HobnobMancer/cazy_webscraper issues and pull requests

#132 - Update ncbi seqs

Pull Request - State: closed - Opened by HobnobMancer about 1 month ago
Labels: enhancement, restructrure, update

#131 - Create a single entry point and add scrape_cazy subcmd

Pull Request - State: closed - Opened by HobnobMancer 3 months ago

#130 - Issues 129 ncbi

Pull Request - State: open - Opened by HobnobMancer 8 months ago
Labels: bug, enhancement, restructrure, update

#129 - Incorrect parsing of NCBI protein version accession

Issue - State: open - Opened by HobnobMancer 9 months ago - 1 comment
Labels: bug, enhancement

#127 - Error during retrieving taxa info from NCBI

Issue - State: closed - Opened by UNIVERSALIONZ 11 months ago - 1 comment
Labels: duplicate

#126 - Issue 120 ncbi

Pull Request - State: closed - Opened by HobnobMancer 12 months ago - 2 comments
Labels: bug

#125 - cazy_webscraper - error downloading database

Issue - State: closed - Opened by bharat1912 12 months ago - 1 comment
Labels: bug, duplicate

#124 - Crashing when retrieving taxs from NCBI - perhaps related to #120

Issue - State: closed - Opened by bharat1912 12 months ago - 1 comment
Labels: bug, duplicate

#123 - Reduced memory demand

Issue - State: open - Opened by HobnobMancer almost 1 year ago - 1 comment
Labels: enhancement

#122 - Incomplete read error

Issue - State: closed - Opened by HobnobMancer about 1 year ago - 3 comments
Labels: bug, duplicate

#121 - Catch incomplete read error

Pull Request - State: closed - Opened by HobnobMancer about 1 year ago
Labels: bug

#120 - Crashing when retrieving taxs from NCBI

Issue - State: closed - Opened by HobnobMancer about 1 year ago - 6 comments
Labels: bug

#119 - Increase unit test coverage

Issue - State: open - Opened by HobnobMancer over 1 year ago
Labels: enhancement, unit tests, long term plan

#118 - Add subcommands

Issue - State: open - Opened by HobnobMancer over 1 year ago - 1 comment
Labels: documentation, enhancement, long term plan

#117 - Update config.yml

Pull Request - State: closed - Opened by HobnobMancer over 1 year ago - 2 comments
Labels: unit tests

#116 - Doc update

Pull Request - State: closed - Opened by HobnobMancer over 1 year ago - 1 comment
Labels: documentation

#115 - Issue 111 + 112 uniprot

Pull Request - State: closed - Opened by HobnobMancer almost 2 years ago - 2 comments
Labels: documentation, enhancement, unit tests

#114 - Unexpected error message when retrieving AA UniProt sequences

Issue - State: closed - Opened by AlejandroSanchezCano almost 2 years ago - 2 comments
Labels: bug, duplicate

#113 - Add batch ncbi tax

Pull Request - State: closed - Opened by HobnobMancer almost 2 years ago - 4 comments
Labels: bug, enhancement, unit tests

#112 - add not on cw_get_uniprot before cw_get_pdb

Pull Request - State: closed - Opened by HobnobMancer almost 2 years ago - 1 comment
Labels: documentation

#111 - No PDB acessions matched and Retrieving no protein structure files

Issue - State: closed - Opened by chagas98 almost 2 years ago - 3 comments
Labels: documentation

#110 - Issue 109

Pull Request - State: closed - Opened by HobnobMancer about 2 years ago
Labels: bug

#109 - Crashes when retrieving seqs from NCBI

Issue - State: closed - Opened by HobnobMancer about 2 years ago
Labels: bug

#108 - Fix tax invalid ids

Pull Request - State: closed - Opened by HobnobMancer about 2 years ago
Labels: bug

#107 - Update imports

Pull Request - State: closed - Opened by HobnobMancer about 2 years ago
Labels: bug

#106 - Update to `sqlalchemy` 2.x

Issue - State: open - Opened by HobnobMancer about 2 years ago - 1 comment
Labels: update, long term plan

#103 - Issue 100 uniprot

Pull Request - State: closed - Opened by HobnobMancer about 2 years ago - 4 comments
Labels: bug, documentation, enhancement, unit tests

#102 - Issue 99

Pull Request - State: closed - Opened by HobnobMancer about 2 years ago - 4 comments
Labels: bug, documentation, unit tests

