McTavishLab/physcraper issues and pull requests

#183 - biopython error

Issue - State: open - Opened by lskatz over 1 year ago

#182 - KeyError: '^ot:ottId'

Issue - State: open - Opened by LunaSare almost 3 years ago

#181 - error with search_taxon ott:417957

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

#180 - Clean code

Pull Request - State: closed - Opened by snacktavish about 3 years ago

#179 - undefined character

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

#178 - output - file with taxon names that are all gaps in input alignment

Issue - State: open - Opened by LunaSare about 3 years ago - 1 comment

#177 - documenttaion - add docker to install instructions

Issue - State: open - Opened by LunaSare about 3 years ago - 1 comment

#176 - add jupyter notebook to dockerfile

Issue - State: open - Opened by LunaSare about 3 years ago - 3 comments

#175 - Write implementation section as md

Issue - State: open - Opened by LunaSare over 3 years ago

#174 - Add a Troubleshooting page

Issue - State: open - Opened by LunaSare over 3 years ago

#173 - automatically generate a file with all citations

Issue - State: open - Opened by LunaSare over 3 years ago

#172 - reviewer 2 - comment 8 - check internal links in docs

Issue - State: closed - Opened by LunaSare over 3 years ago - 1 comment
Labels: pyopensci-review, done

#171 - reviewer 2 - comment 7 - explain polytomy handling in docs

Issue - State: closed - Opened by LunaSare over 3 years ago - 1 comment
Labels: pyopensci-review

#170 - reviewer 2 - comment 6 - tree relabelling

Issue - State: closed - Opened by LunaSare over 3 years ago - 1 comment
Labels: pyopensci-review

#169 - reviewer 2 - comment 5 - clarify mapping is automatic

Issue - State: closed - Opened by LunaSare over 3 years ago - 1 comment
Labels: pyopensci-review

#168 - reviewer 2 - comment 4 - orthologs instead of homologs

Issue - State: closed - Opened by LunaSare over 3 years ago
Labels: pyopensci-review

#167 - reviewer 2 - comment 3 - clarify expectations for users

Issue - State: closed - Opened by LunaSare over 3 years ago - 1 comment
Labels: pyopensci-review

#166 - reviewer 2 - comment 2 - clarify differences with existing tools

Issue - State: closed - Opened by LunaSare over 3 years ago - 1 comment
Labels: pyopensci-review

#165 - reviewer 2 - comment 1 - clarify usability

Issue - State: closed - Opened by LunaSare over 3 years ago - 2 comments
Labels: pyopensci-review

#164 - Clean docs

Pull Request - State: closed - Opened by LunaSare over 3 years ago

#163 - Lint

Pull Request - State: closed - Opened by snacktavish over 3 years ago - 1 comment

#162 - Reqs update

Pull Request - State: closed - Opened by snacktavish over 3 years ago

#161 - Ejm ms rev

Pull Request - State: closed - Opened by snacktavish over 3 years ago - 1 comment

#160 - duplicated taxon names on input alignment file "taxonname.fas"

Issue - State: closed - Opened by LunaSare almost 4 years ago - 1 comment

#159 - Cleanup

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

#158 - homogenize terms across docs

Issue - State: closed - Opened by LunaSare almost 4 years ago - 1 comment

#157 - add physcraper citation to readme and credits on docs

Issue - State: closed - Opened by LunaSare almost 4 years ago - 1 comment

#156 - double 'example commands' section on physcraper run docs needs merging

Issue - State: closed - Opened by LunaSare almost 4 years ago - 1 comment

#155 - reviewer 1 - minor comments

Issue - State: closed - Opened by LunaSare almost 4 years ago - 1 comment

#154 - reviewer 1 - comment 7 - aminoacid alignments

Issue - State: open - Opened by LunaSare almost 4 years ago - 1 comment
Labels: enhancement, pyopensci-review

#153 - reviewer 1 - comment 2 - things labeled as "under construction"

Issue - State: closed - Opened by LunaSare almost 4 years ago - 4 comments
Labels: pyopensci-review

#152 - reviewer 1 - comment 1 - missing things on readme

Issue - State: closed - Opened by LunaSare almost 4 years ago - 2 comments
Labels: pyopensci-review

#151 - toc not showing on readthedocs, only on local build

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

#150 - Supertreebasefix

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

#149 - Pyopensci rev

Pull Request - State: closed - Opened by snacktavish almost 4 years ago

#148 - Reqs update

Pull Request - State: closed - Opened by snacktavish almost 4 years ago

#147 - reviewer 1 - comment 8 - Error on treebase tree

Issue - State: closed - Opened by snacktavish almost 4 years ago - 3 comments
Labels: pyopensci-review

