Code

Add proksee and gff output#139

Code

Merged

jpjarnoux merged 36 commits intodevlabgem/PPanGGOLiN:devfrom gff_outputlabgem/PPanGGOLiN:gff_outputCopy head branch name to clipboardOct 27, 2023

+1,200-333

Commits

Commits on Aug 10, 2023

• add contig length in contig object

  JeanMainguy

  committed
  01619b3

  Copy full SHA for 01619b3

Commits on Aug 11, 2023

• write and read contig length

  JeanMainguy

  committed
  8dfb1ac

  Copy full SHA for 8dfb1ac

• add gff output

  JeanMainguy

  committed
  6d1b6fc

  Copy full SHA for 6d1b6fc

• fix module and Spot loading

  JeanMainguy

  committed
  fc5bca2

  Copy full SHA for fc5bca2

Commits on Aug 30, 2023

• add source information

  JeanMainguy

  committed
  95497b7

  Copy full SHA for 95497b7

Commits on Sep 19, 2023

• Merge remote-tracking branch 'origin/AnnotHDF5Reformat' into gff_output

  JeanMainguy

  committed
  b87a2ee

  Copy full SHA for b87a2ee

Commits on Sep 21, 2023

• add gene line for each CDS ARN

  JeanMainguy

  committed
  d1f2231

  Copy full SHA for d1f2231

• Merge remote-tracking branch 'origin/dev' into gff_output

  JeanMainguy

  committed
  67867c0

  Copy full SHA for 67867c0

Commits on Sep 25, 2023

• adapt proksee panorama code to ppanggolin

  JeanMainguy

  committed
  1dab861

  Copy full SHA for 1dab861

• improve proksee output

  JeanMainguy

  committed
  bffb2b8

  Copy full SHA for bffb2b8

Commits on Oct 2, 2023

• add possibility to add sequences

  JeanMainguy

  committed
  7bcc7a4

  Copy full SHA for 7bcc7a4

Commits on Oct 4, 2023

• Merge remote-tracking branch 'origin/context' into gff_output

  JeanMainguy

  committed
  c1ed656

  Copy full SHA for c1ed656

Commits on Oct 12, 2023

• fix wrong completion calculation in module outputs

  JeanMainguy

  committed
  77c3be8

  Copy full SHA for 77c3be8

Commits on Oct 17, 2023

• Merge branch 'dev' into gff_output

  JeanMainguy

  committed
  0b6f6f4

  Copy full SHA for 0b6f6f4

• remove the need of a proksee template

  JeanMainguy

  committed
  32bd30a

  Copy full SHA for 32bd30a

Commits on Oct 18, 2023

• color module with different colors according their proximity

  JeanMainguy

  committed
  a4795fe

  Copy full SHA for a4795fe

• clean proksee generation code and add type and docstring

  JeanMainguy

  committed
  53dac90

  Copy full SHA for 53dac90

• reuse projection fct to parse genome paths file

  JeanMainguy

  committed
  1e15c31

  Copy full SHA for 1e15c31

Commits on Oct 19, 2023

• add proksee output to projection

  JeanMainguy

  committed
  6f95236

  Copy full SHA for 6f95236

• add sequence to gff file when equired

  JeanMainguy

  committed
  ae013a5

  Copy full SHA for ae013a5

• add gff output in projection cmd

  JeanMainguy

  committed
  7a01e27

  Copy full SHA for 7a01e27

• add argument to output or not gff and proksee

  JeanMainguy

  committed
  fb4fc13

  Copy full SHA for fb4fc13

• add proksee own output dir in write cmd

  JeanMainguy

  committed
  8a13856

  Copy full SHA for 8a13856

Commits on Oct 20, 2023

• Add limit in networkx version for compatibility problem with python3.8

  jpjarnoux

  committed
  334ad70

  Copy full SHA for 334ad70

• fix error in parsing fasta file

  JeanMainguy

  committed
  0c590c6

  Copy full SHA for 0c590c6

• add seq to proksee and gff output for proj cmd

  JeanMainguy

  committed
  a0f6132

  Copy full SHA for a0f6132

• fix bug in proksee output

  JeanMainguy

  committed
  8e447c8

  Copy full SHA for 8e447c8

• add gff and proksee in the gh action

  JeanMainguy

  committed
  a1fb03e

  Copy full SHA for a1fb03e

• fix error in gh action

  JeanMainguy

  committed
  068bbba

  Copy full SHA for 068bbba

Commits on Oct 23, 2023

• resolve some review comment

  jpjarnoux

  committed
  4defeca

  Copy full SHA for 4defeca

• Fix variable name

  jpjarnoux

  committed
  95171ee

  Copy full SHA for 95171ee

• Fix bug in get contig length in gff files

  jpjarnoux

  committed
  5eb755a

  Copy full SHA for 5eb755a

• resolve PR review

  jpjarnoux

  committed
  accd2c1

  Copy full SHA for accd2c1

Commits on Oct 24, 2023

• refac launch of projection

  JeanMainguy

  committed
  61dacfe

  Copy full SHA for 61dacfe

• Refactoring

  jpjarnoux

  committed
  b0b7ef1

  Copy full SHA for b0b7ef1

• Merge branch 'gff_output' of https://github.com/labgem/PPanGGOLiN into gff_output

  jpjarnoux

  committed
  d58a253

  Copy full SHA for d58a253