#101 - API missing opt to include 'kingdoms' in output

Issue - State: closed - Opened by HobnobMancer about 2 years ago
Labels: bug, documentation

#100 - Failing to retrieve UniProt data

Issue - State: closed - Opened by HobnobMancer about 2 years ago - 4 comments
Labels: bug

#99 - Crashes when retrieving NCBI seqs: http.client.IncompleteRead

Issue - State: closed - Opened by HobnobMancer about 2 years ago
Labels: bug, enhancement

#98 - Update closing message

Pull Request - State: closed - Opened by HobnobMancer over 2 years ago - 1 comment
Labels: bug, documentation, unit tests

#97 - Fails to retrieve data from UniProt

Issue - State: closed - Opened by HobnobMancer over 2 years ago
Labels: bug

#96 - Fix inability to parse Entrez.NotXMLError

Pull Request - State: closed - Opened by HobnobMancer over 2 years ago - 1 comment
Labels: bug

#95 - Bio.Entrez NotXMLError

Issue - State: closed - Opened by HobnobMancer over 2 years ago - 1 comment
Labels: bug

#94 - Add getting GTDB taxonomic classifications

Pull Request - State: closed - Opened by HobnobMancer over 2 years ago - 1 comment
Labels: documentation, enhancement, new feature, unit tests

#93 - Issue 92 ncbi taxs

Pull Request - State: closed - Opened by HobnobMancer over 2 years ago - 1 comment
Labels: enhancement

#92 - Use NCBI Tax IDs

Issue - State: closed - Opened by HobnobMancer over 2 years ago
Labels: enhancement

#91 - Get genomes

Pull Request - State: closed - Opened by HobnobMancer over 2 years ago - 1 comment
Labels: documentation, enhancement, new feature, unit tests

#90 - Get ncbi tax lineages

Pull Request - State: closed - Opened by HobnobMancer over 2 years ago - 3 comments
Labels: documentation, enhancement, new feature

#89 - Fix logger

Pull Request - State: closed - Opened by HobnobMancer almost 3 years ago - 1 comment
Labels: bug, enhancement, unit tests

#88 - Fix logger inheritance

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: bug

#87 - KeyError when converting CAZy class abbreviations

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: bug

#86 - Update to circleCI 2.0

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: bug, unit tests, update

#85 - Use uniprot accessions in `get_uniprot_data`

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: enhancement

#84 - Tidy and update docs

Pull Request - State: closed - Opened by HobnobMancer almost 3 years ago - 1 comment
Labels: documentation, enhancement

#83 - Fix parsing config and selecting candidates of interest

Pull Request - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: bug, enhancement

#82 - Add GUI

Issue - State: open - Opened by HobnobMancer almost 3 years ago
Labels: enhancement

#81 - Fix log table contents

Pull Request - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: bug, enhancement

#80 - fix parsing `families` configuration

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: bug

#79 - Fix blank pdb accs

Pull Request - State: closed - Opened by HobnobMancer almost 3 years ago - 1 comment
Labels: bug, enhancement

#78 - selecting proteins matching criteria

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: bug

#77 - handling blank pdb accession from uniprot

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: enhancement, update

#76 - log table contents

Issue - State: closed - Opened by HobnobMancer almost 3 years ago
Labels: documentation, enhancement

#75 - Trouble shoot extract seqs

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago
Labels: bug, documentation, enhancement, update

#74 - Trouble shoot getting data from NCBI

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago
Labels: bug, documentation, enhancement, unit tests

#73 - Trouble shoot uniprot

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago
Labels: bug, documentation, enhancement, update

#72 - Fix output dir making

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago - 1 comment
Labels: bug

#71 - update v number

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

#70 - Update unit tests

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago - 1 comment
Labels: unit tests

#69 - ModuleNotFoundError: No module named 'cazy_webscraper.cazy_webscraper‘

Issue - State: closed - Opened by NaiveLittleTiger about 3 years ago - 1 comment
Labels: bug

#68 - Update unit tests

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago - 1 comment
Labels: unit tests, update

#67 - Get data from UniProt

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago
Labels: enhancement, restructrure, new feature, update

#66 - Add retrieving data from GenBank and PDB

Pull Request - State: closed - Opened by HobnobMancer about 3 years ago
Labels: bug, enhancement, restructrure, new feature, update

