pyranges - 0.0.132

Tagging a "stable" v0 in view of the transition to v1 v0 tagged releases will have long-term documentation in readthedocs

What's Changed

• Spliced subseq2 by @endrebak in https://github.com/pyranges/pyranges/pull/232
• 0.0.112 by @endrebak in https://github.com/pyranges/pyranges/pull/226
• Add subsequence by @marco-mariotti in https://github.com/pyranges/pyranges/pull/240
• Fix gff3 writer by @endrebak in https://github.com/pyranges/pyranges/pull/241
• Changes to make flake8 pass by @endrebak in https://github.com/pyranges/pyranges/pull/242
• Update ghwf by @endrebak in https://github.com/pyranges/pyranges/pull/243
• Fix one-off error for GTF Start coordinates in readgtfrestricted (read_gtf(full=False)) by @SamBryce-Smith in https://github.com/pyranges/pyranges/pull/260
• Trying to autogenerate book with github actions. by @endrebak in https://github.com/pyranges/pyranges/pull/247
• Allow reading empty attribute GTF by @endrebak in https://github.com/pyranges/pyranges/pull/269
• A small update to remove pd.append() warnings by @aallahyar in https://github.com/pyranges/pyranges/pull/279
• Fixed the replace parameter. by @FabrizioG202 in https://github.com/pyranges/pyranges/pull/270
• added step to reorder bed columns based on order in PyRanges object before writing by @fairliereese in https://github.com/pyranges/pyranges/pull/275
• Linked intervals by @marco-mariotti in https://github.com/pyranges/pyranges/pull/266
• Fix UnboundLocalError for 'null' variable by @mkanai in https://github.com/pyranges/pyranges/pull/264
• Docstring update by @marco-mariotti in https://github.com/pyranges/pyranges/pull/290
• Bug fix on subsequence and spliced_subsequence by @marco-mariotti in https://github.com/pyranges/pyranges/pull/294
• 0.0.121 by @endrebak in https://github.com/pyranges/pyranges/pull/300
• Improve genome bounds by @marco-mariotti in https://github.com/pyranges/pyranges/pull/295
• fixed empty attribute bug in readgtf when duplicateattr=True by @fairliereese in https://github.com/pyranges/pyranges/pull/297
• Fix FutureWarning by @y9c in https://github.com/pyranges/pyranges/pull/284
• book: index and tutorial by @marco-mariotti in https://github.com/pyranges/pyranges/pull/318
• Preserve order aallahyar by @endrebak in https://github.com/pyranges/pyranges/pull/319
• hi by @endrebak in https://github.com/pyranges/pyranges/pull/328
• ho by @endrebak in https://github.com/pyranges/pyranges/pull/329
• hi by @endrebak in https://github.com/pyranges/pyranges/pull/330
• hia by @endrebak in https://github.com/pyranges/pyranges/pull/331
• hi by @endrebak in https://github.com/pyranges/pyranges/pull/333
• Update runhypothesistests.yml by @endrebak in https://github.com/pyranges/pyranges/pull/334
• Update runhypothesistests.yml by @endrebak in https://github.com/pyranges/pyranges/pull/335
• Add property tests by @endrebak in https://github.com/pyranges/pyranges/pull/336
• Require fewer property tests on github actions by @endrebak in https://github.com/pyranges/pyranges/pull/337
• Fix tostring2 by @endrebak in https://github.com/pyranges/pyranges/pull/339
• 0.0.128 Fix left join category error #342 by @endrebak in https://github.com/pyranges/pyranges/pull/343
• 342 2 by @endrebak in https://github.com/pyranges/pyranges/pull/344
• New documentation by @marco-mariotti in https://github.com/pyranges/pyranges/pull/347
• RTD bugfix by @marco-mariotti in https://github.com/pyranges/pyranges/pull/350
• Bump urllib3 from 2.0.5 to 2.0.6 in /docs by @dependabot in https://github.com/pyranges/pyranges/pull/352
• Option to automatically rename reserved GTF columns in read_gtf by @fairliereese in https://github.com/pyranges/pyranges/pull/354
• Minor doc edits by @marco-mariotti in https://github.com/pyranges/pyranges/pull/358
• COC by @endrebak in https://github.com/pyranges/pyranges/pull/368
• Del by @endrebak in https://github.com/pyranges/pyranges/pull/369
• Open file fix by @endrebak in https://github.com/pyranges/pyranges/pull/379

New Contributors

• @SamBryce-Smith made their first contribution in https://github.com/pyranges/pyranges/pull/260
• @aallahyar made their first contribution in https://github.com/pyranges/pyranges/pull/279
• @FabrizioG202 made their first contribution in https://github.com/pyranges/pyranges/pull/270
• @fairliereese made their first contribution in https://github.com/pyranges/pyranges/pull/275
• @mkanai made their first contribution in https://github.com/pyranges/pyranges/pull/264
• @y9c made their first contribution in https://github.com/pyranges/pyranges/pull/284
• @dependabot made their first contribution in https://github.com/pyranges/pyranges/pull/352

Full Changelog: https://github.com/pyranges/pyranges/compare/0.0.111...v0

- Python
Published by marco-mariotti almost 2 years ago

pyranges - 0.0.111

- Python
Published by endrebak over 4 years ago

pyranges - 0.0.85

Fix read_gtf.

- Python
Published by endrebak over 5 years ago

pyranges - 0.0.79

- Python
Published by endrebak over 5 years ago

pyranges -

• fix merge print functions
• make pickleable
• add iter as alias for itergrs in pr. namespace
• gr.length() shows nucleotide length (sum of all interval lengths)
• gr.lengths() takes as_dict=False flag to return as vector
• fix slack in join: added columns when joining with itself
• fix print for unstranded pyranges: printed tail and head of first chromosome

- Python
Published by endrebak over 6 years ago

pyranges - 0.0.57

- Python
Published by endrebak over 6 years ago

pyranges - 0.0.56

0.0.56 (25.09.19)

• add possibility of 5-end and 3-end in slack being different/none
• add slack to join-method
• add new_position method to take union or intersection of two pairs of Start/End-columns in pyranges

- Python
Published by endrebak over 6 years ago