fhcrc/taxtastic issues and pull requests

#159 - Modifications to support iqtree.

Pull Request - State: closed - Opened by jgolob about 2 months ago

#158 - Add logic to generate taxonomy4blast.sqlite3 database

Issue - State: open - Opened by dhoogest 4 months ago - 4 comments

#157 - Bump jinja2 from 3.1.2 to 3.1.3

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#156 - ftp download link times out

Issue - State: closed - Opened by nhoffman 11 months ago - 2 comments

#155 - Error is pplacer using taxtastic

Issue - State: closed - Opened by lpipes 11 months ago - 6 comments

#154 - TypeError: MetaData.reflect() missing 1 required positional argument: 'bind'

Issue - State: closed - Opened by lpipes 12 months ago - 1 comment

#153 - 152 faster pg load

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

#152 - Improve efficiency of postgres taxonomy database creation

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

#151 - MetaData.reflect() missing 1 required positional argument: 'bind'

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

#150 - pplacer error when using taxtastic refpkg

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

#149 - Added support for headerless txt files

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

#148 - build docs using a github action

Issue - State: closed - Opened by nhoffman about 2 years ago - 1 comment

#147 - Links in readme file broken

Issue - State: closed - Opened by BenKuhnhaeuser over 2 years ago - 1 comment

#146 - Error building db, fixed using older versions from NCBI

Issue - State: closed - Opened by nickp60 over 2 years ago - 1 comment

#145 - Add tree model (.bestModel) to taxit create refpkg creation

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

#144 - Raxmlng

Pull Request - State: closed - Opened by jgolob about 3 years ago - 2 comments

#143 - Check for circular lineages in taxit new_database

Issue - State: closed - Opened by crosenth about 3 years ago - 1 comment
Labels: Enhancement, Discussion

#142 - Update TaxNode.from_taxtable classmethod to include logic for support of unordered ranks

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

#141 - WIP: minimal adaptations from 0.9.0 release to handle new/unordered ranks

Pull Request - State: closed - Opened by dhoogest about 3 years ago - 2 comments

#140 - closes #134, include is_valid in the fields upserted in add_node fn

Pull Request - State: closed - Opened by dhoogest almost 4 years ago - 2 comments

#139 - improve `new_database` subcommand performance when targeting postgresql db

Issue - State: closed - Opened by dhoogest almost 4 years ago - 8 comments
Labels: Enhancement

#138 - Remove official Python 2 support

Issue - State: closed - Opened by crosenth almost 4 years ago - 3 comments

#137 - 133 new ranks

Pull Request - State: closed - Opened by crosenth about 4 years ago - 5 comments

#136 - ValueError: u'clade' is not in list

Issue - State: closed - Opened by santcamille about 4 years ago - 2 comments

#135 - incorporate new ranks in order specified by @crosenth

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

#134 - update_nodes not incorporating is_valid

Issue - State: closed - Opened by dhoogest about 4 years ago - 9 comments

#133 - taxit new_database fails during node update for newer NCBI db dumps

Issue - State: closed - Opened by dhoogest about 4 years ago - 13 comments

#132 - raxml-ng compatibility

Issue - State: closed - Opened by jgolob about 5 years ago - 2 comments
Labels: Enhancement, Discussion

#131 - 130 raxml regex fix

Pull Request - State: closed - Opened by jgolob about 5 years ago

#130 - raxml regex too permissive

Issue - State: closed - Opened by jgolob about 5 years ago

#129 - update installation instructions

Issue - State: open - Opened by nhoffman about 5 years ago - 1 comment
Labels: Documentation

#128 - taxtable: ValueError: 'section' is not in list

Issue - State: closed - Opened by openpaul about 5 years ago - 3 comments

#127 - taxtable produes malformed column names

Issue - State: closed - Opened by bowmanjeffs over 5 years ago - 2 comments

#126 - Add subcommand 'get-descendants'

Issue - State: closed - Opened by nhoffman over 5 years ago - 1 comment

#125 - Provide regular expression defining named/unnamed externally

Issue - State: closed - Opened by nhoffman over 5 years ago - 1 comment

#124 - ncbi new_database failing unique constrain on `names`

Issue - State: closed - Opened by dhoogest over 5 years ago - 7 comments

#123 - ValueError: Table "nodes" is missing from the input database.

