diff --git a/.buildinfo b/.buildinfo index 895bd7b6..88ce134a 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 7fd5115d475fbca355cfe2b14f6309e1 +config: 2b03fdb29cb7f014b01d408c45b07c8c tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index 5c9c305f..f55e13bc 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -5,14 +5,14 @@ - Overview: module code — pydna 0.0.0.post1+fd8577c documentation + Overview: module code — pydna 0.0.0.post1+0f15ccd documentation - + diff --git a/_modules/pydna.html b/_modules/pydna.html index f9817c61..e9807d72 100644 --- a/_modules/pydna.html +++ b/_modules/pydna.html @@ -5,14 +5,14 @@ - pydna — pydna 0.0.0.post1+fd8577c documentation + pydna — pydna 0.0.0.post1+0f15ccd documentation - + @@ -218,7 +218,7 @@

Source code for pydna

 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "0.0.0-post.1+fd8577c"
+__version__ = "0.0.0-post.1+0f15ccd"
 
 
 # create config directory
diff --git a/_modules/pydna/amplicon.html b/_modules/pydna/amplicon.html
index a6ca394d..27c8f91c 100644
--- a/_modules/pydna/amplicon.html
+++ b/_modules/pydna/amplicon.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.amplicon — pydna 0.0.0.post1+fd8577c documentation
+  pydna.amplicon — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/amplify.html b/_modules/pydna/amplify.html
index ffb4c8e1..3013c4a1 100644
--- a/_modules/pydna/amplify.html
+++ b/_modules/pydna/amplify.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.amplify — pydna 0.0.0.post1+fd8577c documentation
+  pydna.amplify — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/assembly.html b/_modules/pydna/assembly.html
index 49c5e2a7..a68f9b1a 100644
--- a/_modules/pydna/assembly.html
+++ b/_modules/pydna/assembly.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.assembly — pydna 0.0.0.post1+fd8577c documentation
+  pydna.assembly — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/common_sub_strings.html b/_modules/pydna/common_sub_strings.html
index c0cde5f9..496737c6 100644
--- a/_modules/pydna/common_sub_strings.html
+++ b/_modules/pydna/common_sub_strings.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.common_sub_strings — pydna 0.0.0.post1+fd8577c documentation
+  pydna.common_sub_strings — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/contig.html b/_modules/pydna/contig.html
index d422497b..9041f70b 100644
--- a/_modules/pydna/contig.html
+++ b/_modules/pydna/contig.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.contig — pydna 0.0.0.post1+fd8577c documentation
+  pydna.contig — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/design.html b/_modules/pydna/design.html
index 2029ff0f..f323c45d 100644
--- a/_modules/pydna/design.html
+++ b/_modules/pydna/design.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.design — pydna 0.0.0.post1+fd8577c documentation
+  pydna.design — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
@@ -310,7 +310,7 @@ 
Source code for pydna.design
 
 

 [docs]
-def assembly_fragments(f, overlap=35, maxlink=40):
+def assembly_fragments(f, overlap=35, maxlink=40, circular=False):
     """This function return a list of :mod:`pydna.amplicon.Amplicon` objects where
     primers have been modified with tails so that the fragments can be fused in
     the order they appear in the list by for example Gibson assembly or homologous
@@ -637,6 +637,9 @@ 
Source code for pydna.design
     maxlink : int, optional
         Maximum length of spacer sequences that may be present in f. These will be included in tails for designed primers.
 
+    circular : bool, optional
+        If True, the assembly is circular. If False, the assembly is linear.
+
     Returns
     -------
     seqs : list of :mod:`pydna.amplicon.Amplicon` and other Dseqrecord like objects :mod:`pydna.amplicon.Amplicon` objects
@@ -694,6 +697,15 @@ 
Source code for pydna.design
     >>>
 
     """
+
+    # Recursive call for circular assemblies
+    if circular:
+        fragments = assembly_fragments(f + f[0:1], overlap=overlap, maxlink=maxlink, circular=False)
+
+        if hasattr(fragments[0], "template"):
+            fragments[0] = _pcr((fragments[-1].forward_primer, fragments[0].reverse_primer), fragments[0].template)
+        return fragments[:-1]
+
     # sanity check for arguments
     nf = [item for item in f if len(item) > maxlink]
     if not all(hasattr(i[0], "template") or hasattr(i[1], "template") for i in zip(nf, nf[1:])):
@@ -819,11 +831,19 @@ 
Source code for pydna.design
 

 [docs]
 def circular_assembly_fragments(f, overlap=35, maxlink=40):
-    fragments = assembly_fragments(f + f[0:1], overlap=overlap, maxlink=maxlink)
+    """
+    Equivalent to `assembly_fragments` with `circular=True`.
 
