Pos numbering

#45 sjanssen2 closed 7 years ago
5
adding additional unit tests to cover Tomasz pseudo bug, i.e. a bit u…

#44 sjanssen2 closed 7 years ago
5
IMPROVEMENT: split_search should modify output name, if residue numbers in name

#43 tkosciol closed 7 years ago
2
BUG: split_search skips non_match sequences if --frag-len too large

#42 tkosciol closed 7 years ago
9
improved process_fasta.py

#41 qiyunzhu closed 7 years ago
4
REQUEST: process_fasta.extract_sequences should be able to read sequence ranges

#40 tkosciol closed 7 years ago
0
BUG: process_fasta.extract_sequences cannot handle lists of int

#39 tkosciol closed 7 years ago
0
Process fasta

#38 tkosciol closed 7 years ago
4
updated split_search

#37 tkosciol closed 7 years ago
7
handling fusion of two rightmost columns in hit summary lines

#36 sjanssen2 closed 7 years ago
2
IMPROVEMENT: split_sequence non_match fragment length

#35 tkosciol closed 7 years ago
3
IMPROVEMENT: split_sequence naming

#34 tkosciol closed 7 years ago
1
BUG: split_search parsing HHsearch output

#33 tkosciol closed 7 years ago
4
Split search

#32 tkosciol closed 7 years ago
5
Split sequence

#31 sjanssen2 closed 7 years ago
13
cluster Micronota genes: extract representative sequences from clustering

#30 tkosciol closed 7 years ago
1
snakemake: edge cases and extensions

#29 tkosciol closed 7 years ago
1
MMSeqs2 install

#28 tkosciol closed 7 years ago
1