Issue - State: closed - Opened by RyloByte about 6 years ago - 1 comment

#122 - RAxML info parsing bug

Pull Request - State: closed - Opened by jgolob over 6 years ago

#121 - Documentation out of sync with code?

Issue - State: closed - Opened by nylander over 6 years ago - 3 comments

#120 - Handling circular taxonomic lineages

Issue - State: closed - Opened by crosenth over 6 years ago - 1 comment

#119 - Entered LG-model (Fasttree) in lines 116 and 150

Pull Request - State: closed - Opened by sachacoesel over 6 years ago - 1 comment

#118 - update to python 3.6 in docker image

Issue - State: closed - Opened by nhoffman over 6 years ago - 2 comments

#117 - produce table of lineages represented as taxonomic names

Issue - State: closed - Opened by nhoffman over 6 years ago - 1 comment

#116 - taxtastic cohort error

Issue - State: closed - Opened by ghost over 6 years ago - 13 comments

#115 - enforcing python2

Pull Request - State: closed - Opened by crosenth over 6 years ago

#114 - adding psycopg2 to install requirements

Pull Request - State: closed - Opened by dhoogest almost 7 years ago - 2 comments

#113 - Fixed column order and added check for self-reference to root

Pull Request - State: closed - Opened by jgolob almost 7 years ago - 1 comment

#112 - column order and need for self-referrential root

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

#111 - adding schema prefix to queries for postgres compatibility

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

#110 - Consider using ncbi taxcat to process species clades

Issue - State: closed - Opened by crosenth almost 7 years ago

#109 - remove dependency on biopython

Issue - State: closed - Opened by nhoffman almost 7 years ago

#108 - remove dependency on pandas

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

#107 - develop.rst merge from 3 years ago

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

#106 - taxtastic - new versions - in BioConda?

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

#105 - Regular build of a full ncbi taxtable

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

#104 - taxtable column order must be tax_id, parent_id, rank, tax_name, ranks

Issue - State: closed - Opened by nhoffman almost 7 years ago - 1 comment

#103 - create docker image

Issue - State: closed - Opened by nhoffman almost 7 years ago

#102 - Unfiltered taxonomy

Pull Request - State: closed - Opened by dhoogest almost 7 years ago - 1 comment

#101 - add_node(s) refactor

Pull Request - State: closed - Opened by crosenth about 7 years ago

#100 - use recursive cte to calculate lineages

Issue - State: closed - Opened by nhoffman about 7 years ago - 1 comment

#99 - evaluate leaving no_rank taxa in database and expanding on the fly

Issue - State: closed - Opened by nhoffman about 7 years ago - 2 comments

#98 - postgresql database creation

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

#97 - add_ranks subcommand

Issue - State: closed - Opened by crosenth about 7 years ago - 2 comments

#96 - add_names subcommand

Issue - State: closed - Opened by crosenth about 7 years ago - 2 comments

#95 - Update Sphinx docs on latest tagged version

Issue - State: closed - Opened by crosenth about 7 years ago - 1 comment

#94 - commented out regex for excluding 'group' records

Pull Request - State: closed - Opened by dhoogest about 7 years ago - 4 comments

#93 - Remove "group" from UNCLASSIFIED_REGEX_COMPONENTS in ncbi.py

Issue - State: closed - Opened by dhoogest about 7 years ago - 2 comments

#92 - "source" table not updated with add_nodes

Issue - State: open - Opened by nhoffman over 7 years ago - 1 comment

#91 - Populate source table when adding initial data in subcommand ``new_database``

Issue - State: closed - Opened by crosenth over 7 years ago - 1 comment

#90 - PyPI package out of date?

Issue - State: closed - Opened by wwood over 7 years ago - 3 comments

#89 - Is it possible to run pplacer on an IQ-tree?

Issue - State: closed - Opened by AliciaArroyo over 7 years ago - 2 comments

#88 - running taxit error. pkg_resources.DistributionNotFound: xlrd

Issue - State: closed - Opened by blancaverag over 7 years ago - 3 comments