MOB-typer failed to detect plasmid replicons and relaxases for fasta files with certain headers.

[ryotag]

This issue is related to #85, but I opened this new issue because the title of #85 does not reflect the true problem.

I found that MOB-typer failed to detect plasmid replicons and relaxases for fasta files with certain headers.
Here is the file I analyzed. (the file extension is .txt since github does not allow files with .fasta)
KX912253_RC.txt

mob_typer --multi --infile KX912253_RC.fasta --out_file results.tsv returned a tsv file as follows:

sample_id	num_contigs	size	gc	md5	rep_type(s)	rep_type_accession(s)	relaxase_type(s)	relaxase_type_accession(s)	mpf_type	mpf_type_accession(s)	orit_type(s)	orit_accession(s)	predicted_mobility	mash_nearest_neighbor	mash_neighbor_distance	mash_neighbor_identification	primary_cluster_id	secondary_cluster_id	predicted_host_range_overall_rank	predicted_host_range_overall_name	observed_host_range_ncbi_rank	observed_host_range_ncbi_name	reported_host_range_lit_rank	reported_host_range_lit_name	associated_pmid(s)
FRI-2_plasmid_KX912253-RC_Enterobacter_asburiae_strain_H162620587_plasmid_pJF-587__complete_sequence.	1	108672	51.1842977	5bd1577e5eae2824bbb7eb4e9ed6c126	-	-	-	-	-	-	-	-	non-mobilizable	KX912253	0	Enterobacter asburiae	AA414	AI467	genus	Enterobacter	genus	Enterobacter	-	-	-

I changed the header of the fasta file from
>FRI-2_plasmid_KX912253-RC Enterobacter asburiae strain H162620587 plasmid pJF-587, complete sequence.
to
>FRI-2_plasmid_KX912253-RC
Now, I got the following results.

sample_id	num_contigs	size	gc	md5	rep_type(s)	rep_type_accession(s)	relaxase_type(s)	relaxase_type_accession(s)	mpf_type	mpf_type_accession(s)	orit_type(s)	orit_accession(s)	predicted_mobility	mash_nearest_neighbor	mash_neighbor_distance	mash_neighbor_identification	primary_cluster_id	secondary_cluster_id	predicted_host_range_overall_rank	predicted_host_range_overall_name	observed_host_range_ncbi_rank	observed_host_range_ncbi_name	reported_host_range_lit_rank	reported_host_range_lit_name	associated_pmid(s)
FRI-2_plasmid_KX912253-RC	1	108672	51.1842977	5bd1577e5eae2824bbb7eb4e9ed6c126	IncFII,IncR	CP019890_00139,000207__CP025517	MOBF	NC_014107_00160	MPF_F	NC_014107_00125,NC_014107_00126,NC_014107_00127,NC_009425_00108,NC_014107_00135,NC_014107_00139,NC_014107_00145,NC_014107_00146,NC_014107_00154,NC_014107_00155,NC_014107_00137,NC_014107_00159	-	-	conjugative	KX912253	0	Enterobacter asburiae	AA414	AI467	order	Enterobacterales	order	Enterobacterales	family	Enterobacteriaceae	20851899; 23711894

The results seem to be quite different, one without any replicons/relaxases and the other with detected replicons/relaxases.
I'm not sure this is a bug or not, but any help/thoughts are appreciated.

Thank you for your time,

[jrober84]

There seems to be some issues with blast and length of headers. I have implemented a fix in 3.1.0 where all sequences are renamed internally for all of the blast and search calls. Then reported back as the original sequence identifiers.