__maintainer__ = "Björn Johansson"
__email__ = "bjorn_johansson@bio.uminho.pt"
__status__ = "Development" # "Production" #"Prototype"
-__version__ = "0.0.0-post.1+3220013"
+__version__ = "0.0.0-post.1+e87d85a"
# create config directory
diff --git a/_modules/pydna/amplicon.html b/_modules/pydna/amplicon.html
index cc1f81a6..f55d5221 100644
--- a/_modules/pydna/amplicon.html
+++ b/_modules/pydna/amplicon.html
@@ -3,7 +3,7 @@
- pydna.amplicon — pydna 0.0.0.post1+3220013 documentation
+ pydna.amplicon — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/amplify.html b/_modules/pydna/amplify.html
index 7feb6db7..25e4061f 100644
--- a/_modules/pydna/amplify.html
+++ b/_modules/pydna/amplify.html
@@ -3,7 +3,7 @@
- pydna.amplify — pydna 0.0.0.post1+3220013 documentation
+ pydna.amplify — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
@@ -91,7 +91,7 @@ Source code for pydna.amplify
from pydna.utils import flatten as _flatten
# from pydna.utils import memorize as _memorize
-from pydna.utils import rc as _rc
+from pydna.utils import rc as _rc, shift_feature as _shift_feature
from pydna.amplicon import Amplicon as _Amplicon
from pydna.primer import Primer as _Primer
from pydna.seqrecord import SeqRecord as _SeqRecord
@@ -427,6 +427,8 @@ Source code for pydna.amplify
feats = self.template[
fp.position - fp._fp : rp.position + rp._fp
].features # Save features covered by primers
+ shift_amount = len(fp.tail)
+ feats = [_shift_feature(f, shift_amount, None) for f in feats]
tpl = self.template
else:
continue
diff --git a/_modules/pydna/assembly.html b/_modules/pydna/assembly.html
index 2ed58b94..ed173dbd 100644
--- a/_modules/pydna/assembly.html
+++ b/_modules/pydna/assembly.html
@@ -3,7 +3,7 @@
- pydna.assembly — pydna 0.0.0.post1+3220013 documentation
+ pydna.assembly — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/common_sub_strings.html b/_modules/pydna/common_sub_strings.html
index 17dc0b33..7f5f59ef 100644
--- a/_modules/pydna/common_sub_strings.html
+++ b/_modules/pydna/common_sub_strings.html
@@ -3,7 +3,7 @@
- pydna.common_sub_strings — pydna 0.0.0.post1+3220013 documentation
+ pydna.common_sub_strings — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/contig.html b/_modules/pydna/contig.html
index 7640cb28..783c2b5b 100644
--- a/_modules/pydna/contig.html
+++ b/_modules/pydna/contig.html
@@ -3,7 +3,7 @@
- pydna.contig — pydna 0.0.0.post1+3220013 documentation
+ pydna.contig — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/design.html b/_modules/pydna/design.html
index e8783fe6..ae8bf3c6 100644
--- a/_modules/pydna/design.html
+++ b/_modules/pydna/design.html
@@ -3,7 +3,7 @@
- pydna.design — pydna 0.0.0.post1+3220013 documentation
+ pydna.design — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/dseq.html b/_modules/pydna/dseq.html
index de54e3af..a0d2fb2f 100644
--- a/_modules/pydna/dseq.html
+++ b/_modules/pydna/dseq.html
@@ -3,7 +3,7 @@
- pydna.dseq — pydna 0.0.0.post1+3220013 documentation
+ pydna.dseq — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/dseqrecord.html b/_modules/pydna/dseqrecord.html
index 2a101111..afc72d9d 100644
--- a/_modules/pydna/dseqrecord.html
+++ b/_modules/pydna/dseqrecord.html
@@ -3,7 +3,7 @@
- pydna.dseqrecord — pydna 0.0.0.post1+3220013 documentation
+ pydna.dseqrecord — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/editor.html b/_modules/pydna/editor.html
index 2f4e13cc..8ad0adc5 100644
--- a/_modules/pydna/editor.html
+++ b/_modules/pydna/editor.html
@@ -3,7 +3,7 @@
- pydna.editor — pydna 0.0.0.post1+3220013 documentation
+ pydna.editor — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/gel.html b/_modules/pydna/gel.html
index bfdc1e5c..07969529 100644
--- a/_modules/pydna/gel.html
+++ b/_modules/pydna/gel.html
@@ -3,7 +3,7 @@
- pydna.gel — pydna 0.0.0.post1+3220013 documentation
+ pydna.gel — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/genbank.html b/_modules/pydna/genbank.html
index 87a6720c..fd6e1b4d 100644
--- a/_modules/pydna/genbank.html
+++ b/_modules/pydna/genbank.html
@@ -3,7 +3,7 @@
- pydna.genbank — pydna 0.0.0.post1+3220013 documentation
+ pydna.genbank — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/genbankfile.html b/_modules/pydna/genbankfile.html
index e316e7df..b7b7d85e 100644
--- a/_modules/pydna/genbankfile.html
+++ b/_modules/pydna/genbankfile.html
@@ -3,7 +3,7 @@
- pydna.genbankfile — pydna 0.0.0.post1+3220013 documentation
+ pydna.genbankfile — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/genbankfixer.html b/_modules/pydna/genbankfixer.html
index f9afdbad..14893174 100644
