mdshw5/pyfaidx issues and pull requests

#225 - Remove Depsy from README

Pull Request - State: closed - Opened by mdshw5 about 2 months ago - 1 comment

#224 - remove setuptools from runtime dependencies

Pull Request - State: closed - Opened by emollier about 2 months ago - 4 comments

#223 - Add packaging library for #220

Pull Request - State: closed - Opened by mdshw5 4 months ago

#222 - Update documentation for get_seq which uses 1-based closed intervals

Pull Request - State: closed - Opened by eroller 4 months ago - 2 comments

#221 - --transform nucleotide throws KeyError

Issue - State: closed - Opened by kubu4 4 months ago - 2 comments

#220 - Missing library packaging

Issue - State: closed - Opened by nerilbl 6 months ago - 1 comment

#218 - Update develop

Pull Request - State: closed - Opened by mdshw5 8 months ago

#217 - getting UnicodeDecodeError when running faidx with a bed file input

Issue - State: closed - Opened by yonniejon 10 months ago - 8 comments

#216 - Update init.py

Pull Request - State: closed - Opened by rraadd88 11 months ago - 5 comments

#215 - remove old Python 2 hybridation

Pull Request - State: closed - Opened by a-detiste 11 months ago - 2 comments

#214 - Insert indels using mutable option

Issue - State: closed - Opened by anderdnavarro about 1 year ago - 2 comments

#213 - Replace usage of pkg_resources API

Pull Request - State: closed - Opened by mdshw5 about 1 year ago

#212 - DeprecationWarning: pkg_resources

Issue - State: closed - Opened by antonylebechec about 1 year ago - 2 comments
Labels: enhancement

#211 - Incorrect results when used in parallel

Issue - State: closed - Opened by rahul2512 over 1 year ago - 12 comments

#210 - Update codecov action

Pull Request - State: closed - Opened by mdshw5 over 1 year ago

#209 - FastaVariant for checking the reference genome for the VCF file

Issue - State: closed - Opened by shelpuk over 1 year ago - 1 comment
Labels: question

#208 - 27 tests fail on `=pyfaidx-0.7.2.1`

Issue - State: closed - Opened by TheChymera over 1 year ago - 1 comment

#207 - missing setuptools dependency in v0.7.2

Pull Request - State: closed - Opened by mdshw5 almost 2 years ago

#206 - missing setuptools dependency in 0.7.2

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

#205 - 'Sequence.gc' Method for IUPAC bases

Pull Request - State: closed - Opened by Bardia-Masudy almost 2 years ago - 2 comments

#204 - Move the --invert-match example to the top

Pull Request - State: closed - Opened by mdshw5 almost 2 years ago

#203 - Allow supplying no .bed file and creating just the index

Issue - State: closed - Opened by wbazant almost 2 years ago - 2 comments

#202 - fix ResourceWarning: unclosed file

Pull Request - State: closed - Opened by siebrenf almost 2 years ago - 1 comment

#201 - Bump pysam from 0.19.1 to 0.20.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#200 - Switch to pyproject.toml

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

#199 - fix bgzf test failure with biopython 1.80

Pull Request - State: closed - Opened by emollier about 2 years ago - 4 comments

#198 - Add use case for indexing FASTA with suppressed output

Pull Request - State: closed - Opened by mdshw5 about 2 years ago
Labels: enhancement

#197 - Update python versions in CI

Pull Request - State: closed - Opened by mdshw5 about 2 years ago - 1 comment

#196 - Merge changes from #184 to release

Pull Request - State: closed - Opened by mdshw5 over 2 years ago

#195 - Bump minimum python to 3.7

Pull Request - State: closed - Opened by mdshw5 over 2 years ago

#194 - fix: remove seemingly superfluous import of pysam

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

#193 - Implement fsspec handling for indexname

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

#192 - Add indexname kwarg to Faidx and Fasta

Pull Request - State: closed - Opened by mdshw5 over 2 years ago - 1 comment

#191 - Minor change in pytest xfail usage in tests

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

#190 - Add fsspec support

Pull Request - State: closed - Opened by ap-- over 2 years ago - 8 comments

#189 - BED parsing not fully compliant with spec

Issue - State: open - Opened by mdshw5 over 2 years ago
Labels: enhancement, testing

#188 - Add acidbio/bed tests

Pull Request - State: closed - Opened by mdshw5 over 2 years ago

#187 - Version in APT doesn't have correct dependenceis

Issue - State: closed - Opened by CholoTook almost 3 years ago - 2 comments

#186 - Migration to pyproject.toml?

