#1979 Preview: IDT sequence with leading or trailing spaces will not…

… open. (#1980)
epam · May 30, 2024 · b45d44a · b45d44a
1 parent 910d3ca
commit b45d44a
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Showing 3 changed files with 201 additions and 128 deletions.
diff --git a/api/tests/integration/ref/formats/idt_to_ket.py.out b/api/tests/integration/ref/formats/idt_to_ket.py.out
@@ -9,8 +9,8 @@ idt_prefix_suffix.ket:SUCCEED
 idt_singe_32moera_nucleoside.ket:SUCCEED
 idt_single_nucleoside.ket:SUCCEED
 idt_std_phosphates.ket:SUCCEED
-Test '!+-$#12w12r23e32e33': got expected error 'Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3'
-Test '+/5Phos/A': got expected error 'Sugar prefix could not be used with '/5Phos/''
+Test '!+A-$#12w12r23e32e33': got expected error 'Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3'
+Test '+/5Phos/A': got expected error 'Sugar prefix could not be used with modified monomer.'
 Test '/': got expected error 'Unexpected end of data'
 Test '//': got expected error 'Invalid modification: empty string.'
 Test '/32MOErA/T': got expected error 'IDT alias 32MOErA not found at five-prime end position.'
@@ -21,11 +21,13 @@ Test '/a/': got expected error 'Invalid modification: a.'
 Test '/i2MOErA/': got expected error 'IDT alias i2MOErA not found at three-prime end position.'
 Test '/i2MOErA/T': got expected error 'IDT alias i2MOErA not found at five-prime end position.'
 Test 'A*': got expected error 'Invalid IDT sequence: '*' couldn't be the last symbol.'
-Test 'A+/3Phos/': got expected error 'Sugar prefix could not be used with '/3Phos/''
-Test 'Am/3Phos/': got expected error 'Sugar prefix could not be used with '/3Phos/''
-Test 'Ar/3Phos/': got expected error 'Sugar prefix could not be used with '/3Phos/''
+Test 'A*/3Phos/': got expected error 'Phosphor /3Phos/ cannod be modified with '*'.'
+Test 'A+/3Phos/': got expected error 'Sugar prefix could not be used with modified monomer.'
+Test 'Am/3Phos/': got expected error 'Sugar prefix could not be used with modified monomer.'
+Test 'Ar/3Phos/': got expected error 'Sugar prefix could not be used with modified monomer.'
 Test 'T/52MOErA/': got expected error 'IDT alias 52MOErA not found at three-prime end position.'
 Test 'T/5Phos/': got expected error 'IDT alias 5Phos not found at three-prime end position.'
 Test 'T/i2MOErA/': got expected error 'IDT alias i2MOErA not found at three-prime end position.'
-Test 'm/5Phos/A': got expected error 'Sugar prefix could not be used with '/5Phos/''
-Test 'r/5Phos/A': got expected error 'Sugar prefix could not be used with '/5Phos/''
+Test 'm/5Phos/A': got expected error 'Sugar prefix could not be used with modified monomer.'
+Test 'r+A': got expected error 'Sugar prefix 'r' whithout base.'
+Test 'r/5Phos/A': got expected error 'Sugar prefix could not be used with modified monomer.'
diff --git a/api/tests/integration/tests/formats/idt_to_ket.py b/api/tests/integration/tests/formats/idt_to_ket.py
@@ -29,9 +29,9 @@ def find_diff(a, b):
 ref_path = joinPathPy("ref/", __file__)
 
 idt_data = {
-    "idt_single_nucleoside": "A",
-    "idt_bases": "ATCGUI",
-    "idt_prefix_suffix": "mA*rT*+C*G*+UrImA",
+    "idt_single_nucleoside": "  A  ",
+    "idt_bases": "  ATCGUI  ",
+    "idt_prefix_suffix": "  mA*rT*+C*G*+UrImA  ",
     "idt_modifications": "/52MOErA/*/i2MOErA//32MOErA/",
     "idt_52moera_with_3phos": "/52MOErA//3Phos/",
     "idt_singe_32moera_nucleoside": "/32MOErA/",
@@ -60,10 +60,11 @@ def find_diff(a, b):
         print(diff)
 
 idt_errors = {
-    "!+-$#12w12r23e32e33": "Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3",
+    "!+A-$#12w12r23e32e33": "Invalid symbols in the sequence: !,-,$,#,1,2,w,1,2,2,3,e,3,2,e,3,3",
     "/": "Unexpected end of data",
     "//": "Invalid modification: empty string.",
     "/a/": "Invalid modification: a.",
+    "r+A": "Sugar prefix 'r' whithout base.",
     "A*": "Invalid IDT sequence: '*' couldn't be the last symbol.",
     "/i2MOErA/": "IDT alias i2MOErA not found at three-prime end position.",
     "/i2MOErA/T": "IDT alias i2MOErA not found at five-prime end position.",
@@ -74,12 +75,13 @@ def find_diff(a, b):
     "/3Phos/T": "IDT alias 3Phos not found at three-prime end position.",
     "T/5Phos/": "IDT alias 5Phos not found at three-prime end position.",
     "/5Phos/*A": "/5Phos/ cannot be modified to 'sP'",
-    "r/5Phos/A": "Sugar prefix could not be used with '/5Phos/'",
-    "+/5Phos/A": "Sugar prefix could not be used with '/5Phos/'",
-    "m/5Phos/A": "Sugar prefix could not be used with '/5Phos/'",
-    "Ar/3Phos/": "Sugar prefix could not be used with '/3Phos/'",
-    "A+/3Phos/": "Sugar prefix could not be used with '/3Phos/'",
-    "Am/3Phos/": "Sugar prefix could not be used with '/3Phos/'",
+    "r/5Phos/A": "Sugar prefix could not be used with modified monomer.",
+    "+/5Phos/A": "Sugar prefix could not be used with modified monomer.",
+    "m/5Phos/A": "Sugar prefix could not be used with modified monomer.",
+    "Ar/3Phos/": "Sugar prefix could not be used with modified monomer.",
+    "A+/3Phos/": "Sugar prefix could not be used with modified monomer.",
+    "Am/3Phos/": "Sugar prefix could not be used with modified monomer.",
+    "A*/3Phos/": "Phosphor /3Phos/ cannod be modified with '*'.",
 }
 for idt_seq in sorted(idt_errors.keys()):
     error = idt_errors[idt_seq]