####VERBOSE OPTION GIVEN

#MAIN ARGUMENTS
sequence_file: nem_zotus_assign.fasta
blast_database: nem_mendocino
taxonomy_file: tax_nematodes.tsv

#Filtering OPTIONS
blast_hits_to_consider: 10.0
sway_from_best_hit: 0.5
phylum_level_cutoff: 80
family_level_cutoff: 90
species_level_cutoff: 97
length_of_hit_cutoff: 0
proportion_of_query_coverage: 0.0
blast e-value cutoff: 1e-10

Other OPTIONS
BLAST_file given?: None
BLAST flavor: blastn
BLAST evalue cutoff: 1e-10
BLAST threads: 24
NCBI flag?: False
Output dir: Assigned_Taxonomy/
Param file: None

###Program Start

#Taxonomy Categories
superkingdom:subkingdom:sub_subkingdom:kingdom:tmp1:tmp2:phylum:class:family:genus:species:tmp3:tmp4:tmp5:tmp6
#The below levels should match the target, i.e. species_level = species
Species_level =  14 = tmp6
Family_level =  10 = species
Phylum_level =  7 = class

Running blast on input sequences (this step takes the longest, maybe run overnight)
#BLAST COMMAND
blastn -query nem_zotus_assign.fasta -db nem_mendocino -num_threads 24 -evalue 1e-10 -out Assigned_Taxonomy/blast_output_custom_format.tsv -outfmt 6 qseqid qlen sseqid pident length qstart qend sstart send evalue bitscore slen staxids
Parsing taxonomy file and storing info in dictionary (might take a moment if using nt database)
Parsing Blast and Assigning Taxonomy

########################
#BLAST LINE : Zotu7	350	KF357370.1	99.429	350	1	350	33	382	0.0	636	549	N/A
#BLAST LINE : Zotu7	350	AB376942.1	97.959	343	8	350	1	343	4.30e-172	595	507	N/A
#BLAST LINE : Zotu7	350	AY593941.1	97.143	350	1	350	16	364	2.00e-170	590	1713	N/A
#BLAST LINE : Zotu7	350	LC222904.1	96.875	352	1	350	9	360	7.19e-170	588	1693	N/A
#BLAST LINE : Zotu7	350	HQ999619.1	96.857	350	1	350	31	380	2.59e-169	586	526	N/A
#BLAST LINE : Zotu7	350	HQ999617.1	96.857	350	1	350	31	380	2.59e-169	586	526	N/A
#BLAST LINE : Zotu7	350	AY593940.1	96.857	350	1	350	16	365	2.59e-169	586	1716	N/A
#BLAST LINE : Zotu7	350	LT601482.1	93.429	350	1	350	23	370	9.57e-149	518	392	N/A
#BLAST LINE : Zotu7	350	AB921837.1	96.785	311	40	350	1	310	9.57e-149	518	474	N/A
#BLAST LINE : Zotu7	350	MH302873.1	94.720	322	29	350	3	323	3.47e-143	499	535	N/A

ASSIGNING TAXONOMY FOR Zotu7 total hits passing initial filters = 10
KF357370.1 99.429 --> CAPTURED after percent sway filter
## Providing consensus taxonomy up to level 14 : tmp6
99.429_1 k__Eukaryota;

Taxonomy Assignment for Zotu7 = k__Eukaryota:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined:undetermined


######
#BLAST LINE : Zotu14	350	KU992904.1	98.571	350	1	350	16	365	2.55e-179	619	1747	N/A
#BLAST LINE : Zotu14	350	KU992903.1	98.571	350	1	350	16	365	2.55e-179	619	1746	N/A
#BLAST LINE : Zotu14	350	AY384571.1	97.668	343	8	350	1	342	7.19e-170	588	475	N/A
#BLAST LINE : Zotu14	350	MG921285.1	96.857	350	1	350	16	364	9.30e-169	584	1747	N/A
#BLAST LINE : Zotu14	350	MG921284.1	96.857	350	1	350	16	364	9.30e-169	584	1747	N/A
#BLAST LINE : Zotu14	350	MG921283.1	96.857	350	1	350	16	364	9.30e-169	584	1747	N/A
#BLAST LINE : Zotu14	350	MG921282.1	96.857	350	1	350	16	364	9.30e-169	584	1747	N/A
#BLAST LINE : Zotu14	350	AY284831.1	94.857	350	1	350	16	363	4.39e-157	545	1725	N/A
#BLAST LINE : Zotu14	350	FN394812.1	94.571	350	1	350	517	170	2.04e-155	540	564	N/A
#BLAST LINE : Zotu14	350	FN394809.1	94.571	350	1	350	46	393	2.04e-155	540	562	N/A

ASSIGNING TAXONOMY FOR Zotu14 total hits passing initial filters = 10
KU992904.1 98.571 --> CAPTURED after percent sway filter
KU992903.1 98.571 --> CAPTURED after percent sway filter
## Providing consensus taxonomy up to level 14 : tmp6
98.571_1 k__Eukaryota;p__Nematoda;c__Enoplea;o__Dorylaimida;f__Tylencholaimidae;g__Tylencholaimus;
98.571_2 k__Eukaryota;p__Nematoda;c__Enoplea;o__Dorylaimida;f__Tylencholaimidae;g__Tylencholaimus;