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

#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

#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

#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

#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

#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

#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

#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