v0.29.1 - mutate and cosmic overhaul

• gget mutate:
  • gget mutate has been simplified to focus on taking as input a list of mutations and associated reference genome with corresponding annotation information, and produce as output the sequences with the mutation incorporated and a short region of surrounding context. For the full functionality of the previous version and how it integrates in the context of a novel variant screening pipeline, visit the varseek repository being developed by members of the gget team at https://github.com/pachterlab/varseek.git.
  • Added additional information to returned data frames as described here: #169
• gget cosmic:
  • Major restructuring of the gget cosmic module to adhere to new login requirements set by COSMIC
  • New arguments email and password were added to allow the user to manually enter their login credentials without required input for data download
  • Default changed: gget_mutate=False
  • Deprecated argument: entity
  • Argument mutation_class is now cosmic_project
• gget bgee:
  • type="orthologs" is now the default, removing the need to specify the type argument when calling orthologs
  • Allow querying multiple genes at once.
• gget diamond:
  • Now supports translated alignment of nucleotide sequences to amino acid reference sequences using the --translated flag.
• gget elm:
  • Improved server error handling.