Code

Issue 99#102

Code

Merged

HobnobMancer merged 69 commits intomasterHobnobMancer/cazy_webscraper:masterfrom issue_99HobnobMancer/cazy_webscraper:issue_99Copy head branch name to clipboardJan 11, 2023

+975-263

Commits

Commits on Nov 15, 2022

• term program if closing early

  HobnobMancer

  committed
  94ee1be

  Copy full SHA for 94ee1be

• add opt to use seqs from FASTA file

  Show description for c258475
  HobnobMancer

  committed
  c258475

  Copy full SHA for c258475

• shorten line lengths

  HobnobMancer

  committed
  53d2506

  Copy full SHA for 53d2506

• update docs with new CLI args

  HobnobMancer

  committed
  d53203c

  Copy full SHA for d53203c

• add tutorial for using genbank seq cahce

  HobnobMancer

  committed
  ec6cb54

  Copy full SHA for ec6cb54

• cache seqs as retrieved. refactorise code

  HobnobMancer

  committed
  8c41446

  Copy full SHA for 8c41446

• compress the cache directory once done

  HobnobMancer

  committed
  cf3e395

  Copy full SHA for cf3e395

• update version num

  HobnobMancer

  committed
  c504074

  Copy full SHA for c504074

• update installation instructions

  HobnobMancer

  committed
  3f84d95

  Copy full SHA for 3f84d95

• update closing message unit tests

  HobnobMancer

  committed
  d01a69f

  Copy full SHA for d01a69f

• correct add to append for list

  HobnobMancer

  committed
  b396a49

  Copy full SHA for b396a49

• add logging messages

  HobnobMancer

  committed
  b7c2f41

  Copy full SHA for b7c2f41

Commits on Nov 16, 2022

• IncompleteRead error capture when posting ids

  HobnobMancer

  committed
  6512e0e

  Copy full SHA for 6512e0e

• ignore blank links in the acc file

  HobnobMancer

  committed
  297e1c3

  Copy full SHA for 297e1c3

Commits on Nov 29, 2022

• use re to retrieve ncbi accessions

  HobnobMancer

  committed
  908dcce

  Copy full SHA for 908dcce

• add unit tests and remove unused imports

  HobnobMancer

  committed
  8e0bbd1

  Copy full SHA for 8e0bbd1

• update unit tests

  HobnobMancer

  committed
  7546238

  Copy full SHA for 7546238

Commits on Jan 11, 2023

• fix merge conflicts

  HobnobMancer

  committed
  8f28199

  Copy full SHA for 8f28199

• update version number

  HobnobMancer

  committed
  91422ea

  Copy full SHA for 91422ea

• refactor funcs

  HobnobMancer

  committed
  36c482b

  Copy full SHA for 36c482b

• define missing logger

  HobnobMancer

  committed
  9faaae0

  Copy full SHA for 9faaae0

• update parser

  Show description for c503b5a
  HobnobMancer

  committed
  c503b5a

  Copy full SHA for c503b5a

• get protein acc for gene name

  Show description for f38925f
  HobnobMancer

  committed
  f38925f

  Copy full SHA for f38925f

• update dict keys to separte gene and protein names

  HobnobMancer

  committed
  50d559e

  Copy full SHA for 50d559e

• retrieve gene names from uniprot to link gene names and genbank protein version accessions

