From 2a3a9ab2f4a921db1c5d69a55bd12b08c9051fb5 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 22 Oct 2020 11:53:48 +0200
Subject: [PATCH] Prepare module now returns the output info file
---
PanACoTA/prepare_module/download_genomes_func.py | 1 -
PanACoTA/prepare_module/filter_genomes.py | 4 ++--
PanACoTA/subcommands/prepare.py | 4 +++-
3 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/PanACoTA/prepare_module/download_genomes_func.py b/PanACoTA/prepare_module/download_genomes_func.py
index e820316c..ffda0958 100644
--- a/PanACoTA/prepare_module/download_genomes_func.py
+++ b/PanACoTA/prepare_module/download_genomes_func.py
@@ -142,7 +142,6 @@ def download_from_refseq(species_linked, NCBI_species, NCBI_taxid, levels, outdi
logger.error(error_message)
sys.exit(1)
nb_gen, db_dir = to_database(outdir)
- logger.info(f"Downloaded {nb_gen} genomes.")
return db_dir, nb_gen
diff --git a/PanACoTA/prepare_module/filter_genomes.py b/PanACoTA/prepare_module/filter_genomes.py
index aa3d7167..b56e9a18 100755
--- a/PanACoTA/prepare_module/filter_genomes.py
+++ b/PanACoTA/prepare_module/filter_genomes.py
@@ -227,7 +227,7 @@ def iterative_mash(sorted_genomes, genomes, outdir, species_linked, min_dist, ma
progressbar.Counter(), "/{}".format(nbgen), ' ',
progressbar.Timer(), ' - '
]
- bar = progressbar.ProgressBar(widgets=widgets, max_value=len(to_try), term_width=100).start()
+ bar = progressbar.ProgressBar(widgets=widgets, max_value=len(to_try), term_width=79).start()
done = 0
while len(to_try) > 1:
@@ -504,4 +504,4 @@ def write_outputfiles(genomes, sorted_genomes, genomes_removed, outdir, gspecies
disf.write(utils.list_to_str([genome] + info))
logger.info(f"Final list of genomes in the dataset: {list_file}")
logger.info(f"List of genomes discarded by minhash steps: {discard_file}")
- return 0
+ return list_file
diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py
index ebe85ea6..9f4d221b 100644
--- a/PanACoTA/subcommands/prepare.py
+++ b/PanACoTA/subcommands/prepare.py
@@ -266,8 +266,10 @@ def main(cmd, NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_ref
removed = fg.iterative_mash(sorted_genomes, genomes, outdir, species_linked,
min_dist, max_dist, threads, quiet)
# Write list of genomes kept, and list of genomes discarded by mash step
- fg.write_outputfiles(genomes, sorted_genomes, removed, outdir, species_linked, min_dist, max_dist)
+ info_file = fg.write_outputfiles(genomes, sorted_genomes, removed, outdir, species_linked,
+ min_dist, max_dist)
logger.info("End")
+ return info_file
def build_parser(parser):
--
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