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Add proksee and gff output #139

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merged 36 commits into from
Oct 27, 2023
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01619b3
add contig length in contig object
JeanMainguy Aug 10, 2023
8dfb1ac
write and read contig length
JeanMainguy Aug 11, 2023
6d1b6fc
add gff output
JeanMainguy Aug 11, 2023
fc5bca2
fix module and Spot loading
JeanMainguy Aug 11, 2023
95497b7
add source information
JeanMainguy Aug 30, 2023
b87a2ee
Merge remote-tracking branch 'origin/AnnotHDF5Reformat' into gff_output
JeanMainguy Sep 19, 2023
d1f2231
add gene line for each CDS ARN
JeanMainguy Sep 21, 2023
67867c0
Merge remote-tracking branch 'origin/dev' into gff_output
JeanMainguy Sep 21, 2023
1dab861
adapt proksee panorama code to ppanggolin
JeanMainguy Sep 25, 2023
bffb2b8
improve proksee output
JeanMainguy Sep 25, 2023
7bcc7a4
add possibility to add sequences
JeanMainguy Oct 2, 2023
c1ed656
Merge remote-tracking branch 'origin/context' into gff_output
JeanMainguy Oct 4, 2023
77c3be8
fix wrong completion calculation in module outputs
JeanMainguy Oct 12, 2023
0b6f6f4
Merge branch 'dev' into gff_output
JeanMainguy Oct 17, 2023
32bd30a
remove the need of a proksee template
JeanMainguy Oct 17, 2023
a4795fe
color module with different colors according their proximity
JeanMainguy Oct 18, 2023
53dac90
clean proksee generation code and add type and docstring
JeanMainguy Oct 18, 2023
1e15c31
reuse projection fct to parse genome paths file
JeanMainguy Oct 18, 2023
6f95236
add proksee output to projection
JeanMainguy Oct 19, 2023
ae013a5
add sequence to gff file when equired
JeanMainguy Oct 19, 2023
7a01e27
add gff output in projection cmd
JeanMainguy Oct 19, 2023
fb4fc13
add argument to output or not gff and proksee
JeanMainguy Oct 19, 2023
8a13856
add proksee own output dir in write cmd
JeanMainguy Oct 19, 2023
334ad70
Add limit in networkx version for compatibility problem with python3.8
jpjarnoux Oct 20, 2023
0c590c6
fix error in parsing fasta file
JeanMainguy Oct 20, 2023
a0f6132
add seq to proksee and gff output for proj cmd
JeanMainguy Oct 20, 2023
8e447c8
fix bug in proksee output
JeanMainguy Oct 20, 2023
a1fb03e
add gff and proksee in the gh action
JeanMainguy Oct 20, 2023
068bbba
fix error in gh action
JeanMainguy Oct 20, 2023
4defeca
resolve some review comment
jpjarnoux Oct 23, 2023
95171ee
Fix variable name
jpjarnoux Oct 23, 2023
5eb755a
Fix bug in get contig length in gff files
jpjarnoux Oct 23, 2023
accd2c1
resolve PR review
jpjarnoux Oct 23, 2023
61dacfe
refac launch of projection
JeanMainguy Oct 23, 2023
b0b7ef1
Refactoring
jpjarnoux Oct 24, 2023
d58a253
Merge branch 'gff_output' of https://github.com/labgem/PPanGGOLiN int…
jpjarnoux Oct 24, 2023
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fix bug in proksee output
JeanMainguy committed Oct 20, 2023
commit 8e447c8a8bd2201d20f4d3a08d6180fc800be63b
6 changes: 3 additions & 3 deletions ppanggolin/formats/writeFlat.py
Original file line number Diff line number Diff line change
@@ -646,7 +646,7 @@ def write_proksee(output: Path, fasta: Path = None, anno: Path = None):
If genome sequences are provided in a FASTA file or annotations in a separate file, they will be used in the generation
of ProkSee data for each organism to add sequences data to proksee files.
"""

proksee_outdir = output / "proksee"
if not os.path.exists(proksee_outdir):
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os.makedirs(proksee_outdir)
@@ -670,7 +670,7 @@ def write_proksee(output: Path, fasta: Path = None, anno: Path = None):

for organism in pan.organisms:
if organisms_file:
genome_sequences = read_genome_file(org_dict[organism.name]['path'], organism.name)
genome_sequences = read_genome_file(org_dict[organism.name]['path'], organism)
else:
genome_sequences = None

@@ -684,7 +684,7 @@ def write_proksee(output: Path, fasta: Path = None, anno: Path = None):
genome_sequences=genome_sequences)



logging.getLogger().info("Done writing the proksee files")

def manage_module_colors(modules: List[Module], window_size:int=50) -> Dict[Module, str]:
"""