althonos/pyhmmer issues and pull requests

#83 - Update index.rst

Pull Request - State: open - Opened by jolespin 24 days ago

#82 - Question about extract columns from hmmsearch domain output

Issue - State: open - Opened by Xinpeng021001 2 months ago - 1 comment
Labels: question

#81 - TopHits from Binary I/O

Issue - State: open - Opened by arajkovic 3 months ago - 2 comments
Labels: question

#80 - ValueError: Could Not Determine Alphabet of File When Using digital=True in esl.SequenceFile

Issue - State: closed - Opened by BioGavin 4 months ago - 2 comments
Labels: question

#79 - Running the hmmsearch

Issue - State: open - Opened by SergeyBaikal 4 months ago - 3 comments
Labels: question

#78 - Record query object in every `TopHits` object.

Pull Request - State: closed - Opened by althonos 4 months ago - 1 comment

#77 - Get AllHits instead of TopHits

Issue - State: closed - Opened by jpjarnoux 5 months ago - 2 comments
Labels: question

#76 - Provide the description of an HMM

Issue - State: closed - Opened by oschwengers 5 months ago - 13 comments
Labels: enhancement

#75 - Difference in e-value between HMMER and pyHMMER

Issue - State: open - Opened by jpjarnoux 5 months ago - 3 comments
Labels: question

#74 - Parameter to remove insert column in `hmmalign`

Issue - State: open - Opened by apcamargo 6 months ago
Labels: enhancement

#73 - Return a single TopHits object when passing a single hmm to hmmsearch

Issue - State: open - Opened by alex-hh 6 months ago
Labels: enhancement, question

#72 - "Erroneous" type warning?

Issue - State: closed - Opened by leoburgy 7 months ago - 3 comments
Labels: bug

#71 - PyHmmer sets CPU float behaviour globally, potentially causing issues in other libraries

Issue - State: closed - Opened by jakobnissen 7 months ago - 2 comments
Labels: bug, building

#70 - Uninformative error when input hmm file contains profiles with different alphabets

Issue - State: closed - Opened by Sann5 9 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 9 months ago - 1 comment
Labels: bug, external

#68 - [question] PyInfernal?

Issue - State: open - Opened by tomdstanton 10 months ago - 3 comments
Labels: question

#67 - [Bug] Pickling and unpickling an HMM object changes the cutoff values

Issue - State: closed - Opened by jolespin 10 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 10 months ago - 2 comments
Labels: question

#65 - Apply cutoffs for domains

Issue - State: open - Opened by apcamargo 11 months ago - 3 comments

#64 - Guess bit_cutoffs in hmmsearch

Issue - State: open - Opened by jpjarnoux 11 months ago

#64 - Guess bit_cutoffs in hmmsearch

Issue - State: open - Opened by jpjarnoux 11 months ago

#63 - pyhmmer.hmmer.hmmsearch is always slower than using hmmsearch directly

Issue - State: closed - Opened by Gmar999 11 months ago - 9 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 11 months ago - 2 comments
Labels: bug

#61 - HMMSearch block and freeze

Issue - State: closed - Opened by jpjarnoux 12 months ago - 5 comments
Labels: bug

#60 - Hmmsearch callback tqdm update

Issue - State: closed - Opened by jpjarnoux 12 months ago - 4 comments
Labels: bug

#59 - Expose ppline in Alignment class

Pull Request - State: closed - Opened by arajkovic about 1 year ago - 3 comments
Labels: enhancement

#58 - cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```

Issue - State: open - Opened by erfanshekarriz about 1 year ago - 1 comment
Labels: question

#58 - cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```

Issue - State: open - Opened by erfanshekarriz about 1 year ago - 1 comment

#57 - [Feature Request] Internally assigning Z for ```HMM``` class

Issue - State: open - Opened by erfanshekarriz about 1 year ago - 1 comment

#57 - [Feature Request] Internally assigning Z for ```HMM``` class

Issue - State: open - Opened by erfanshekarriz about 1 year ago - 3 comments

#56 - Save the DigitalSequenceBlock as pickle

Issue - State: closed - Opened by chtsai0105 over 1 year ago - 4 comments
Labels: question

#56 - Save the DigitalSequenceBlock as pickle

Issue - State: closed - Opened by chtsai0105 over 1 year ago - 6 comments
Labels: question

#55 - Scoring a set of sequences with HMM

Issue - State: closed - Opened by paoslaos over 1 year ago - 3 comments
Labels: question

#54 - Added new publication to the .rst

Pull Request - State: closed - Opened by halanzi over 1 year ago - 1 comment
Labels: documentation

#54 - Added new publication to the .rst

Pull Request - State: closed - Opened by halanzi over 1 year ago - 1 comment
Labels: documentation

#53 - `hmmscan` gets confused about short monotone sequences' alphabet. ( assumes `Amino`, actually `RNA`)

Issue - State: closed - Opened by rtviii over 1 year ago - 7 comments
Labels: question

#52 - Update plan7.pyx

Pull Request - State: closed - Opened by rtviii over 1 year ago - 2 comments

#51 - Batch the hmmsearch output

Issue - State: open - Opened by chtsai0105 over 1 year ago - 3 comments
Labels: question

#51 - Batch the hmmsearch output

Issue - State: closed - Opened by chtsai0105 over 1 year ago - 5 comments
Labels: question

#50 - Aborted (core dumped) occurred while doing translate

Issue - State: closed - Opened by chtsai0105 over 1 year ago - 3 comments
Labels: bug

#49 - Best way to Read in/Search Over Many Many HMMs?

