From 9123655f4a80b45afee435e4750925e7dd9fd00d Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Tue, 8 Oct 2019 13:09:44 +0200
Subject: [PATCH] Change output filename when QC only
---
PanACoTA/utils.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index 108df9d1..f922cbdc 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -448,7 +448,7 @@ def write_genomes_info(genomes, kept_genomes, list_file, res_path, qc=False):
# if QC, there is no 'discarded genome', just write information on all analyzed genomes
else:
outdisc = os.path.join(res_path,
- "info-genomes-" + ".".join(name_lst.split(".")[:-1]) + ".lst")
+ "ALL-GENOMES-info-" + ".".join(name_lst.split(".")[:-1]) + ".lst")
logger.info("Writing information on genomes in {}".format(outdisc))
with open(outdisc, "w") as outdf:
outdf.write("\t".join(["orig_name", "to_annotate", "gsize", "nb_conts", "L90"]) + "\n")
@@ -481,7 +481,7 @@ def write_lstinfo(list_file, genomes, outdir):
with open(outlst, "w") as outf:
outf.write("\t".join(["gembase_name", "orig_name", "to_annotate", "gsize",
"nb_conts", "L90"]) + "\n")
- for genome, values in sorted(genomes.items(), key=sort_genomes):
+ for genome, values in sorted(genomes.items(), key=sort_genomes_byname_l90_nbcont):
gembase, _, to_annote, gsize, nbcont, l90 = [str(x) for x in values]
to_annote_file = os.path.basename(to_annote)
outf.write("\t".join([gembase, genome, to_annote_file, gsize, nbcont, l90]) + "\n")
--
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