From 09f9e75890e340487cffd433abaf4d65d82434a9 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 10 Oct 2019 12:06:46 +0200
Subject: [PATCH] Complete docstring on parameter types
---
PanACoTA/utils.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index f922cbdc..7d343e67 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -1084,9 +1084,9 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
Returns
-------
tuple
- - List of all contigs with their original and new name:
+ - List of all contigs with their original and new name: (list of str)
["contig1'\t'orig_name1", "contig2'\t'orig_name2" ...]
- - List of all contigs with their size:
+ - List of all contigs with their size: (list of str)
["contig1'\t'size1", "contig2'\t'size2" ...]
"""
# Initialize variables
@@ -1095,9 +1095,9 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
contig_num = 1
# contig size
cont_size = 0
- # List of contigs [<name>\t<orig_name>]
+ # List of contigs (str) [<name>\t<orig_name>]
contigs = []
- # List of contigs with their sizes [<name>\t<size>]
+ # List of contigs (str) with their sizes [<name>\t<size>]
sizes = []
# Name of previous contig (to put to contigs, as we need to wait for the next
# contig to know the size of the previous one)
@@ -1124,6 +1124,7 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
contigs.append(cor)
grf.write(cont)
grf.write(seq)
+
prev_cont = ">" + gembase_name + "." + str(contig_num).zfill(4)
prev_orig_name = line
contig_num += 1
--
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