Ecosyste.ms: Issues
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GitHub / althonos/pyhmmer issues and pull requests
#74 - Parameter to remove insert column in `hmmalign`
Issue -
State: open - Opened by apcamargo about 2 months ago
#73 - Return a single TopHits object when passing a single hmm to hmmsearch
Issue -
State: open - Opened by alex-hh about 2 months ago
#72 - "Erroneous" type warning?
Issue -
State: closed - Opened by leoburgy 2 months ago
- 2 comments
Labels: bug
#71 - PyHmmer sets CPU float behaviour globally, potentially causing issues in other libraries
Issue -
State: open - Opened by jakobnissen 2 months ago
- 1 comment
Labels: bug, building
#70 - Uninformative error when input hmm file contains profiles with different alphabets
Issue -
State: closed - Opened by Sann5 4 months ago
- 2 comments
Labels: bug
#69 - BUG: `plan7.HMM.validate()` fails to raise exceptions with ill formatted hmm profiles
Issue -
State: open - Opened by Sann5 4 months ago
- 1 comment
Labels: bug, external
#68 - [question] PyInfernal?
Issue -
State: open - Opened by tomdstanton 5 months ago
- 3 comments
Labels: question
#67 - [Bug] Pickling and unpickling an HMM object changes the cutoff values
Issue -
State: closed - Opened by jolespin 5 months ago
- 5 comments
Labels: bug
#66 - [Question] What does does `included` and `reported` mean in pyhmmer.plan7.Hit?
Issue -
State: closed - Opened by jolespin 5 months ago
- 2 comments
Labels: question
#65 - Apply cutoffs for domains
Issue -
State: open - Opened by apcamargo 6 months ago
- 2 comments
#64 - Guess bit_cutoffs in hmmsearch
Issue -
State: open - Opened by jpjarnoux 6 months ago
#64 - Guess bit_cutoffs in hmmsearch
Issue -
State: open - Opened by jpjarnoux 6 months ago
#63 - pyhmmer.hmmer.hmmsearch is always slower than using hmmsearch directly
Issue -
State: closed - Opened by Gmar999 7 months ago
- 6 comments
Labels: bug, question
#62 - `pyhmmer.nhmmer` throws error when the number of FASTA seqs is larger than 64
Issue -
State: closed - Opened by moshi4 7 months ago
- 2 comments
Labels: bug
#61 - HMMSearch block and freeze
Issue -
State: closed - Opened by jpjarnoux 7 months ago
- 5 comments
Labels: bug
#60 - Hmmsearch callback tqdm update
Issue -
State: closed - Opened by jpjarnoux 7 months ago
- 4 comments
Labels: bug
#59 - Expose ppline in Alignment class
Pull Request -
State: closed - Opened by arajkovic 8 months ago
- 3 comments
Labels: enhancement
#58 - cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```
Issue -
State: open - Opened by erfanshekarriz 10 months ago
- 1 comment
Labels: question
#58 - cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```
Issue -
State: open - Opened by erfanshekarriz 10 months ago
- 1 comment
#57 - [Feature Request] Internally assigning Z for ```HMM``` class
Issue -
State: open - Opened by erfanshekarriz 10 months ago
- 1 comment
#57 - [Feature Request] Internally assigning Z for ```HMM``` class
Issue -
State: open - Opened by erfanshekarriz 10 months ago
- 3 comments
#56 - Save the DigitalSequenceBlock as pickle
Issue -
State: closed - Opened by chtsai0105 11 months ago
- 4 comments
Labels: question
#56 - Save the DigitalSequenceBlock as pickle
Issue -
State: closed - Opened by chtsai0105 11 months ago
- 6 comments
Labels: question
#55 - Scoring a set of sequences with HMM
Issue -
State: closed - Opened by paoslaos 11 months ago
- 3 comments
Labels: question
#54 - Added new publication to the .rst
Pull Request -
State: closed - Opened by halanzi 12 months ago
- 1 comment
Labels: documentation
#54 - Added new publication to the .rst
Pull Request -
State: closed - Opened by halanzi 12 months ago
- 1 comment
Labels: documentation
#53 - `hmmscan` gets confused about short monotone sequences' alphabet. ( assumes `Amino`, actually `RNA`)
Issue -
State: closed - Opened by rtviii 12 months ago
- 7 comments
Labels: question
#52 - Update plan7.pyx
Pull Request -
State: closed - Opened by rtviii 12 months ago
- 2 comments
#51 - Batch the hmmsearch output
Issue -
State: open - Opened by chtsai0105 about 1 year ago
- 3 comments
Labels: question
#51 - Batch the hmmsearch output
Issue -
State: closed - Opened by chtsai0105 about 1 year ago
- 5 comments
Labels: question
#50 - Aborted (core dumped) occurred while doing translate
Issue -
State: closed - Opened by chtsai0105 about 1 year ago
- 3 comments
Labels: bug
#49 - Best way to Read in/Search Over Many Many HMMs?