#146 - reviwer 1 - comment 6 - Progress bar for blast runs

Issue - State: open - Opened by snacktavish almost 4 years ago - 1 comment
Labels: enhancement, pyopensci-review

#145 - reviewer 1 - comment 5 - function documentation

Issue - State: closed - Opened by snacktavish almost 4 years ago - 1 comment
Labels: pyopensci-review

#144 - reviewer 1 - comment 4 - alternative alignment options

Issue - State: closed - Opened by snacktavish almost 4 years ago - 1 comment
Labels: pyopensci-review

#143 - reviewer 1 - comment 3 - Anaconda/virtualenv

Issue - State: closed - Opened by snacktavish almost 4 years ago - 2 comments
Labels: pyopensci-review

#142 - Pylint

Pull Request - State: closed - Opened by snacktavish about 4 years ago

#141 - Docs

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#140 - Update location of instructions when blast db is old

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

#139 - No ingroup fix

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

#138 - Tree not found?

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

#137 - ot_ws_wrapper NoneType

Issue - State: open - Opened by mkandziora over 4 years ago - 3 comments

#136 - add do_not_align option

Issue - State: open - Opened by snacktavish over 4 years ago

#135 - Pylint

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#134 - fix write info bug

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#133 - writeinfofiles is not defined

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

#132 - no_est functionality

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

#131 - own data example not working

Issue - State: closed - Opened by mkandziora over 4 years ago - 2 comments

#130 - Pyopensci

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#129 - output nexml

Issue - State: open - Opened by snacktavish over 4 years ago

#128 - Documentation updates

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

#127 - Relabel

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#126 - Treetaxon

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#125 - Api key

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#124 - relabel script

Issue - State: open - Opened by snacktavish over 4 years ago - 1 comment
Labels: enhancement

#123 - organize MDs

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

#122 - Ownfile

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#121 - Tutorial

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#120 - OpenTree names for no ncbi

Issue - State: open - Opened by snacktavish over 4 years ago

#119 - Update blocklist

Issue - State: closed - Opened by snacktavish over 4 years ago

#118 - take outgroup tips or taxa as inputs for conflict

Issue - State: closed - Opened by snacktavish over 4 years ago

#117 - Repeat

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#116 - Check Treebase downloads for concatenated loci

Issue - State: open - Opened by snacktavish over 4 years ago

#115 - Define namespace

Issue - State: open - Opened by snacktavish over 4 years ago

#114 - Helpers

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#113 - Check dates of blast files

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

#112 - Align

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#111 - Automate updating taxonomy and ottids in synth

Issue - State: open - Opened by snacktavish over 4 years ago

#110 - Check if phylogeny information exists in OpenTree

Issue - State: open - Opened by snacktavish over 4 years ago

#109 - no branch lengths on trees dowloaded from OpenTree

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

#108 - not recognizing blasted sequences

Issue - State: open - Opened by LunaSare over 4 years ago

#107 - alignment import fail

Issue - State: open - Opened by LunaSare over 4 years ago

#106 - Dev

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#105 - weird error on cluster for study pg_238 tree109, aln Tr5276-M3938-mod.nex

Issue - State: closed - Opened by LunaSare over 4 years ago - 2 comments

#104 - Bootstrap

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#103 - pass in boot reps and other related params

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

#102 - rooting when search taxon is inclusive of initial outgroup

Issue - State: open - Opened by LunaSare over 4 years ago

#101 - NCBI id of 0

Issue - State: open - Opened by snacktavish over 4 years ago

#100 - Conflict

Pull Request - State: closed - Opened by snacktavish over 4 years ago

#99 - Check rooting and ingroup from OpenTree

Issue - State: open - Opened by snacktavish over 4 years ago

#98 - muscle error on profile alignment

Issue - State: open - Opened by LunaSare over 4 years ago - 1 comment

#97 - Conflict script ideas

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

#95 - manually downloaded alignment not read

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

#94 - treepath missing

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

#92 - Handle Nones in config

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

#77 - Disambiguate different genes associated with same tree

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

#76 - Exit on local blast

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

#67 - Update taxonomy to ott 3.1

Issue - State: closed - Opened by snacktavish about 5 years ago - 2 comments

#65 - Last blasted is not getting updated correctly

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

#26 - Setup Automatic testing on TravisCI.

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

#14 - Doc strings for all functions

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

#7 - check for required files

Issue - State: closed - Opened by snacktavish about 7 years ago

#6 - organize dependencies

Issue - State: closed - Opened by snacktavish about 7 years ago

#4 - taxon namesspace error

Issue - State: closed - Opened by shchurch about 8 years ago - 2 comments

#3 - cut error & assigns to LIFE

Issue - State: closed - Opened by shchurch over 8 years ago - 1 comment

GitHub / McTavishLab/physcraper issues and pull requests