diff testMock.py @ 4:61158f32e5c3 draft

planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 18 Apr 2025 09:56:13 +0000
parents 41ac63b5d221
children 5b16f2911491
line wrap: on
line diff
--- a/testMock.py	Fri Apr 11 13:22:51 2025 +0000
+++ b/testMock.py	Fri Apr 18 09:56:13 2025 +0000
@@ -46,6 +46,7 @@
         CREATE TABLE sample (
             fragment TEXT PRIMARY KEY,
             sequence TEXT,
+            annotation TEXT,
             metadata_1 TEXT,
             metadata_2 TEXT
         );
@@ -53,13 +54,80 @@
 
     # Insert mock data
     cursor.executemany('''
-        INSERT INTO sample (fragment, sequence, metadata_1, metadata_2) VALUES (%s, %s, %s, %s);
-    ''', [
-        ('ACP10001AaCbbBS', 'seq for ACP10001AaCbbBS', 'Metadata1 for ACP10001AaCbbBS', 'Metadata2 for ACP10001AaCbbBS'),
-        ('CFP10002AaCbbBS', 'seq for CFP10002AaCbbBS', 'Metadata1 for CFP10002AaCbbBS', 'Metadata2 for CFP10002AaCbbBS'),
-        ('XYZ10003AaCbbBS', 'seq for XYZ10003AaCbbBS', 'Metadata1 for XYZ10003AaCbbBS', 'Metadata2 for XYZ10003AaCbbBS'),
-        ('QWE10004AaCbbBS', 'seq for QWE10004AaCbbBS', 'Metadata1 for QWE10004AaCbbBS', 'Metadata2 for QWE10004AaCbbBS')
-    ])
+    INSERT INTO sample (fragment, sequence, annotation, metadata_1, metadata_2)
+    VALUES (%s, %s, %s, %s, %s);
+''', [
+    (
+        'ACP10001AaCbbBS',
+        '''ORIGIN
+1 atggccattg taatgggccg ctgaaagggt gcccggatca ctttcgctgt ttcgacgttg
+61 gcttggtccc agcggcggca ccgagctggg tagcggtcag gagctgcttc gcgtgagcgg
+121 ctgccagggc agctgacgcc gctgcgcgca gctgcgcatg
+''',
+        '''LOCUS       ACP10001AaCbbBS                150 bp ds-DNA     circular SYN 14-SEP-2017
+FEATURES             Location/Qualifiers
+     CDS             5..150
+                     /vntifkey="1"
+                     /label=mock_gene_A
+     misc_feature    160..240
+                     /vntifkey="11"
+                     /label=mock_feature_A
+''',
+        'Metadata1 for ACP10001AaCbbBS', 'Metadata2 for ACP10001AaCbbBS'
+    ),
+    (
+        'CFP10002AaCbbBS',
+        '''ORIGIN
+1 ggatccgtaa atcggtttac ggtgcgttat gatctgtgaa acgccagcag cgcgcggtat
+61 ctcgacgtaa agcggttgca cgtgatggtt gccggcatgc ctgtgcgtga atggctgtgg
+121 ccggtacgtt gagcggcgtg
+''',
+        '''LOCUS       CFP10002AaCbbBS                130 bp ds-DNA     circular SYN 14-SEP-2017
+FEATURES             Location/Qualifiers
+     CDS             10..130
+                     /vntifkey="2"
+                     /label=mock_gene_B
+     misc_feature    complement(140..220)
+                     /vntifkey="12"
+                     /label=mock_feature_B
+''',
+        'Metadata1 for CFP10002AaCbbBS', 'Metadata2 for CFP10002AaCbbBS'
+    ),
+    (
+        'XYZ10003AaCbbBS',
+        '''ORIGIN
+1 tccgtttggg ccgttggttc cgtccggttg gggttttcgc gctgtggccg gatccggttg
+61 gcttttggcg ggggcgggtt cgtttttttc cggctttggg ccgggccgtt
+''',
+        '''LOCUS       XYZ10003AaCbbBS                120 bp ds-DNA     circular SYN 14-SEP-2017
+FEATURES             Location/Qualifiers
+     CDS             15..115
+                     /vntifkey="3"
+                     /label=mock_gene_C
+     misc_feature    130..210
+                     /vntifkey="13"
+                     /label=mock_feature_C
+''',
+        'Metadata1 for XYZ10003AaCbbBS', 'Metadata2 for XYZ10003AaCbbBS'
+    ),
+    (
+        'QWE10004AaCbbBS',
+        '''ORIGIN
+1 atgtttgctg gggcgatgct ggggctgctt tgttggcgcc gttttggtgg tgtttggttc
+61 tgctggggcc gggcgtgttt cgcgttggcg cgtgcgcgtt
+''',
+        '''LOCUS       QWE10004AaCbbBS                130 bp ds-DNA     circular SYN 14-SEP-2017
+FEATURES             Location/Qualifiers
+     CDS             20..130
+                     /vntifkey="4"
+                     /label=mock_gene_D
+     misc_feature    complement(145..225)
+                     /vntifkey="14"
+                     /label=mock_feature_D
+''',
+        'Metadata1 for QWE10004AaCbbBS', 'Metadata2 for QWE10004AaCbbBS'
+    )
+])
 
     conn.commit()
     print("Mock data inserted into 'sample' table.")