Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / pycogent/pycogent issues and pull requests
#115 - Please port to Python3
Issue -
State: closed - Opened by tillea about 5 years ago
- 1 comment
#114 - add pyproject.toml
Pull Request -
State: closed - Opened by grandynguyen almost 6 years ago
- 1 comment
#113 - BUG/DOC: test and fix for Canberra-Adkins
Pull Request -
State: closed - Opened by wasade about 6 years ago
- 2 comments
#112 - Incompatibility with latest matplotlib
Issue -
State: closed - Opened by tillea over 6 years ago
- 4 comments
#111 - Pycogent on a local database
Issue -
State: closed - Opened by MarijkeVM almost 7 years ago
- 2 comments
#110 - Sorting `envs`/`env_names` in `fast_unifrac`/`_fast_unifrac_setup` should be optional
Issue -
State: closed - Opened by riemannzetagambit almost 7 years ago
- 1 comment
#109 - PyCogent can't connect to ENSEMBL Metazoa coredb
Issue -
State: closed - Opened by ghost about 7 years ago
- 1 comment
#108 - Trim terminal stop codons with partial sequences
Issue -
State: closed - Opened by santiagoha about 7 years ago
- 1 comment
#107 - [Question] Releasing code under BSD instead of GPL
Issue -
State: closed - Opened by campenr over 7 years ago
- 3 comments
#106 - update code to work with Python 3.x
Issue -
State: closed - Opened by fizwit over 7 years ago
- 1 comment
#105 - Add numpy dependency for setup.py to be installed it automatically
Pull Request -
State: closed - Opened by TaskeHAMANO over 7 years ago
- 3 comments
#104 - cogent Genome does not fetch data from ensembl version 86 and onwards
Issue -
State: closed - Opened by vladie0 over 7 years ago
- 4 comments
#103 - Random failures of test suite
Issue -
State: closed - Opened by tillea almost 8 years ago
- 9 comments
#102 - Test failure with FastTree 2.1.9
Issue -
State: closed - Opened by tillea about 8 years ago
- 3 comments
#101 - Test failures for cd-hit when trying to build Debian package
Issue -
State: closed - Opened by tillea about 8 years ago
- 5 comments
#100 - No 1.9 release tarball available
Issue -
State: closed - Opened by nieder about 8 years ago
- 2 comments
#99 - Using pip to upgrade gives this error : Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-UvtXdd/cogent/
Issue -
State: closed - Opened by miklou over 8 years ago
- 12 comments
#98 - Table 'ensembl_compara_84.member' doesn't exist") 'DESCRIBE member' ()"
Issue -
State: closed - Opened by chirrie over 8 years ago
- 5 comments
#97 - error message when running own pdb files
Issue -
State: closed - Opened by mlynekg3 over 8 years ago
- 2 comments
#96 - Can node labels be parsed as edge values?
Issue -
State: closed - Opened by lczech over 8 years ago
- 1 comment
#95 - About taxon_ids_to_names_and_lineages() in ncbi.py
Issue -
State: closed - Opened by sulsj over 8 years ago
- 1 comment
#94 - iPython Error - UnsupportedOperation: IOStream has no fileno.
Issue -
State: closed - Opened by mbiokyle29 over 8 years ago
- 4 comments
#93 - Cogent not installing with tox
Issue -
State: closed - Opened by mbiokyle29 over 8 years ago
- 2 comments
#92 - BirthDeathModel/RangeNode: tree nodes are not labelled.
Issue -
State: closed - Opened by ropermpv over 8 years ago
- 1 comment
#91 - Create Unifrac fast_p_test_iter and fast_unifrac_permutations_iter
Pull Request -
State: closed - Opened by blankenberg almost 9 years ago
- 4 comments
#90 - cogent ensembl, exon.Location/transcript.Location represents wrong data
Issue -
State: closed - Opened by vladie0 about 9 years ago
- 10 comments
#89 - error with compara and recent Ensembl releases
Issue -
State: closed - Opened by lassancejm about 9 years ago
- 2 comments
#88 - License of pycogent
Issue -
State: closed - Opened by yuharasatoshi about 9 years ago
- 1 comment
#87 - [getFeatures] UnboundLocalError: local variable 'coord' referenced before assignment
Issue -
State: closed - Opened by raonyguimaraes over 9 years ago
- 2 comments
#86 - Retrieving all gene IDs for a given species
Issue -
State: closed - Opened by gawbul almost 10 years ago
- 4 comments
Labels: question
#85 - Non-stationary model which, at equilibrium, would be reversible
Issue -
State: closed - Opened by sarahparks almost 10 years ago
- 2 comments
#84 - Numpy comparison with None future warning forebodes trouble.
