From 972eb235f72114e56d0a550d741e155e70f3802a Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 22 Oct 2020 12:14:28 +0200
Subject: [PATCH] Annotate now returns lstinfo and #genomes
---
PanACoTA/subcommands/annotate.py | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/PanACoTA/subcommands/annotate.py b/PanACoTA/subcommands/annotate.py
index 616c2a1c..51baddb4 100755
--- a/PanACoTA/subcommands/annotate.py
+++ b/PanACoTA/subcommands/annotate.py
@@ -340,7 +340,6 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn
# Here, both are the same, as we take given sequences as is.
genomes = utils.read_genomes_info(from_info, name, date, logger)
-
# STEP 2. keep only genomes with 'good' (according to user thresholds) L90 and nb_contigs
# genomes = {genome: [spegenus.date, orig_seq, path_to_splitSequence, size, nbcont, l90]}
# Plot L90 and nb_contigs distributions
@@ -380,7 +379,7 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn
# kept_genomes = {genome: [gembase_name, path_to_origfile, path_split_gembase,
# gsize, nbcont, L90]}
# Write lstinfo file (list of genomes kept with info on L90 etc.)
- utils.write_lstinfo(list_file, kept_genomes, res_dir)
+ outlst = utils.write_lstinfo(list_file, kept_genomes, res_dir)
# STEP 4. Annotate all kept genomes
results = pfunc.run_annotation_all(kept_genomes, threads, force, res_annot_dir,
@@ -409,13 +408,12 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn
# Generate database (folders Proteins, Genes, Replicons, LSTINFO)
skipped_format = ffunc.format_genomes(results_ok, res_dir, res_annot_dir,
prodigal_only, threads, quiet=quiet)
- print(skipped_format)
# At least one genome could not be formatted -> warn user
if skipped_format:
utils.write_warning_skipped(skipped_format, do_format=True, prodigal_only=prodigal_only,
logfile = logfile_base)
logger.info("Annotation step done.")
- return 0
+ return outlst, len(kept_genomes) - len(skipped) - len(skipped_format)
def build_parser(parser):
--
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