phac-nml · mattheww95 · Jun 19, 2024 · Jun 17, 2024 · Jun 17, 2024 · Jun 19, 2024
diff --git a/locidex/classes/extractor.py b/locidex/classes/extractor.py
@@ -25,7 +25,6 @@ def __init__(self,df,seq_data,sseqid_col,queryid_col,qstart_col,qend_col,qlen_co
         self.df = self.recursive_filter_redundant_queries(self.df, 'locus_name', sseqid_col, bitscore_col, 
                                                           sort_cols, ascending_cols, overlap_threshold=1)
 
-
         self.df = self.extend(self.df,sseqid_col, queryid_col, qstart_col, qend_col, sstart_col,send_col,slen_col, qlen_col, bitscore_col, overlap_threshold=overlap_thresh)
         self.df = self.set_extraction_pos(self.df, sstart_col, send_col)
         loci_ranges = self.group_by_locus(self.df,sseqid_col, queryid_col,qlen_col,extend_threshold_ratio)
@@ -413,7 +412,6 @@ def extend(self,df,seqid_col, queryid_col, qstart_col, qend_col, sstart_col,send
         df = df.sort_values(sort_cols, ascending=ascending_cols).reset_index(drop=True)
         queries = df[queryid_col].to_list()
 
-
         #Remove incomplete hits when complete ones are present
         filtered = []
         for query in queries:
@@ -425,10 +423,6 @@ def extend(self,df,seqid_col, queryid_col, qstart_col, qend_col, sstart_col,send
             else:
                 filtered.append(subset)
         df = pd.concat(filtered, ignore_index=True)
-        trunc_records = df[df['is_complete'] == False]
-        if len(trunc_records) == 0:
-            return df
-
         is_extended = []
         five_p_ext = []
         three_p_ext = []

diff --git a/tests/test_data/genomes/G1.fasta b/tests/test_data/genomes/G1.fasta
diff --git a/tests/test_data/genomes/G10.fasta b/tests/test_data/genomes/G10.fasta
diff --git a/tests/test_data/genomes/G11.fasta b/tests/test_data/genomes/G11.fasta
diff --git a/tests/test_data/genomes/G12.fasta b/tests/test_data/genomes/G12.fasta
diff --git a/tests/test_data/genomes/G13.fasta b/tests/test_data/genomes/G13.fasta
diff --git a/tests/test_data/genomes/G14.fasta b/tests/test_data/genomes/G14.fasta
diff --git a/tests/test_data/genomes/G2.fasta b/tests/test_data/genomes/G2.fasta
diff --git a/tests/test_data/genomes/G3.fasta b/tests/test_data/genomes/G3.fasta
diff --git a/tests/test_data/genomes/G4.fasta b/tests/test_data/genomes/G4.fasta
diff --git a/tests/test_data/genomes/G5.fasta b/tests/test_data/genomes/G5.fasta
diff --git a/tests/test_data/genomes/G6.fasta b/tests/test_data/genomes/G6.fasta
diff --git a/tests/test_data/genomes/G7.fasta b/tests/test_data/genomes/G7.fasta
diff --git a/tests/test_data/genomes/G8.fasta b/tests/test_data/genomes/G8.fasta
diff --git a/tests/test_data/genomes/G9.fasta b/tests/test_data/genomes/G9.fasta
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.fasta b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.fasta
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.ndb b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.ndb
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nhr b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nhr
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nin b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nin
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.njs b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.njs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "nucleotide",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "locidex_db/blast/nucleotide/nucleotide.fasta",
+  "number-of-letters": 22641,
+  "number-of-sequences": 20,
+  "last-updated": "2024-06-06T08:43:00",
+  "number-of-volumes": 1,
+  "bytes-total": 44532,
+  "bytes-to-cache": 6046,
+  "files": [
+    "nucleotide.ndb",
+    "nucleotide.nhr",
+    "nucleotide.nin",
+    "nucleotide.not",
+    "nucleotide.nsq",
+    "nucleotide.ntf",
+    "nucleotide.nto"
+  ]
+}
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.not b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.not
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nsq b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nsq
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.ntf b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.ntf
diff --git a/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nto b/tests/test_data/outputs/db/blast/nucleotide/nucleotide.nto
diff --git a/tests/test_data/outputs/db/blast/protein/protein.fasta b/tests/test_data/outputs/db/blast/protein/protein.fasta
@@ -0,0 +1,40 @@
+>0
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+>1
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+>2
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+>3
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+>4
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+>5
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+>6
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+>7
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+>8
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+>9
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+>10
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+>11
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+>12
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+>13
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+>14
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+>15
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+>16
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+>17
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+>18
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+>19
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diff --git a/tests/test_data/outputs/db/blast/protein/protein.pdb b/tests/test_data/outputs/db/blast/protein/protein.pdb
diff --git a/tests/test_data/outputs/db/blast/protein/protein.phr b/tests/test_data/outputs/db/blast/protein/protein.phr
diff --git a/tests/test_data/outputs/db/blast/protein/protein.pin b/tests/test_data/outputs/db/blast/protein/protein.pin
diff --git a/tests/test_data/outputs/db/blast/protein/protein.pjs b/tests/test_data/outputs/db/blast/protein/protein.pjs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "protein",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "locidex_db/blast/protein/protein.fasta",
+  "number-of-letters": 7547,
+  "number-of-sequences": 20,
+  "last-updated": "2024-06-06T08:43:00",
+  "number-of-volumes": 1,
+  "bytes-total": 46334,
+  "bytes-to-cache": 7848,
+  "files": [
+    "protein.pdb",
+    "protein.phr",
+    "protein.pin",
+    "protein.pot",
+    "protein.psq",
+    "protein.ptf",
+    "protein.pto"
+  ]
+}
diff --git a/tests/test_data/outputs/db/blast/protein/protein.pot b/tests/test_data/outputs/db/blast/protein/protein.pot
diff --git a/tests/test_data/outputs/db/blast/protein/protein.psq b/tests/test_data/outputs/db/blast/protein/protein.psq
diff --git a/tests/test_data/outputs/db/blast/protein/protein.ptf b/tests/test_data/outputs/db/blast/protein/protein.ptf
diff --git a/tests/test_data/outputs/db/blast/protein/protein.pto b/tests/test_data/outputs/db/blast/protein/protein.pto
diff --git a/tests/test_data/outputs/db/config.json b/tests/test_data/outputs/db/config.json
@@ -0,0 +1,12 @@
+{
+    "db_name": "Locidex Test Database",
+    "db_version": "1.0.0",
+    "db_date": "2024/06/06",
+    "db_author": "James Robertson",
+    "db_desc": "Using Salmonella GCA_000007545.2 as source data",
+    "db_num_seqs": 20,
+    "is_nucl": true,
+    "is_prot": true,
+    "nucleotide_db_name": "nucleotide",
+    "protein_db_name": "protein"
+}