Issue - State: closed - Opened by gbouras13 over 1 year ago - 3 comments
Labels: duplicate, question

#48 - Load more than 1024 HMM files

Issue - State: closed - Opened by chtsai0105 over 1 year ago - 2 comments
Labels: question

#47 - De-increment nincluded/nreported after merge

Pull Request - State: closed - Opened by zdk123 over 1 year ago - 10 comments

#46 - Reported/Included domain counts are doubled after TopHits merge

Issue - State: closed - Opened by zdk123 over 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 almost 2 years ago - 5 comments
Labels: question

#39 - Generating sequences

Issue - State: closed - Opened by mireklzicar almost 2 years ago - 1 comment
Labels: enhancement

#38 - Conflict with numba

Issue - State: closed - Opened by seanrjohnson almost 2 years ago - 3 comments
Labels: building

#37 - Error raised from C code: fseeko() failed, eslESYS (status code 12)

Issue - State: closed - Opened by k-krakowski almost 2 years ago - 1 comment
Labels: bug

#36 - segmentation fault in hmmalign

Issue - State: closed - Opened by ChristophKnapp almost 2 years ago - 8 comments
Labels: bug

#35 - Proposal to add `pyhmmer.jackhmmer` function

Pull Request - State: closed - Opened by zdk123 almost 2 years ago - 5 comments

#34 - Fix iterate hmm

Pull Request - State: closed - Opened by zdk123 almost 2 years ago - 6 comments
Labels: bug

#33 - Query type is mis-specified in `iterate_hmm`

Issue - State: closed - Opened by zdk123 almost 2 years ago
Labels: bug

#32 - search_hmm with --cut-ga

Issue - State: closed - Opened by willhuynh11 almost 2 years ago - 2 comments
Labels: question

#31 - Save sequence name after translation

Pull Request - State: closed - Opened by valentynbez about 2 years ago - 10 comments
Labels: bug

#30 - Pass query name to translated sequences

Issue - State: closed - Opened by valentynbez about 2 years ago
Labels: enhancement

#29 - Bioconda update to v0.7.0 is blocked

Issue - State: closed - Opened by jhahnfeld about 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 about 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 about 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 over 2 years ago - 4 comments
Labels: documentation, enhancement

#25 - search_hmm results in segmentation fault

Issue - State: closed - Opened by snerligit over 2 years ago - 2 comments
Labels: bug, question

#24 - Multiple HMMFiles

Issue - State: closed - Opened by zdk123 over 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 over 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 almost 3 years ago - 1 comment
Labels: documentation

#19 - ValueError: Could not build HMM: Unable to name the HMM.

Issue - State: closed - Opened by eloyvallinaes almost 3 years ago - 5 comments
Labels: question

#18 - pip install pyhmmer fail for M1

Issue - State: closed - Opened by tmsincomb almost 3 years ago - 11 comments
Labels: question, building, external

#17 - zip argument #1 must support iteration error + other question

Issue - State: open - Opened by willhuynh11 almost 3 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 almost 3 years ago - 15 comments
Labels: enhancement

#15 - ImportError: Cannot install pyhmmer in ubuntu

Issue - State: closed - Opened by yongjuntan about 3 years ago - 3 comments
Labels: building

#14 - Fix transition probabilities produced by `Builder.build_msa`

Pull Request - State: closed - Opened by althonos about 3 years ago
Labels: bug

#13 - Implement long targets pipeline for consistent `nhmmer` results

Pull Request - State: closed - Opened by althonos over 3 years ago - 1 comment
Labels: enhancement

#12 - nhmmer reports Alphabet mismatch

Issue - State: closed - Opened by fbosnic over 3 years ago - 3 comments
Labels: bug

#11 - Bioconda Install Error: Unsatisfiable Error

Issue - State: closed - Opened by CCranney over 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 over 3 years ago - 3 comments
Labels: question

#9 - Is it possible to get/apply cutoffs?

Issue - State: closed - Opened by zdk123 over 3 years ago - 3 comments
Labels: enhancement

#8 - Use hpc_hmmsearch

Issue - State: open - Opened by apcamargo over 3 years ago - 6 comments
Labels: enhancement

#7 - Could not parse file: Line 20: illegal character -

Issue - State: closed - Opened by JediKnightChan over 3 years ago - 2 comments
Labels: bug, external

#6 - [ImgBot] Optimize images

Pull Request - State: closed - Opened by imgbot[bot] almost 4 years ago - 1 comment

#5 - new empty HMM segfaults when saved to file

Issue - State: closed - Opened by RuneBlaze almost 4 years ago - 3 comments
Labels: bug, external

#4 - search_hmm finds 0 hits

Issue - State: closed - Opened by GiancarloCroce almost 4 years ago - 5 comments
Labels: bug, invalid

#3 - build hmm from multiple sequence alignment

Issue - State: closed - Opened by tijeco almost 4 years ago - 7 comments
Labels: enhancement

#2 - Add code to allow `phmmer` search pipelines

Pull Request - State: closed - Opened by althonos about 4 years ago
Labels: enhancement

#1 - Rewrite `setup.py` to allow compiling C libraries without `autotools`

Pull Request - State: closed - Opened by althonos over 4 years ago - 1 comment
Labels: building

GitHub / althonos/pyhmmer issues and pull requests