--- a/_modules/pydna/genbankfixer.html
+++ b/_modules/pydna/genbankfixer.html
@@ -3,7 +3,7 @@
- pydna.genbankfixer — pydna 0.0.0.post1+3220013 documentation
+ pydna.genbankfixer — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/genbankrecord.html b/_modules/pydna/genbankrecord.html
index d8b34256..05d53fa6 100644
--- a/_modules/pydna/genbankrecord.html
+++ b/_modules/pydna/genbankrecord.html
@@ -3,7 +3,7 @@
- pydna.genbankrecord — pydna 0.0.0.post1+3220013 documentation
+ pydna.genbankrecord — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/myprimers.html b/_modules/pydna/myprimers.html
index ed8979d3..96b93e68 100644
--- a/_modules/pydna/myprimers.html
+++ b/_modules/pydna/myprimers.html
@@ -3,7 +3,7 @@
- pydna.myprimers — pydna 0.0.0.post1+3220013 documentation
+ pydna.myprimers — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/parsers.html b/_modules/pydna/parsers.html
index bb5aca3f..611e346a 100644
--- a/_modules/pydna/parsers.html
+++ b/_modules/pydna/parsers.html
@@ -3,7 +3,7 @@
- pydna.parsers — pydna 0.0.0.post1+3220013 documentation
+ pydna.parsers — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/primer.html b/_modules/pydna/primer.html
index 223d3910..5970de96 100644
--- a/_modules/pydna/primer.html
+++ b/_modules/pydna/primer.html
@@ -3,7 +3,7 @@
- pydna.primer — pydna 0.0.0.post1+3220013 documentation
+ pydna.primer — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/readers.html b/_modules/pydna/readers.html
index de79996a..9845b602 100644
--- a/_modules/pydna/readers.html
+++ b/_modules/pydna/readers.html
@@ -3,7 +3,7 @@
- pydna.readers — pydna 0.0.0.post1+3220013 documentation
+ pydna.readers — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/seqrecord.html b/_modules/pydna/seqrecord.html
index 75d3e705..a2b576c5 100644
--- a/_modules/pydna/seqrecord.html
+++ b/_modules/pydna/seqrecord.html
@@ -3,7 +3,7 @@
- pydna.seqrecord — pydna 0.0.0.post1+3220013 documentation
+ pydna.seqrecord — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/threading_timer_decorator_exit.html b/_modules/pydna/threading_timer_decorator_exit.html
index f71b5b5e..18a682ac 100644
--- a/_modules/pydna/threading_timer_decorator_exit.html
+++ b/_modules/pydna/threading_timer_decorator_exit.html
@@ -3,7 +3,7 @@
- pydna.threading_timer_decorator_exit — pydna 0.0.0.post1+3220013 documentation
+ pydna.threading_timer_decorator_exit — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/tm.html b/_modules/pydna/tm.html
index fb2859fd..ffcb8aa1 100644
--- a/_modules/pydna/tm.html
+++ b/_modules/pydna/tm.html
@@ -3,7 +3,7 @@
- pydna.tm — pydna 0.0.0.post1+3220013 documentation
+ pydna.tm — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/_modules/pydna/utils.html b/_modules/pydna/utils.html
index 3a216f2f..f149cb41 100644
--- a/_modules/pydna/utils.html
+++ b/_modules/pydna/utils.html
@@ -3,7 +3,7 @@
- pydna.utils — pydna 0.0.0.post1+3220013 documentation
+ pydna.utils — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
@@ -159,6 +159,8 @@ Source code for pydna.utils
"""docstring."""
newparts = []
strand = original_location.strand
+ if lim is None:
+ lim = _sys.maxsize
for part in original_location.parts:
new_start = (part.start + shift) % lim
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
index 53a68b92..086c6356 100644
--- a/_static/documentation_options.js
+++ b/_static/documentation_options.js
@@ -1,5 +1,5 @@
const DOCUMENTATION_OPTIONS = {
- VERSION: '0.0.0.post1+3220013',
+ VERSION: '0.0.0.post1+e87d85a',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/genindex.html b/genindex.html
index a0a2e826..71f8b384 100644
--- a/genindex.html
+++ b/genindex.html
@@ -3,7 +3,7 @@
- Index — pydna 0.0.0.post1+3220013 documentation
+ Index — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/index.html b/index.html
index 617f8f15..e5608932 100644
--- a/index.html
+++ b/index.html
@@ -4,7 +4,7 @@
- Welcome to pydna’s documentation! — pydna 0.0.0.post1+3220013 documentation
+ Welcome to pydna’s documentation! — pydna 0.0.0.post1+e87d85a documentation
@@ -15,7 +15,7 @@
-
+
diff --git a/py-modindex.html b/py-modindex.html
index 1df27f3f..c281abb4 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -3,7 +3,7 @@
- Python Module Index — pydna 0.0.0.post1+3220013 documentation
+ Python Module Index — pydna 0.0.0.post1+e87d85a documentation
@@ -14,7 +14,7 @@
-
+
diff --git a/search.html b/search.html
index 3cbacfc8..adb35302 100644
--- a/search.html
+++ b/search.html
@@ -3,7 +3,7 @@
- Search — pydna 0.0.0.post1+3220013 documentation
+ Search — pydna 0.0.0.post1+e87d85a documentation
@@ -15,7 +15,7 @@
-
+