Issue -
State: closed - Opened by gbouras13 about 1 year ago
- 3 comments
Labels: duplicate, question
#48 - Load more than 1024 HMM files
Issue -
State: closed - Opened by chtsai0105 about 1 year ago
- 2 comments
Labels: question
#47 - De-increment nincluded/nreported after merge
Pull Request -
State: closed - Opened by zdk123 about 1 year ago
- 10 comments
#46 - Reported/Included domain counts are doubled after TopHits merge
Issue -
State: closed - Opened by zdk123 about 1 year ago
- 2 comments
Labels: bug
#45 - Production stable or WIP
Issue -
State: open - Opened by oschwengers over 1 year ago
- 1 comment
Labels: question
#44 - PyHmmer installation error
Issue -
State: closed - Opened by RSweeney25 over 1 year ago
- 1 comment
Labels: question
#43 - `incE` not being respected
Issue -
State: closed - Opened by EvanKomp over 1 year ago
- 2 comments
Labels: question
#42 - Error while running nhmmer
Issue -
State: closed - Opened by theabhirath over 1 year ago
- 3 comments
Labels: bug
#41 - CPUs not being utilized
Issue -
State: closed - Opened by EvanKomp over 1 year ago
- 8 comments
Labels: bug
#40 - PyHMMER 0.8.0 TMD should be 0 for last node
Issue -
State: closed - Opened by jamaliki over 1 year ago
- 5 comments
Labels: question
#39 - Generating sequences
Issue -
State: closed - Opened by mireklzicar over 1 year ago
- 1 comment
Labels: enhancement
#38 - Conflict with numba
Issue -
State: closed - Opened by seanrjohnson over 1 year ago
- 3 comments
Labels: building
#37 - Error raised from C code: fseeko() failed, eslESYS (status code 12)
Issue -
State: closed - Opened by k-krakowski over 1 year ago
- 1 comment
Labels: bug
#36 - segmentation fault in hmmalign
Issue -
State: closed - Opened by ChristophKnapp over 1 year ago
- 8 comments
Labels: bug
#35 - Proposal to add `pyhmmer.jackhmmer` function
Pull Request -
State: closed - Opened by zdk123 over 1 year ago
- 5 comments
#34 - Fix iterate hmm
Pull Request -
State: closed - Opened by zdk123 over 1 year ago
- 6 comments
Labels: bug
#33 - Query type is mis-specified in `iterate_hmm`
Issue -
State: closed - Opened by zdk123 over 1 year ago
Labels: bug
#32 - search_hmm with --cut-ga
Issue -
State: closed - Opened by willhuynh11 over 1 year ago
- 2 comments
Labels: question
#31 - Save sequence name after translation
Pull Request -
State: closed - Opened by valentynbez over 1 year ago
- 10 comments
Labels: bug
#30 - Pass query name to translated sequences
Issue -
State: closed - Opened by valentynbez over 1 year ago
Labels: enhancement
#29 - Bioconda update to v0.7.0 is blocked
Issue -
State: closed - Opened by jhahnfeld almost 2 years ago
- 3 comments
Labels: building, external
#28 - Suggestion: Add esl-reformat as method to convert MSA to stockholm format
Issue -
State: closed - Opened by jpjarnoux almost 2 years ago
- 4 comments
Labels: question
#27 - Possibility to filter alignment results on coverage between HMM and target
Issue -
State: open - Opened by jpjarnoux almost 2 years ago
- 6 comments
Labels: question
#26 - hmmsearch gathering/trusted/noise cutoffs doesn't apply to single domains (i.e., --domT)
Issue -
State: closed - Opened by satriaphd almost 2 years ago
- 4 comments
Labels: documentation, enhancement
#25 - search_hmm results in segmentation fault
Issue -
State: closed - Opened by snerligit about 2 years ago
- 2 comments
Labels: bug, question
#24 - Multiple HMMFiles
Issue -
State: closed - Opened by zdk123 about 2 years ago
- 2 comments
Labels: documentation, enhancement
#23 - how to search HMM file with multiple profiles, ie Pfam?
