From ea85c66d4935c2cfd9370148a0dd867a020e888b Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Tue, 5 Oct 2021 11:48:00 +0200
Subject: [PATCH] change tab to space between rep name and info in Replicons
directory
---
PanACoTA/utils.py | 4 ++--
.../test_runprodigal_small_H299.gff | 2 +-
.../res_formatAll/prodigal/Replicons/test_runprokka_H299.fna | 2 +-
.../exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff | 2 +-
.../res_formatAll/prodigal/gff3/test_runprokka_H299.gff | 2 +-
.../res_formatAll/prokka/Replicons/test.0417.00002.fna | 2 +-
.../res_formatAll/prokka/Replicons/test_runprokka_H299.fna | 2 +-
.../exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff | 2 +-
.../res_formatAll/prokka/gff3/test_runprokka_H299.gff | 2 +-
9 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index 17f1e582..61e3ad99 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -1148,7 +1148,7 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile, logger):
# - add its name with its original name to
# - write header ("<contig name> <size>") to replicon file
if prev_cont:
- cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
+ cont = " ".join([prev_cont, str(cont_size)]) + "\n"
prevcont_nohead = prev_cont.split(">")[1]
prev_orig_name_nohead = prev_orig_name.split(">")[1]
if prev_orig_name_nohead:
@@ -1172,7 +1172,7 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile, logger):
cont_size += len(line.strip())
# Write last contig, if there is one (if gpath not empty)
if prev_cont:
- cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
+ cont = " ".join([prev_cont, str(cont_size)]) + "\n"
prevcont_nohead = "".join(prev_cont.split(">")[1:])
prev_orig_name_nohead = prev_orig_name.split(">")[1]
if prev_orig_name_nohead:
diff --git a/test/data/annotate/exp_files/H299_H561.fasta_small-prodigalRes/test_runprodigal_small_H299.gff b/test/data/annotate/exp_files/H299_H561.fasta_small-prodigalRes/test_runprodigal_small_H299.gff
index 5b758314..50732984 100644
--- a/test/data/annotate/exp_files/H299_H561.fasta_small-prodigalRes/test_runprodigal_small_H299.gff
+++ b/test/data/annotate/exp_files/H299_H561.fasta_small-prodigalRes/test_runprodigal_small_H299.gff
@@ -1,4 +1,4 @@
-##gff-version 3
+##gff-version 3
# Sequence Data: seqnum=1;seqlen=3480;seqhdr="H561_S27 L001_R1_001_(paired)_contig_1"
# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
H561_S27 Prodigal_v2.6.3 CDS 3 140 31.2 - 0 ID=1_1;partial=10;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.580;conf=99.92;score=31.21;cscore=19.39;sscore=11.82;rscore=11.19;uscore=-3.31;tscore=3.95;
diff --git a/test/data/annotate/exp_files/res_formatAll/prodigal/Replicons/test_runprokka_H299.fna b/test/data/annotate/exp_files/res_formatAll/prodigal/Replicons/test_runprokka_H299.fna
index d3a4a198..dc5aac7a 100644
--- a/test/data/annotate/exp_files/res_formatAll/prodigal/Replicons/test_runprokka_H299.fna
+++ b/test/data/annotate/exp_files/res_formatAll/prodigal/Replicons/test_runprokka_H299.fna
@@ -1,4 +1,4 @@
->test_runprokka_H299.0001 3480
+>test_runprokka_H299.0001 3480
AGCAGCACGCTTTTTAATCCGTCCACCGGACCTTCAACCGGCCCTTCGCTGATGGCATCG
ATCACACTCAGCAGCTGCGTGGACTTCAGGTTGTCCTTCGCTTCGCGCGGGGTATGCCCC
TTACTGCTGCCTTTACCCATTCGTCATGCTCCATAAACGATAAAACCGCCCGGAGGCGGT
diff --git a/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff b/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff
index 1529acfc..ba4e9adb 100644
--- a/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff
+++ b/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff
@@ -1,4 +1,4 @@
-##gff-version 3
+##gff-version 3
##sequence-region test.0417.00002.0001 1 9603
##sequence-region test.0417.00002.0002 1 22446
##sequence-region test.0417.00002.0003 1 51012
diff --git a/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test_runprokka_H299.gff b/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test_runprokka_H299.gff
index 447289fb..b9cc64fa 100644
--- a/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test_runprokka_H299.gff
+++ b/test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test_runprokka_H299.gff
@@ -1,4 +1,4 @@
-##gff-version 3
+##gff-version 3
##sequence-region test_runprokka_H299.0001 1 3480
##sequence-region test_runprokka_H299.0002 1 7080
##sequence-region test_runprokka_H299.0003 1 2583
diff --git a/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test.0417.00002.fna b/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test.0417.00002.fna
index 1375f72f..6ca8e489 100644
--- a/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test.0417.00002.fna
+++ b/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test.0417.00002.fna
@@ -1,4 +1,4 @@
->test.0417.00002.0001 9603
+>test.0417.00002.0001 9603
TCTCATACTACCCAATTTCTTAAAAGTGCAAATTTGTGAAGCTTATCCTGTTATTATTTT
AAGTTTCATGCCAAATTCTCTCACCAGATAATGCCGCCCTCTTCCGAAAAATAATCAAGA
GGCCAAACAATATCTAAAATGATACAACTGTATCTATTCCCCTGAAAAATACATTATTCA
diff --git a/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test_runprokka_H299.fna b/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test_runprokka_H299.fna
index d3a4a198..dc5aac7a 100644
--- a/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test_runprokka_H299.fna
+++ b/test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test_runprokka_H299.fna
@@ -1,4 +1,4 @@
->test_runprokka_H299.0001 3480
+>test_runprokka_H299.0001 3480
AGCAGCACGCTTTTTAATCCGTCCACCGGACCTTCAACCGGCCCTTCGCTGATGGCATCG
ATCACACTCAGCAGCTGCGTGGACTTCAGGTTGTCCTTCGCTTCGCGCGGGGTATGCCCC
TTACTGCTGCCTTTACCCATTCGTCATGCTCCATAAACGATAAAACCGCCCGGAGGCGGT
diff --git a/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff b/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff
index de76a5c3..e674cb2c 100644
--- a/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff
+++ b/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff
@@ -1,4 +1,4 @@
-##gff-version 3
+##gff-version 3
##sequence-region test.0417.00002.0001 1 9603
##sequence-region test.0417.00002.0002 1 22446
##sequence-region test.0417.00002.0003 1 51012
diff --git a/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test_runprokka_H299.gff b/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test_runprokka_H299.gff
index aa8c22d7..f444a497 100644
--- a/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test_runprokka_H299.gff
+++ b/test/data/annotate/exp_files/res_formatAll/prokka/gff3/test_runprokka_H299.gff
@@ -1,4 +1,4 @@
-##gff-version 3
+##gff-version 3
##sequence-region test_runprokka_H299.0001 1 3480
##sequence-region test_runprokka_H299.0002 1 7080
##sequence-region test_runprokka_H299.0003 1 2583
--
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