Issue - State: closed - Opened by palao almost 3 years ago - 7 comments

#185 - Remove deprecated argument to random.shuffle

Pull Request - State: closed - Opened by mdshw5 almost 3 years ago

#184 - pathlib.Path can be passed to Fasta and Faidx

Pull Request - State: closed - Opened by palao almost 3 years ago - 5 comments

#183 - Using a pathlib.Path object as filename

Issue - State: closed - Opened by palao almost 3 years ago - 5 comments
Labels: enhancement, help-wanted

#182 - python3.8 pip install with --user, on mac, doesn't install faidx script

Issue - State: closed - Opened by rsharris about 3 years ago - 4 comments
Labels: investigating

#181 - Transition from Travis-CI to GH actions

Issue - State: closed - Opened by mdshw5 about 3 years ago - 1 comment

#180 - Variant fasta non ref chr

Pull Request - State: closed - Opened by lldelisle about 3 years ago - 5 comments

#179 - fetch a chromosome on a FastaVariant which is not part of the vcf raises an error

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

#178 - fix RC

Pull Request - State: closed - Opened by y9c over 3 years ago - 2 comments

#177 - fool proof faidx .bed file documentation

Issue - State: closed - Opened by darked89 over 3 years ago - 1 comment

#176 - Feature request: get sequence length

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

#175 - Make FASTA index creation atomic

Pull Request - State: closed - Opened by mdshw5 over 3 years ago
Labels: enhancement

#174 - Incomplete index

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

#173 - Header longer than actual fasta header

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

#172 - Fix TypeError with faidx --transform nucleotide

Pull Request - State: closed - Opened by jvierstra almost 4 years ago - 1 comment

#171 - How to specify how the consensus sequence should be built?

Issue - State: closed - Opened by larahurban almost 4 years ago - 2 comments

#170 - Make line endings survive round-trip

Issue - State: open - Opened by mdshw5 almost 4 years ago
Labels: enhancement, might do, known

#169 - Load an existing .fai?

Issue - State: closed - Opened by rickbeeloo about 4 years ago - 1 comment
Labels: question

#168 - Implement fsspec in place of open

Pull Request - State: closed - Opened by hardingnj over 4 years ago - 13 comments

#167 - Device or resource busy

Issue - State: closed - Opened by nick-youngblut over 4 years ago - 4 comments

#166 - Fix write_fai

Pull Request - State: closed - Opened by folded over 4 years ago - 1 comment

#165 - usage on google cloud storage and more general file handling

Issue - State: closed - Opened by hardingnj over 4 years ago - 1 comment

#164 - Support for constructing and using GZI format files for BGZF compressed FASTA

Pull Request - State: open - Opened by mdshw5 over 4 years ago - 2 comments
Labels: enhancement

#163 - Minor improvement in integer indexing Fasta class.

Pull Request - State: closed - Opened by C-nit over 4 years ago - 2 comments
Labels: enhancement, testing

#162 - question for Iterator mode

Issue - State: closed - Opened by yhgon over 4 years ago - 2 comments
Labels: question, known

#161 - Enable pyfaidx to accept gcp paths for compressed fasta files

Issue - State: open - Opened by archanaraja over 4 years ago - 2 comments

#160 - Index failes if more than one empty line

Issue - State: open - Opened by openpaul almost 5 years ago - 3 comments
Labels: bug

#159 - Unhandled exception when opening header only file

Issue - State: closed - Opened by openpaul almost 5 years ago - 6 comments

#158 - implement Sequence.eq

Pull Request - State: closed - Opened by Maarten-vd-Sande almost 5 years ago - 4 comments

#157 - Fasta instances should have a len method

Issue - State: closed - Opened by mdshw5 almost 5 years ago
Labels: enhancement

#156 - Fasta more dict-like behaviour

Pull Request - State: closed - Opened by Maarten-vd-Sande almost 5 years ago - 12 comments