Issue -
State: closed - Opened by nextgenusfs about 2 years ago
- 2 comments
Labels: documentation, question
#22 - [QUESTION] How to run hmmsearch and save results using pyhmmer ?
Issue -
State: closed - Opened by alienzj over 2 years ago
- 3 comments
Labels: question
#21 - Work with multiprocessing
Issue -
State: closed - Opened by jpjarnoux over 2 years ago
- 6 comments
Labels: question
#20 - bytes type needed for name in TextSequence example
Pull Request -
State: closed - Opened by tmsincomb over 2 years ago
- 1 comment
Labels: documentation
#19 - ValueError: Could not build HMM: Unable to name the HMM.
Issue -
State: closed - Opened by eloyvallinaes over 2 years ago
- 5 comments
Labels: question
#18 - pip install pyhmmer fail for M1
Issue -
State: closed - Opened by tmsincomb over 2 years ago
- 11 comments
Labels: question, building, external
#17 - zip argument #1 must support iteration error + other question
Issue -
State: open - Opened by willhuynh11 over 2 years ago
- 1 comment
Labels: question
#16 - Recommended settings for searching a small number of profiles against a large database
Issue -
State: closed - Opened by seanrjohnson over 2 years ago
- 15 comments
Labels: enhancement
#15 - ImportError: Cannot install pyhmmer in ubuntu
Issue -
State: closed - Opened by yongjuntan over 2 years ago
- 3 comments
Labels: building
#14 - Fix transition probabilities produced by `Builder.build_msa`
Pull Request -
State: closed - Opened by althonos almost 3 years ago
Labels: bug
#13 - Implement long targets pipeline for consistent `nhmmer` results
Pull Request -
State: closed - Opened by althonos almost 3 years ago
- 1 comment
Labels: enhancement
#12 - nhmmer reports Alphabet mismatch
Issue -
State: closed - Opened by fbosnic almost 3 years ago
- 3 comments
Labels: bug
#11 - Bioconda Install Error: Unsatisfiable Error
Issue -
State: closed - Opened by CCranney almost 3 years ago
- 4 comments
Labels: bug
#10 - ValueError: Could not determine format of file: '/dbfs/mnt/LuxC.sto'
Issue -
State: open - Opened by lzhangUT about 3 years ago
- 3 comments
Labels: question
#9 - Is it possible to get/apply cutoffs?
Issue -
State: closed - Opened by zdk123 about 3 years ago
- 3 comments
Labels: enhancement
#8 - Use hpc_hmmsearch
Issue -
State: open - Opened by apcamargo about 3 years ago
- 6 comments
Labels: enhancement
#7 - Could not parse file: Line 20: illegal character -
Issue -
State: closed - Opened by JediKnightChan about 3 years ago
- 2 comments
Labels: bug, external
#6 - [ImgBot] Optimize images
Pull Request -
State: closed - Opened by imgbot[bot] over 3 years ago
- 1 comment
#5 - new empty HMM segfaults when saved to file
Issue -
State: closed - Opened by RuneBlaze over 3 years ago
- 3 comments
Labels: bug, external
#4 - search_hmm finds 0 hits
Issue -
State: closed - Opened by GiancarloCroce over 3 years ago
- 5 comments
Labels: bug, invalid
#3 - build hmm from multiple sequence alignment
Issue -
State: closed - Opened by tijeco over 3 years ago
- 7 comments
Labels: enhancement
#2 - Add code to allow `phmmer` search pipelines
Pull Request -
State: closed - Opened by althonos over 3 years ago
Labels: enhancement
#1 - Rewrite `setup.py` to allow compiling C libraries without `autotools`
Pull Request -
State: closed - Opened by althonos almost 4 years ago
- 1 comment
Labels: building