change tab to space between rep name and info in Replicons directory

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:

test/data/annotate/exp_files/H299_H561.fasta_small-prodigalRes/test_runprodigal_small_H299.gff

-##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;

test/data/annotate/exp_files/res_formatAll/prodigal/Replicons/test_runprokka_H299.fna

->test_runprokka_H299.0001	3480
+>test_runprokka_H299.0001 3480
 AGCAGCACGCTTTTTAATCCGTCCACCGGACCTTCAACCGGCCCTTCGCTGATGGCATCG
 ATCACACTCAGCAGCTGCGTGGACTTCAGGTTGTCCTTCGCTTCGCGCGGGGTATGCCCC
 TTACTGCTGCCTTTACCCATTCGTCATGCTCCATAAACGATAAAACCGCCCGGAGGCGGT

test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff

-##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

test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test_runprokka_H299.gff

-##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

test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test.0417.00002.fna

->test.0417.00002.0001	9603
+>test.0417.00002.0001 9603
 TCTCATACTACCCAATTTCTTAAAAGTGCAAATTTGTGAAGCTTATCCTGTTATTATTTT
 AAGTTTCATGCCAAATTCTCTCACCAGATAATGCCGCCCTCTTCCGAAAAATAATCAAGA
 GGCCAAACAATATCTAAAATGATACAACTGTATCTATTCCCCTGAAAAATACATTATTCA

test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test_runprokka_H299.fna

->test_runprokka_H299.0001	3480
+>test_runprokka_H299.0001 3480
 AGCAGCACGCTTTTTAATCCGTCCACCGGACCTTCAACCGGCCCTTCGCTGATGGCATCG
 ATCACACTCAGCAGCTGCGTGGACTTCAGGTTGTCCTTCGCTTCGCGCGGGGTATGCCCC
 TTACTGCTGCCTTTACCCATTCGTCATGCTCCATAAACGATAAAACCGCCCGGAGGCGGT

test/data/annotate/exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff

-##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

test/data/annotate/exp_files/res_formatAll/prokka/gff3/test_runprokka_H299.gff

-##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