Issue -
State: closed - Opened by BenKaehler almost 10 years ago
#83 - 2013 Lost connection to MySQL server during query
Issue -
State: closed - Opened by guillermomarco about 10 years ago
- 3 comments
#82 - MinimalFastqParser error when strict=True
Issue -
State: closed - Opened by zz2liu about 10 years ago
- 2 comments
#81 - Running Nystrom MDS with a dissimilarity matrix
Issue -
State: closed - Opened by kulkarnik about 10 years ago
- 1 comment
#80 - Support for newer releases of Ensembl
Issue -
State: closed - Opened by merenlin over 10 years ago
- 2 comments
#79 - Looking for a SNP on a certain position
Issue -
State: closed - Opened by finswimmer over 10 years ago
#78 - RefSeq Transcript IDs from Ensembl Transcripts
Issue -
State: closed - Opened by guillermomarco over 10 years ago
- 1 comment
#77 - KEGG cookbook documentation
Issue -
State: closed - Opened by guillermomarco over 10 years ago
- 1 comment
#76 - 1024 - MySQL too many connections
Issue -
State: closed - Opened by guillermomarco over 10 years ago
- 2 comments
#75 - How to get a region of genome from ensembl?
Issue -
State: closed - Opened by boxiangliu over 10 years ago
- 3 comments
#74 - test
Issue -
State: closed - Opened by boxiangliu over 10 years ago
#73 - unable to query Ensembl
Issue -
State: closed - Opened by boxiangliu over 10 years ago
- 2 comments
Labels: question
#72 - Error Installing PyCogent
Issue -
State: closed - Opened by Gaby1212 over 10 years ago
- 1 comment
#71 - Fix error in Heip E index computation
Pull Request -
State: closed - Opened by ggonnella over 10 years ago
- 7 comments
#70 - Checking if a CDS is incomplete
Issue -
State: closed - Opened by jergosh over 10 years ago
- 3 comments
Labels: question
#69 - To get the DNA sequence for a given ENSP
Issue -
State: closed - Opened by alanwilter almost 11 years ago
- 2 comments
Labels: enhancement
#68 - Fixing default arguments for "params" parameter
Pull Request -
State: closed - Opened by adamrp almost 11 years ago
- 2 comments
#67 - fixed bug - we don't actually want to change WorkingDir
Pull Request -
State: closed - Opened by gregcaporaso almost 11 years ago
- 2 comments
#66 - cogent.app.util.CommandLineApplication TmpDir defaults to /tmp
Issue -
State: closed - Opened by gregcaporaso almost 11 years ago
Labels: bug
#65 - improved output file names (ported fix from qiime's pycogent backports) and gives user control over temp file location
Pull Request -
State: closed - Opened by gregcaporaso almost 11 years ago
- 2 comments
#64 - uclust app controller allows user to pass temp dir
Pull Request -
State: closed - Opened by gregcaporaso almost 11 years ago
- 2 comments
#63 - Update scripting guidelines documentation
Issue -
State: closed - Opened by gregcaporaso almost 11 years ago
#62 - cogent.app.uclust.uclust_search_and_align_from_fasta_filepath needs to take a temp directory and pass it to get_tmp_filename
Issue -
State: closed - Opened by gregcaporaso almost 11 years ago
#61 - fix to make default temp dir in get_tmp_filename work across platforms
Pull Request -
State: closed - Opened by gregcaporaso almost 11 years ago
- 2 comments
#60 - get_tmp_filename should not hardcode tmp_dir='/tmp'
Issue -
State: closed - Opened by gregcaporaso almost 11 years ago
#59 - pip install cogent doesn't work when numpy isn't installed
Issue -
State: closed - Opened by gregcaporaso almost 11 years ago
- 1 comment
#58 - Updated exception handling syntax to new coding style...
Pull Request -
State: closed - Opened by mikerobeson almost 11 years ago
- 2 comments
#57 - paired-end joining app controllers updated for better QIIME compatibility.
Pull Request -
State: closed - Opened by mikerobeson almost 11 years ago
- 1 comment
#56 - fixed path issue in 'join_paired_end_reads_seqprep' function
Pull Request -
State: closed - Opened by mikerobeson almost 11 years ago
- 8 comments
#55 - Updates Cogent to use Makeblastdb instead of the deprecated formatdb
Pull Request -
State: closed - Opened by zachcp almost 11 years ago
- 4 comments
#54 - pycogent.org domain expired
Issue -
State: closed - Opened by JensTimmerman almost 11 years ago
- 1 comment
#53 - additional tests of cogent.maths.stats.rarefaction.subsample_multinomial
Issue -
State: closed - Opened by jairideout almost 11 years ago
- 1 comment
#50 - RTAX: sanity check unique mapping from read IDs to amplicon IDs
Pull Request -
State: closed - Opened by davidsoergel almost 11 years ago
- 3 comments
#48 - Does not build
Issue -
State: closed - Opened by evolvedmicrobe about 11 years ago
- 1 comment
#47 - Paired-end assembly app controllers.
