test for virsorter2

bin/parse_viral_pred.py

@@ -186,7 +186,7 @@ def parse_virus_sorter(sorter_files):
     return high_confidence, low_confidence, prophages
 
 
-def parse_virus_sorter2(sorter_files):
+def parse_virus_sorter2(sorter_files, vs_cutoff):
     """Extract high, low and prophages confidence Records from virus sorter results.
     High confidence are contigs with confidence score >= confidence cutoff (0.9 per default).
     Low confidence are contigs with confidence score < confidence cutoff and > 0.5.
@@ -222,6 +222,7 @@ def parse_virus_sorter2(sorter_files):
     prophages = dict()
 
     final_boundary_file, final_score_file, final_combined_fa_file = "", "", ""
+    print('SORTER',sorter_files)
     for i in sorter_files:
         if "final-viral-boundary.tsv" in i:
             final_boundary_file = i
@@ -250,15 +251,15 @@ def parse_virus_sorter2(sorter_files):
         if not circular or not max_score:
             continue
         circular = circular.startswith('circular')
+
         if 'partial' in record.id:
             # add the prophage position within the contig
+            record.id = clean_name
             prophages.setdefault(clean_name, []).append(
                 Record(record, "prophage", circular, prange)
             )
-
         record.id = clean_name
-
-        if float(max_score) >= float(args.vs_cutoff):
+        if float(max_score) >= float(vs_cutoff):
             high_confidence[record.id] = Record(record, "high_confidence", circular)
         else:
             low_confidence[record.id] = Record(record, "low_confidence", circular)
@@ -270,7 +271,7 @@ def parse_virus_sorter2(sorter_files):
     return high_confidence, low_confidence, prophages
 
 
-def merge_annotations(pprmeta, finder, sorter, sorter2, assembly):
+def merge_annotations(pprmeta, finder, sorter, sorter2, assembly, vs_cutoff):
     """Parse VirSorter, VirFinder and PPR-Meta outputs and merge the results.
     High confidence viral contigs:
     -  VirSorter reported as categories 1 and 2
@@ -291,19 +292,20 @@ def merge_annotations(pprmeta, finder, sorter, sorter2, assembly):
     pprmeta_lc = parse_pprmeta(pprmeta)
     finder_lc, finder_lowestc = parse_virus_finder(finder)
     sorter_hc, sorter_lc, sorter_prophages = parse_virus_sorter(sorter) if sorter is not None else parse_virus_sorter2(
-        sorter2)
+        sorter2, vs_cutoff)
 
     for seq_record in SeqIO.parse(assembly, "fasta"):
-        # HC
-        if seq_record.id in sorter_hc:
-            hc_predictions_contigs.append(sorter_hc.get(seq_record.id).get_seq_record())
         # Pro
-        elif seq_record.id in sorter_prophages:
+        # TODO: check this decision because for VirSorter2 sequence can be in 2 categories
+        if seq_record.id in sorter_prophages:
             # a contig may have several prophages
             # for prophages write the record as it holds the
             # sliced fasta
             for record in sorter_prophages.get(seq_record.id):
                 prophage_predictions_contigs.append(record.get_seq_record())
+        # HC
+        if seq_record.id in sorter_hc:
+            hc_predictions_contigs.append(sorter_hc.get(seq_record.id).get_seq_record())
         # LC
         elif seq_record.id in finder_lc:
             lc_predictions_contigs.append(seq_record)
@@ -331,7 +333,7 @@ def main(pprmeta, finder, sorter, sorter2, assembly, outdir, vs_cutoff, prefix=F
         sorter_hc,
         sorter_lc,
         sorter_prophages,
-    ) = merge_annotations(pprmeta, finder, sorter, sorter2, assembly)
+    ) = merge_annotations(pprmeta, finder, sorter, sorter2, assembly, vs_cutoff)
 
     at_least_one = False
     name_prefix = ""

pytest.ini

@@ -1,4 +1,5 @@
 [pytest]
 pythonpath = . bin
 norecursedirs = cwl/*
-addopts= --git-aware --symlink --color=no
+
+##addopts= --git-aware --symlink --color=no

