update gh action with new write commands

labgem · Oct 24, 2023 · 0ef1c36 · 0ef1c36
1 parent e7da676
commit 0ef1c36
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -67,7 +67,8 @@ jobs:
         ppanggolin spot -p stepbystep/pangenome.h5 --spot_graph --overlapping_match 2 --set_size 3 --exact_match_size 1
         ppanggolin draw -p stepbystep/pangenome.h5 --draw_spots -o stepbystep -f
         ppanggolin module -p stepbystep/pangenome.h5 --transitive 4 --size 3 --jaccard 0.86 --dup_margin 0.05
-        ppanggolin write_pangenome -p stepbystep/pangenome.h5 --output stepbystep -f --soft_core 0.9 --dup_margin 0.06 --gff --proksee --gexf --light_gexf --csv --Rtab --projection --stats --partitions --compress --json --regions --spots --borders --families_tsv --cpu 1 --fasta organisms.fasta.list --gff --proksee 
+        ppanggolin write_pangenome -p stepbystep/pangenome.h5 --output stepbystep -f --soft_core 0.9 --dup_margin 0.06  --gexf --light_gexf --csv --Rtab --stats --partitions --compress --json --regions --spots --borders --families_tsv --cpu 1 
+        ppanggolin write_genomes  -p stepbystep/pangenome.h5 --output stepbystep -f --fasta organisms.fasta.list --gff --proksee --table
         ppanggolin fasta -p stepbystep/pangenome.h5 --output stepbystep -f --prot_families all --gene_families shell --regions all --fasta organisms.fasta.list --gff --proksee
         ppanggolin draw -p stepbystep/pangenome.h5 --draw_spots --spots all -o stepbystep -f
         ppanggolin metrics -p stepbystep/pangenome.h5 --genome_fluidity --info_modules --no_print_info -f --log metrics.log

diff --git a/ppanggolin/formats/writeFlatGenomes.py b/ppanggolin/formats/writeFlatGenomes.py
@@ -16,7 +16,7 @@
 import csv
 import random
 from tqdm import tqdm
-
+import time
 
 import networkx as nx
 from plotly.express.colors import qualitative
@@ -44,7 +44,7 @@ def count_neighbors_partitions(gene_family:GeneFamily):
     nb_pers = 0
     nb_shell = 0
     nb_cloud = 0
-    
+
     for neighbor in gene_family.neighbors:
         if neighbor.named_partition == "persistent":
             nb_pers += 1
@@ -374,7 +374,8 @@ def write_flat_genome_files(pangenome: Pangenome, output: Path, cpu: int = 1,
             contig_to_rgp[rgp.contig].append(rgp)
             rgp_to_spot_id = {rgp:f"spot_{spot.ID}" for spot in pangenome.spots for rgp in spot.regions}
 
-
+    start_writing = time.time()
+
     for organism in  tqdm(pangenome.organisms, total=pangenome.number_of_organisms, unit="organism", disable=disable_bar):
 
         logging.getLogger("PPanGGOLiN").debug(f"Writing genome annotations for {organism.name}")
@@ -408,6 +409,9 @@ def write_flat_genome_files(pangenome: Pangenome, output: Path, cpu: int = 1,
             write_org_file(org=organism, output=org_outdir, compress=compress,
                        add_regions=needRegions, add_modules=needModules, add_spots=needSpots)
 
+    writing_time = time.time() - start_writing
+    logging.getLogger("PPanGGOLiN").debug(f"writing_time for {pangenome.number_of_organisms} genomes: {writing_time} seconds")
+
 
 def launch(args: argparse.Namespace):
     """