#65 - Updating CAZy

Pull Request - State: closed - Opened by HobnobMancer over 3 years ago - 1 comment
Labels: documentation, enhancement, restructrure, new feature, update

#64 - change relationship to one-to-many

Pull Request - State: closed - Opened by HobnobMancer over 3 years ago - 2 comments
Labels: bug, enhancement, restructrure

#63 - Incorrect DB schema

Issue - State: closed - Opened by HobnobMancer over 3 years ago
Labels: bug, enhancement

#62 - None standard database table naming format

Issue - State: closed - Opened by HobnobMancer over 3 years ago
Labels: bug, enhancement

#61 - Where is the downloaded data?

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: bug, enhancement

#60 - More (and more useful) information with `-v`/`--verbose`

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: enhancement

#59 - Version numbering out of sync on `PyPI` and `bioconda`

Issue - State: closed - Opened by widdowquinn over 3 years ago - 1 comment
Labels: bug

#58 - Tidy docs

Pull Request - State: closed - Opened by widdowquinn over 3 years ago - 2 comments
Labels: documentation

#57 - Expand NCBI taxonomy data

Issue - State: closed - Opened by HobnobMancer over 3 years ago
Labels: enhancement, new feature

#56 - make minor restructure change to README.md

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

#55 - Use Semantic Versioning

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: documentation, enhancement

#54 - replace hand-written shields/badges

Pull Request - State: closed - Opened by widdowquinn over 3 years ago
Labels: documentation

#53 - Tidy docs

Pull Request - State: closed - Opened by widdowquinn over 3 years ago - 1 comment
Labels: documentation

#52 - highlight complete download warning

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

#51 - Tidy docs

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

#50 - Allow the user to determine the software version

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: enhancement

#49 - Do not make complete download of CAZy the default operation

Issue - State: closed - Opened by widdowquinn over 3 years ago - 2 comments
Labels: enhancement

#48 - Tidy docs

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

#47 - Handling CAZymes with no GenBank accession

Issue - State: closed - Opened by HobnobMancer over 3 years ago
Labels: enhancement, new feature

#46 - 'cazy_webscraper.py' is in 'scraper' directory

Issue - State: closed - Opened by LFLWilson over 3 years ago - 5 comments

#45 - Refinements and tweaks

Pull Request - State: closed - Opened by HobnobMancer over 3 years ago - 1 comment
Labels: bug, documentation, enhancement

#44 - fixes issue #43 - remove .egg-info from repo

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

#43 - Remove `cazy_webscraper.egg-info/` from repo

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: bug

#42 - Use `cazy_webscraper` rather than `cazy_webscraper.py` as the command.

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: enhancement

#41 - When writing output files, create missing parent directories

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: enhancement

#40 - `.vscode` directory can be removed from repository

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: enhancement

#39 - `--families` option does not work as stated in tutorial

Issue - State: closed - Opened by widdowquinn over 3 years ago - 2 comments
Labels: bug, documentation, could not reproduce

#38 - Parse config unit tests

Pull Request - State: closed - Opened by HobnobMancer over 3 years ago
Labels: unit tests

#37 - Include paths in error messages when filenotfound errors are raised

Pull Request - State: closed - Opened by HobnobMancer over 3 years ago - 1 comment
Labels: enhancement

#36 - [ERROR] [scraper.utilities.parse_configuration]: Could not open the CAZy synonym dictionary

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

#35 - Potentially streamlined scraping

Issue - State: closed - Opened by HobnobMancer almost 4 years ago - 3 comments
Labels: enhancement

#34 - Add sql db

Pull Request - State: closed - Opened by HobnobMancer almost 4 years ago
Labels: enhancement, restructrure, new feature

#33 - Add rapid scraping

Pull Request - State: closed - Opened by HobnobMancer almost 4 years ago - 1 comment
Labels: enhancement

#32 - Tutorials

Issue - State: closed - Opened by HobnobMancer almost 4 years ago - 1 comment
Labels: documentation, enhancement

#31 - BLAST database from GenBank retrieval

Issue - State: closed - Opened by HobnobMancer almost 4 years ago
Labels: enhancement

#30 - Basic validation against public CAZy site

Issue - State: closed - Opened by widdowquinn about 4 years ago
Labels: enhancement

GitHub / HobnobMancer/cazy_webscraper issues and pull requests