tests/parse_viral_fixtures/base_fixtures/virsorter2/final-viral-boundary.tsv

@@ -0,0 +1,7 @@
+seqname	trim_orf_index_start	trim_orf_index_end	trim_bp_start	trim_bp_end	trim_pr	trim_pr_max	prox_orf_index_start	prox_orf_index_end	prox_bp_start	prox_bp_end	prox_pr	prox_pr_max	partial	full_orf_index_start	full_orf_index_end	full_bp_start	full_bp_end	pr_full	arc	bac	euk	vir	mix	unaligned	hallmark_cnt	group	shape	seqname_new	final_max_score	final_max_score_group
+phage_1	1	13	3	23076	1.0	1.0	1	13	3	23076	NA	NA	0	1	13	3	23076	1.0	0.0	0.0	0.0	84.6	0.0	15.4	7	dsDNAphage	linear	seq91||full	1.0	dsDNAphage
+phage_2	1	30	1	23146	1.0	1.0	1	30	1	23146	NA	NA	0	1	30	1	23146	1.0	0.0	0.0	0.0	93.3	0.0	6.7	11	dsDNAphage	linear	seq90||full	1.0	dsDNAphage
+hc_1	1	65	92	47657	1.0	1.0	1	65	92	47657	NA	NA	0	1	65	92	47657	1.0	0.0	0.0	0.0	87.7	0.0	12.3	3	dsDNAphage	circular	seq9||full	1.0	dsDNAphage
+hc_2	1	33	61	20731	0.727	0.76	1	34	61	23816	NA	NA	0	1	34	61	23816	0.72	0.0	0.0	2.9	88.2	5.9	2.9	0	dsDNAphage	linear	seq78||full	0.727	dsDNAphage
+lc_1	1	25	2	24532	0.993	0.993	1	25	2	24532	NA	NA	0	1	25	2	24532	0.993	0.0	0.0	0.0	60.0	0.0	40.0	2	dsDNAphage	linear	seq72||full	0.993	dsDNAphage
+lc_2	1	36	2	25058	0.947	0.96	1	36	2	25058	NA	NA	0	1	36	2	25058	0.947	0.0	0.0	0.0	86.1	2.8	11.1	0	dsDNAphage	circular	seq70||full	0.947	dsDNAphage

tests/parse_viral_fixtures/base_fixtures/virsorter2/final-viral-combined.fa

@@ -0,0 +1,14 @@
+>phage_1||partial
+AAA
+>phage_2||1_partial
+GGG
+>hc_1||full
+TTT
+>hc_2||lt2gene
+T
+>lc_1||full
+C
+>lc_2||lt2gene
+AA
+>lc_3||full
+GG

tests/parse_viral_fixtures/base_fixtures/virsorter2/final-viral-score.tsv

@@ -0,0 +1,8 @@
+seqname	dsDNAphage	ssDNA	max_score	max_score_group	length	hallmark	viral	cellular
+phage_1||partial	0.913	0.053	0.7	dsDNAphage	105648	0	67.800	1.300
+phage_2||1_partial	1.000	0.087	1.000	dsDNAphage	62420	2	66.000	0.000
+hc_1||full	0.987	0.027	0.987	dsDNAphage	57882	15	83.000	1.900
+hc_2||lt2gene	1.000	0.413	1.000	dsDNAphage	47566	3	87.700	0.000
+lc_1||full	1.000	0.173	0.8	dsDNAphage	45193	1	85.500	0.000
+lc_2||lt2gene	1.000	0.513	0.5	dsDNAphage	45227	4	74.000	0.000
+seq10||lt2gene	nan	nan	nan	dsDNAphage	5899	1	100.000	0.000

tests/parse_viral_fixtures/virsorter_precedence/virsorter2/expected/high_confidence_viral_contigs.fna → tests/parse_viral_fixtures/virsorter_precedence/expected_vs2/high_confidence_viral_contigs.fna

@@ -10,9 +10,5 @@ TTT
 G
 >seq6
 C
->seq7|phage-circular
-T
->seq8
-AA
 >seq9
 GG