rigdenlab/crops issues and pull requests

#144 - docs language='en'

Pull Request - State: open - Opened by jjavier-bm 5 months ago

#143 - add myst_parser in exchange of recommonmark 2

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

#142 - add myst_parser in exchange of recommonmark

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

#141 - minor fix in new .readthedocs.yaml

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

#140 - Read the docs update

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

#139 - fix write seq filename bug

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

#138 - Fix bug

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

#137 - version update

Pull Request - State: closed - Opened by jjavier-bm almost 2 years ago

#136 - Revert "add remove_ligands option"

Pull Request - State: closed - Opened by jjavier-bm almost 2 years ago

#135 - add remove_ligands option

Pull Request - State: closed - Opened by jjavier-bm almost 2 years ago

#134 - Ligands, renumbering and alignment

Pull Request - State: closed - Opened by jjavier-bm almost 2 years ago

#133 - improvements Mar-Apr 2023

Pull Request - State: closed - Opened by jjavier-bm almost 2 years ago

#132 - small fix

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#131 - Preparation for new release

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#130 - fix crops headers

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: bug

#129 - debugging sort option in cropseq.py

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: bug

#128 - debugging uniprot server-only option

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: bug

#127 - add tests for UP threshold to ops.py

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: testing

#126 - Update docs - fixtures 1

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#125 - Update docs

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#124 - Update docstrings and minor fixes 1

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: documentation, enhancement

#123 - seq length tests ops.py

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#122 - add final tests ops.py

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#121 - add final tests sequence.py

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#120 - Tests sequence.py

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#119 - modify .gitignore and add python 3.10 for testing

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago - 1 comment

#118 - add seqback to renumber_needleman + interval tests

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#117 - Modify commands + subsets for all + intintervals tests

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: enhancement, testing

#116 - Add Option to extract a few sequences from large fasta file

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#115 - fix input cropmap

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: bug

#114 - fix pdb parser name

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: bug

#113 - update biopython requirements

Pull Request - State: closed - Opened by FilomenoSanchez over 2 years ago - 1 comment

#112 - Splitseqs Command Added

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#111 - fix ID case sensitive issues

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: bug

#110 - stringparsing, tests of parsers and taggers

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago

#109 - add seq & str parsing from strings

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: enhancement

#108 - Make Needleman-Wunsch optional

Pull Request - State: closed - Opened by jjavier-bm over 2 years ago
Labels: enhancement

#107 - Minor fix

Pull Request - State: closed - Opened by FilomenoSanchez over 2 years ago
Labels: bug

#106 - Use Needleman-Wunsch to renumber structures if original algorithm fails

Pull Request - State: closed - Opened by FilomenoSanchez over 2 years ago

#105 - open file safely at parsers

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#104 - more flexible sequence-structure match

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#103 - little fix to retrieve_id function

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#102 - add intervals to sequence

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#101 - minor edit sequences, add msa slots to sequence

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#100 - improvement of set cropmaps 4 & 5

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#99 - Improvement of set_cropmaps

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#98 - minor fix urllib 2

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#97 - use urllib instead of urllib3

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#96 - minor fixes including use of os.linesep

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#95 - remove about module from docs

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#94 - various fixes

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#93 - doc fix test

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#92 - Sequence classes remade

Pull Request - State: closed - Opened by jjavier-bm almost 3 years ago

#91 - Cropmaps and guess type added

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

#90 - typo correction in parsers.py

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

#89 - addition of mapfiles in command line

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

#88 - addition of mapfiles in parsers.py and sequence.py

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

#87 - minor fixes

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

#86 - Uniprot online fasta db added

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

#85 - backmapping

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

#84 - Multiple sequence files

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

#83 - sequence debugging2

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

#82 - sequence debugging

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

#81 - add requirements to pip installation

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

#80 - new install and palette

Pull Request - State: closed - Opened by jjavier-bm almost 4 years ago
Labels: documentation, enhancement