  HobnobMancer

  committed
  28c290a

  Copy full SHA for 28c290a

• add missing option to choices for the api

  HobnobMancer

  committed
  f72ad97

  Copy full SHA for f72ad97

• add new args to parser

  Show description for 055b947
  HobnobMancer

  committed
  055b947

  Copy full SHA for 055b947

• update version number

  HobnobMancer

  committed
  3c10e02

  Copy full SHA for 3c10e02

• update citation information

  HobnobMancer

  committed
  ca7be8b

  Copy full SHA for ca7be8b

• fix unit tests for expand.unprot

  HobnobMancer

  committed
  8e234c5

  Copy full SHA for 8e234c5

• fix unit tests for parsers

  HobnobMancer

  committed
  de5a920

  Copy full SHA for de5a920

• update requirements. use bioservices for the new uniprot api

  HobnobMancer

  committed
  aeb48d4

  Copy full SHA for aeb48d4

• do not retry invalid gene names

  HobnobMancer

  committed
  e3cbe5b

  Copy full SHA for e3cbe5b

• update documentation

  Show description for f80b6ac
  HobnobMancer

  committed
  f80b6ac

  Copy full SHA for f80b6ac

• update documentation

  Show description for 3ec8477
  HobnobMancer

  committed
  3ec8477

  Copy full SHA for 3ec8477

• map gene names when couldn't be retrieved from uniprot

  HobnobMancer

  committed
  1b36121

  Copy full SHA for 1b36121

• use the uniprot mapping service

  Show description for 8174df8
  HobnobMancer

  committed
  8174df8

  Copy full SHA for 8174df8

• correct typo in variable name genebank to genbank

  HobnobMancer

  committed
  ec0e0ed

  Copy full SHA for ec0e0ed

• mock getting gene names

  HobnobMancer

  committed
  8bfac94

  Copy full SHA for 8bfac94

• mockmapping accessions

  HobnobMancer

  committed
  43994ec

  Copy full SHA for 43994ec

• correct key names to get genbank acc from uniprot dict

  HobnobMancer

  committed
  6befcfd

  Copy full SHA for 6befcfd

• check the retrieved gbk acc is in the local db before adding protein data

  HobnobMancer

  committed
  9d4a721

  Copy full SHA for 9d4a721

• log addition of data to the local db

  HobnobMancer

  committed
  d3fa24d

  Copy full SHA for d3fa24d

• check the retrieved gbk acc is in the local db before adding protein data

  HobnobMancer

  committed
  e64489e

  Copy full SHA for e64489e

• update variable name to print gbk not in lcoal db

  HobnobMancer

  committed
  3a1e5b4

  Copy full SHA for 3a1e5b4

• update unit tests

  HobnobMancer

  committed
  82e9baf

  Copy full SHA for 82e9baf

• cache uniprot accessions that could not be mapped to genbank

  HobnobMancer

  committed
  d2ff454

  Copy full SHA for d2ff454

• expand error catching when querying ncbi

  Show description for c8474e2
  HobnobMancer

  committed
  c8474e2

  Copy full SHA for c8474e2

• move ncbi-calling funcs to ncbi mod

  Show description for ec3d6d4
  HobnobMancer

  committed
  ec3d6d4

  Copy full SHA for ec3d6d4

• update imports for getting prot seqs

  HobnobMancer

  committed
  2d0822b

  Copy full SHA for 2d0822b

• process invalids containing batches after processing failed connection batches. Process each separetly

  HobnobMancer

  committed
  75f3405

  Copy full SHA for 75f3405

• update version number

  HobnobMancer

  committed
  a70c2b9

  Copy full SHA for a70c2b9

• log when cache and downloaded seqs don't match

  Show description for 9a896e7
  HobnobMancer

  committed
  9a896e7

  Copy full SHA for 9a896e7

• correct syntax errors

  Show description for d4ecf03
  HobnobMancer

  committed
  d4ecf03

  Copy full SHA for d4ecf03

• add missing args to func calls

  HobnobMancer

  committed
  b0f1384

  Copy full SHA for b0f1384

• add missing IncompeteRead import

  HobnobMancer

  committed
  53198c1

  Copy full SHA for 53198c1

• add missing IncompeteRead import

  HobnobMancer

  committed
  6bb4849

  Copy full SHA for 6bb4849

• correct . to , typo

  HobnobMancer

  committed
  2af7469

  Copy full SHA for 2af7469

• add missing args param to func calls

  HobnobMancer

  committed
  3119346

  Copy full SHA for 3119346

• use joined list as str as failed connections key

  HobnobMancer

  committed
  8ce63b6

  Copy full SHA for 8ce63b6

• correct typos success to successful

  HobnobMancer

  committed
  63f869b

  Copy full SHA for 63f869b

• correct old var name to new var name: gbk_acc_to_retrieve to acc_to_retrieve

  HobnobMancer

  committed
  2d08be9

  Copy full SHA for 2d08be9

• correct list to set: successful_accessions

  HobnobMancer

  committed
  771b3d1

  Copy full SHA for 771b3d1

• remove whitespace from ids

  HobnobMancer

  committed
  79350d2

  Copy full SHA for 79350d2

• fix failed_connections bug

  Show description for 94d59d1
  HobnobMancer

  committed
  94d59d1

  Copy full SHA for 94d59d1

• update docs on cache files

  HobnobMancer

  committed
  4324751

  Copy full SHA for 4324751

• Merge branch 'master' into issue_99

  HobnobMancer

  authored
  35c2fd8

  Copy full SHA for 35c2fd8

• change sqlalchemy requirement to fix v num

  HobnobMancer

  committed
  b8268e5

  Copy full SHA for b8268e5

• Merge branch 'issue_99' of https://github.com/HobnobMancer/cazy_webscraper into issue_99

  HobnobMancer

  committed
  b3b9dc4

  Copy full SHA for b3b9dc4