change to normal strings instead of raw strings

pydna-group · Jan 26, 2025 · 7dad56b · 7dad56b
1 parent 4740475
commit 7dad56b
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Showing 2 changed files with 38 additions and 36 deletions.
diff --git a/src/pydna/tm.py b/src/pydna/tm.py
@@ -12,7 +12,7 @@
 from Bio.SeqUtils import MeltingTemp as _mt
 from Bio.SeqUtils import gc_fraction as _GC
 
-import textwrap as _textwrap
+from textwrap import dedent as _dedent
 from pydna._pretty import pretty_str as _pretty_str
 
 # See the documentation for Bio.SeqUtils.MeltingTemp for more details
@@ -160,12 +160,12 @@ def program(amplicon, tm=tm_default, ta=ta_default):
     extension_time_taq = max(30, int(taq_extension_rate * len(amplicon) / 1000))
     # seconds
 
-    f = _textwrap.dedent(
-        r"""
+    f = _dedent(
+        """\
         |95°C|95°C               |    |tmf:{tmf:.1f}
         |____|_____          72°C|72°C|tmr:{tmr:.1f}
-        |3min|30s  \ {ta:.1f}°C _____|____|{rate}s/kb
-        |    |      \______/{0:2}:{1:0>2}|5min|GC {GC}%
+        |3min|30s  \\ {ta:.1f}°C _____|____|{rate}s/kb
+        |    |      \\______/{0:2}:{1:0>2}|5min|GC {GC}%
         |    |       30s         |    |{size}bp
         """.format(
             rate=taq_extension_rate,
@@ -226,14 +226,14 @@ def dbd_program(amplicon, tm=tm_dbd, ta=ta_dbd):
     tmr = tm(amplicon.reverse_primer.footprint)
 
     if tmf >= 69.0 and tmr >= 69.0:
-        f = _textwrap.dedent(
-            r"""
-                              |98°C|98°C      |    |tmf:{tmf:.1f}
-                              |____|____      |    |tmr:{tmr:.1f}
-                              |30s |10s \ 72°C|72°C|{rate}s/kb
-                              |    |     \____|____|GC {GC_prod}%
-                              |    |     {0:2}:{1:0>2}|5min|{size}bp
-                              """.format(
+        f = _dedent(
+            """\
+                    |98°C|98°C      |    |tmf:{tmf:.1f}
+                    |____|____      |    |tmr:{tmr:.1f}
+                    |30s |10s \\ 72°C|72°C|{rate}s/kb
+                    |    |     \\____|____|GC {GC_prod}%
+                    |    |     {0:2}:{1:0>2}|5min|{size}bp
+                    """.format(
                 rate=PfuSso7d_extension_rate,
                 tmf=tmf,
                 tmr=tmr,
@@ -243,12 +243,12 @@ def dbd_program(amplicon, tm=tm_dbd, ta=ta_dbd):
             )
         ).strip()
     else:
-        f = _textwrap.dedent(
-            r"""
+        f = _dedent(
+            """\
              |98°C|98°C               |    |tmf:{tmf:.1f}
              |____|_____          72°C|72°C|tmr:{tmr:.1f}
-             |30s |10s  \ {ta:.1f}°C _____|____|{rate}s/kb
-             |    |      \______/{0:2}:{1:0>2}|5min|GC {GC}%
+             |30s |10s  \\ {ta:.1f}°C _____|____|{rate}s/kb
+             |    |      \\______/{0:2}:{1:0>2}|5min|GC {GC}%
              |    |       10s         |    |{size}bp
              """.format(
                 rate=PfuSso7d_extension_rate,

diff --git a/tests/test_module_amplicon.py b/tests/test_module_amplicon.py
@@ -86,25 +86,27 @@ def test_amplicon_dbd():
 
     assert repr(prod) == "Amplicon(1505)"
 
-    fig = r"""
-    |95°C|95°C               |    |tmf:77.1
-    |____|_____          72°C|72°C|tmr:80.9
-    |3min|30s  \ 64.6°C _____|____|45s/kb
-    |    |      \______/ 1:07|5min|GC 51%
-    |    |       30s         |    |1505bp
-    """
-    fig = dedent(fig).strip()
-    assert str(prod.program()) == fig
-
-    fig = r"""
-    |98°C|98°C      |    |tmf:71.6
-    |____|____      |    |tmr:75.3
-    |30s |10s \ 72°C|72°C|15s/kb
-    |    |     \____|____|GC 51%
-    |    |      0:22|5min|1505bp
-    """
-    fig = dedent(fig).strip()
-    assert str(prod.dbd_program()) == fig
+    fig = dedent(
+        """\
+                 |95°C|95°C               |    |tmf:77.1
+                 |____|_____          72°C|72°C|tmr:80.9
+                 |3min|30s  \\ 64.6°C _____|____|45s/kb
+                 |    |      \\______/ 1:07|5min|GC 51%
+                 |    |       30s         |    |1505bp"""
+    )
+
+    assert str(prod.program()) == fig.strip()
+
+    fig = dedent(
+        """\
+                 |98°C|98°C      |    |tmf:71.6
+                 |____|____      |    |tmr:75.3
+                 |30s |10s \\ 72°C|72°C|15s/kb
+                 |    |     \\____|____|GC 51%
+                 |    |      0:22|5min|1505bp"""
+    )
+
+    assert str(prod.dbd_program()) == fig.strip()
 
 
 def test_amplicon_dbd_low_gc():