Pull Request -
State: closed - Opened by mikerobeson about 11 years ago
- 36 comments
#46 - Paired-end assembly app controllers.
Pull Request -
State: closed - Opened by mikerobeson about 11 years ago
- 4 comments
#45 - Fetching IDs with unknown species from Ensembl
Issue -
State: closed - Opened by jergosh about 11 years ago
- 1 comment
#44 - Why are we not allowed to relabel the root node of a tree?
Issue -
State: closed - Opened by BenKaehler about 11 years ago
#42 - Subtracted 18 (hydrate) from all ProteinWeights as this is already added...
Pull Request -
State: closed - Opened by jonatanfan about 11 years ago
- 9 comments
#41 - have gamma return a float when x=2
Pull Request -
State: closed - Opened by wasade about 11 years ago
- 1 comment
#40 - uclust application controller does not properly report out of memory errors
Issue -
State: closed - Opened by wasade about 11 years ago
- 1 comment
#39 - pycogent 1.5.3 fails some tests on OS X 10.7
Issue -
State: closed - Opened by nieder about 11 years ago
#37 - Exception in DenseAligment __init__ method
Issue -
State: closed - Opened by krcurtis over 11 years ago
- 1 comment
#36 - A small bugfix enabling half-bounded optimisation to work as intended.
Pull Request -
State: closed - Opened by pm67nz over 11 years ago
- 4 comments
#34 - BLAT app controller doesn't report out-of-memory errors
Issue -
State: closed - Opened by jairideout over 11 years ago
Labels: bug
#33 - Update coding guidelines to include the new option types
Issue -
State: closed - Opened by josenavas over 11 years ago
#32 - Core db doesn't exist for 'Mustela putorius furo'
Issue -
State: closed - Opened by jergosh over 11 years ago
- 4 comments
#31 - pycogent alters numpy error handling globally?
Issue -
State: closed - Opened by yarden over 11 years ago
#29 - is there any stockholm format parser in cogent?
Issue -
State: closed - Opened by RNAer over 11 years ago
- 2 comments
#28 - allow "." as gap in sequence parser
Issue -
State: closed - Opened by RNAer over 11 years ago
- 4 comments
Labels: enhancement
#27 - fixed bug in setMaxTipTipDistance
Pull Request -
State: closed - Opened by wasade over 11 years ago
- 7 comments
#26 - logical error in CommandLineApplication.getTmpFilename?
Issue -
State: closed - Opened by GavinHuttley over 11 years ago
Labels: bug
#24 - Handling Tempfiles
Issue -
State: closed - Opened by finswimmer over 11 years ago
- 1 comment
Labels: enhancement
#22 - Implemented a getTranscriptByStableId method in response to issue #21
Pull Request -
State: closed - Opened by gawbul over 11 years ago
- 4 comments
#20 - Why isn't Windows supported?
Issue -
State: closed - Opened by finswimmer over 11 years ago
- 4 comments
Labels: question
#18 - RefSeq attribute
Issue -
State: closed - Opened by yvancouver over 11 years ago
- 2 comments
#16 - TestCase.assertFloatEqual doesn't handle infinity correctly
Issue -
State: closed - Opened by jairideout over 11 years ago
- 2 comments
Labels: bug
#15 - Fixed an ApplicationError when using a different working directory with cd_hit app controller
Pull Request -
State: closed - Opened by ctSkennerton over 11 years ago
- 4 comments
#13 - How to calculate the similarity between two gene sequences?
Issue -
State: closed - Opened by skylersun over 11 years ago
- 10 comments
#12 - Bug Fixed: name.py might parse wrong when the species name has more than 2 words
Pull Request -
State: closed - Opened by skylersun over 11 years ago
- 4 comments
#11 - Input parser specific for fasta quality files
Pull Request -
State: closed - Opened by ctSkennerton over 11 years ago
- 3 comments
#9 - QIIME dev does not play nice with PyCogent dev
Issue -
State: closed - Opened by adamrp over 11 years ago
#8 - added a test while investigating issue #7
Pull Request -
State: closed - Opened by gregcaporaso over 11 years ago
- 2 comments
#6 - NCBI database tests fail
Issue -
State: closed - Opened by jairideout over 11 years ago
- 1 comment
Labels: bug
#5 - usearch v5.2.236
Issue -
State: closed - Opened by jairideout over 11 years ago
- 1 comment
Labels: question
#4 - Added warning message when os.rmdir cannot remove temporary training dir
Pull Request -
State: closed - Opened by kylebittinger over 11 years ago
#3 - MODIFIED blat and test_blat to take genetic code as param
Pull Request -
State: closed - Opened by adamrp over 11 years ago
- 7 comments
#2 - port SF feature requests and bug reports to GitHub
Issue -
State: closed - Opened by gregcaporaso almost 12 years ago
#1 - update docs to point to GitHub rather than Sourceforge
Issue -
State: closed - Opened by gregcaporaso almost 12 years ago
- 1 comment