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Add proksee and gff output #139

Merged
merged 36 commits into from
Oct 27, 2023
Merged

Add proksee and gff output #139

merged 36 commits into from
Oct 27, 2023

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JeanMainguy
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This pull request introduces the ability to generate genomes with pangenome annotations in both GFF format and JSON PROKSEE format.

  • These new output options are accessible through the 'write' and 'projection' commands.
  • Additionally, users have the option to include sequences in these formats.

JeanMainguy and others added 28 commits August 10, 2023 17:21
@JeanMainguy
add contig length in contig object
01619b3
@JeanMainguy
write and read contig length
8dfb1ac
@JeanMainguy
add gff output
6d1b6fc
@JeanMainguy
fix module and Spot loading
fc5bca2
@JeanMainguy
add source information
95497b7
@JeanMainguy
Merge remote-tracking branch 'origin/AnnotHDF5Reformat' into gff_output
b87a2ee
@JeanMainguy
add gene line for each CDS ARN
d1f2231
@JeanMainguy
Merge remote-tracking branch 'origin/dev' into gff_output
67867c0
@JeanMainguy
adapt proksee panorama code to ppanggolin
1dab861
@JeanMainguy
improve proksee output
bffb2b8
@JeanMainguy
add possibility to add sequences
7bcc7a4
@JeanMainguy
Merge remote-tracking branch 'origin/context' into gff_output
c1ed656
@JeanMainguy
fix wrong completion calculation in module outputs
77c3be8
@JeanMainguy
Merge branch 'dev' into gff_output
0b6f6f4
@JeanMainguy
remove the need of a proksee template
32bd30a
@JeanMainguy
color module with different colors according their proximity
a4795fe
@JeanMainguy
clean proksee generation code and add type and docstring
53dac90
@JeanMainguy
reuse projection fct to parse genome paths file
1e15c31
@JeanMainguy
add proksee output to projection
6f95236
@JeanMainguy
add sequence to gff file when equired
ae013a5
@JeanMainguy
add gff output in projection cmd
7a01e27
@JeanMainguy
add argument to output or not gff and proksee
fb4fc13
@JeanMainguy
add proksee own output dir in write cmd
8a13856
@jpjarnoux
Add limit in networkx version for compatibility problem with python3.8
334ad70
@JeanMainguy
fix error in parsing fasta file
0c590c6
@JeanMainguy
add seq to proksee and gff output for proj cmd
a0f6132
@JeanMainguy
fix bug in proksee output
8e447c8
@JeanMainguy
add gff and proksee in the gh action
a1fb03e
@JeanMainguy JeanMainguy reopened this Oct 20, 2023
@JeanMainguy JeanMainguy marked this pull request as ready for review October 20, 2023 12:13
jpjarnoux
jpjarnoux reviewed Oct 23, 2023
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jpjarnoux
jpjarnoux reviewed Oct 23, 2023
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@jpjarnoux jpjarnoux mentioned this pull request Oct 27, 2023
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@jpjarnoux jpjarnoux linked an issue Oct 27, 2023 that may be closed by this pull request
Gbk files #128
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@jpjarnoux jpjarnoux merged commit faf2e50 into dev Oct 27, 2023
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@jpjarnoux jpjarnoux deleted the gff_output branch October 27, 2023 08:03
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Gbk files
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@JeanMainguy @jpjarnoux