#155 - Support zero-length sequences

Pull Request - State: closed - Opened by prihoda about 5 years ago - 3 comments
Labels: enhancement

#154 - --split-files

Issue - State: closed - Opened by nservant about 5 years ago - 2 comments
Labels: bug, enhancement

#153 - BGZip slow performance near end of chromosomes

Issue - State: open - Opened by davmlaw over 5 years ago - 3 comments

#152 - Cannot use FastaVariant without genotype

Issue - State: closed - Opened by victorlin over 5 years ago - 2 comments
Labels: wontfix

#151 - FIX bgzip link

Pull Request - State: closed - Opened by VarIr over 5 years ago - 1 comment

#150 - False duplicate key error

Issue - State: closed - Opened by Benjamin-Lee almost 6 years ago - 1 comment

#149 - Make pyfaidx available on py3.7

Issue - State: closed - Opened by VidJa almost 6 years ago - 2 comments

#148 - fix misformatted line in README

Pull Request - State: closed - Opened by hsiaoyi0504 almost 6 years ago - 1 comment

#147 - ImportError: BioPython >= 1.73 must be installed to read block gzip files.

Issue - State: closed - Opened by fungs about 6 years ago - 6 comments

#146 - UnicodeDecodeError while reading file: how to explicit decode format?

Issue - State: closed - Opened by LucaCappelletti94 about 6 years ago - 3 comments

#145 - Python 3.7: RuntimeError: generator raised StopIteration

Issue - State: closed - Opened by tillea about 6 years ago - 3 comments

#144 - Parser breaks if FASTA file does not contain >

Issue - State: closed - Opened by Benjamin-Lee about 6 years ago - 6 comments

#143 - Add support for reading from S3

Pull Request - State: closed - Opened by palakpsheth about 6 years ago

#142 - allow -v to be specified alongside -g

Pull Request - State: closed - Opened by daler about 6 years ago - 3 comments

#141 - Carriage return breaks parsing

Issue - State: closed - Opened by Benjamin-Lee over 6 years ago - 8 comments

#140 - The default_seq argument is not supported with using BGZF compression.

Issue - State: closed - Opened by UnkindPartition over 6 years ago - 4 comments
Labels: bug

#139 - Obtain numpy array for sequence

Issue - State: closed - Opened by alimanfoo over 6 years ago - 8 comments

#138 - Pass build_index to Fasta constructor

Pull Request - State: closed - Opened by marcelm almost 7 years ago - 5 comments

#137 - Large faidx. Huge memory usage?

Issue - State: closed - Opened by aswarren almost 7 years ago - 4 comments

#136 - Rewrite documentation

Issue - State: open - Opened by mdshw5 almost 7 years ago

#135 - Pull changes from issue #134

Pull Request - State: closed - Opened by mdshw5 almost 7 years ago

#134 - Option for failing if index not found

Issue - State: closed - Opened by marcelm almost 7 years ago - 10 comments

#133 - Fasta to Bed

Issue - State: closed - Opened by atfields almost 7 years ago - 2 comments

#132 - Tiny typo: diffent -> different

Issue - State: closed - Opened by croth1 almost 7 years ago - 2 comments

#131 - Recursion error when with bfgz files

Issue - State: closed - Opened by arivers almost 7 years ago - 9 comments

#130 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by mdshw5 almost 7 years ago

#129 - FastaVariant example not working

Issue - State: closed - Opened by daquang almost 7 years ago - 6 comments

#128 - `Sequence.gc` methods that consider IUPAC nucleotide ambiguity

Issue - State: open - Opened by mdshw5 about 7 years ago

#127 - initial version of spliced sequence retrieval

Pull Request - State: closed - Opened by simonvh about 7 years ago - 5 comments
Labels: enhancement

#126 - Create or load htslib .fai and .gzi index files when using BGZF files

Issue - State: closed - Opened by KwatMDPhD about 7 years ago - 12 comments
Labels: enhancement

#125 - BGZF recursion issue

Issue - State: closed - Opened by KwatMDPhD about 7 years ago - 11 comments

GitHub / mdshw5/pyfaidx issues and pull requests