Code

Add metadata from annotation files#227

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jpjarnoux merged 25 commits intodevlabgem/PPanGGOLiN:devfrom improve_metadatalabgem/PPanGGOLiN:improve_metadataCopy head branch name to clipboardJun 3, 2024

+851-148

Commits

Commits on May 17, 2024

• refactor fct to parse gbff

  JeanMainguy

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  eab0de5

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• add unit test to test read_org_gff and co

  JeanMainguy

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  5e8730c

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• fix type in function of annotate

  JeanMainguy

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  3f4ac17

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• fix type in function of annotate again

  JeanMainguy

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  d9b0922

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• manage db_xref for CDS feature as previously

  JeanMainguy

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  2e8777d

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Commits on May 21, 2024

• extract and add metadata from annotation file

  JeanMainguy

  committed
  3416707

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Commits on May 22, 2024

• metadata extracted from GBFF files changes expected file

  JeanMainguy

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  24434c1

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• extract info and add them as metadata from GFF files

  JeanMainguy

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Commits on May 23, 2024

• add write_metadata cmd to write metadata as TSV files

  JeanMainguy

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  950847e

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• improve log, comments, docstring

  JeanMainguy

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  d9dc1ef

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• downgrade log to prevent unnecessary warning in write_metadata cmd

  JeanMainguy

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  ea9bd43

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• fix wrong attr used to get contig

  JeanMainguy

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  976d720

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• add doc for write_metadata

  JeanMainguy

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  25827a7

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• tiny improvement of metadata doc

  JeanMainguy

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  d14f482

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Commits on May 24, 2024

• clarify, fix typo and give example in metadata doc

  JeanMainguy

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  e9fdf0d

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• add write_metadata cmd in CI

  JeanMainguy

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  d45cb4e

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• add db_xref in metadata of GBFF files

  JeanMainguy

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  d92207e

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Commits on May 27, 2024

• set pangenome status on metadata if some have been really added

  JeanMainguy

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  986e8a3

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• add genome metadata to contig meta in proksee and remove None value

  JeanMainguy

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  5c963d3

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• manage dbxref in GFF the same way as in GBFF

  JeanMainguy

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  471ae1e

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• add method to check if an element has some metadata associated

  JeanMainguy

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  b54a242

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• exclude step that check nb of cores in the local launch

  JeanMainguy

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  63183c3

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• Merge branch 'AnnotJoin' into improve_metadata

  JeanMainguy

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  cf5d5ee

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• fix bad merging..

  JeanMainguy

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  6ca28c7

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Commits on Jun 3, 2024

• Change in response to PR comments

  jpjarnoux

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  7d8f707

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