-    if hasattr(fragments[0], "template"):
-        fragments[0] = _pcr((fragments[-1].forward_primer, fragments[0].reverse_primer), fragments[0].template)
-    return fragments[:-1]

+    Deprecated, kept for backward compatibility. Use `assembly_fragments` with `circular=True` instead.
+    """
+    import warnings
+
+    warnings.warn(
+        "The circular_assembly_fragments function is deprecated. Use assembly_fragments with circular=True instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return assembly_fragments(f, overlap=overlap, maxlink=maxlink, circular=True)

 
 
 
diff --git a/_modules/pydna/dseq.html b/_modules/pydna/dseq.html
index 8f794e27..4ee6672a 100644
--- a/_modules/pydna/dseq.html
+++ b/_modules/pydna/dseq.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.dseq — pydna 0.0.0.post1+fd8577c documentation
+  pydna.dseq — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/dseqrecord.html b/_modules/pydna/dseqrecord.html
index ce8b71d9..263c4f44 100644
--- a/_modules/pydna/dseqrecord.html
+++ b/_modules/pydna/dseqrecord.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.dseqrecord — pydna 0.0.0.post1+fd8577c documentation
+  pydna.dseqrecord — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/editor.html b/_modules/pydna/editor.html
index 3043c604..a98daf47 100644
--- a/_modules/pydna/editor.html
+++ b/_modules/pydna/editor.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.editor — pydna 0.0.0.post1+fd8577c documentation
+  pydna.editor — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/gel.html b/_modules/pydna/gel.html
index 53f26420..ed1e7448 100644
--- a/_modules/pydna/gel.html
+++ b/_modules/pydna/gel.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.gel — pydna 0.0.0.post1+fd8577c documentation
+  pydna.gel — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/genbank.html b/_modules/pydna/genbank.html
index 4eaf17e8..b08cd9a0 100644
--- a/_modules/pydna/genbank.html
+++ b/_modules/pydna/genbank.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.genbank — pydna 0.0.0.post1+fd8577c documentation
+  pydna.genbank — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/genbankfile.html b/_modules/pydna/genbankfile.html
index 96f8d213..c212d7f1 100644
--- a/_modules/pydna/genbankfile.html
+++ b/_modules/pydna/genbankfile.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.genbankfile — pydna 0.0.0.post1+fd8577c documentation
+  pydna.genbankfile — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/genbankfixer.html b/_modules/pydna/genbankfixer.html
index e1ba0d6e..6510d1be 100644
--- a/_modules/pydna/genbankfixer.html
+++ b/_modules/pydna/genbankfixer.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.genbankfixer — pydna 0.0.0.post1+fd8577c documentation
+  pydna.genbankfixer — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/genbankrecord.html b/_modules/pydna/genbankrecord.html
index 3ab78165..ec64e2be 100644
--- a/_modules/pydna/genbankrecord.html
+++ b/_modules/pydna/genbankrecord.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.genbankrecord — pydna 0.0.0.post1+fd8577c documentation
+  pydna.genbankrecord — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/myprimers.html b/_modules/pydna/myprimers.html
index ff43082b..919ad0f9 100644
--- a/_modules/pydna/myprimers.html
+++ b/_modules/pydna/myprimers.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.myprimers — pydna 0.0.0.post1+fd8577c documentation
+  pydna.myprimers — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/parsers.html b/_modules/pydna/parsers.html
index 1304b79b..ea059e60 100644
--- a/_modules/pydna/parsers.html
+++ b/_modules/pydna/parsers.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.parsers — pydna 0.0.0.post1+fd8577c documentation
+  pydna.parsers — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/primer.html b/_modules/pydna/primer.html
index c027b265..09f9c495 100644
--- a/_modules/pydna/primer.html
+++ b/_modules/pydna/primer.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.primer — pydna 0.0.0.post1+fd8577c documentation
+  pydna.primer — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/readers.html b/_modules/pydna/readers.html
index 7e41d7fb..410d3b01 100644
--- a/_modules/pydna/readers.html
+++ b/_modules/pydna/readers.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.readers — pydna 0.0.0.post1+fd8577c documentation
+  pydna.readers — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/seqrecord.html b/_modules/pydna/seqrecord.html
index acee26e7..ac045348 100644
--- a/_modules/pydna/seqrecord.html
+++ b/_modules/pydna/seqrecord.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.seqrecord — pydna 0.0.0.post1+fd8577c documentation
+  pydna.seqrecord — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/threading_timer_decorator_exit.html b/_modules/pydna/threading_timer_decorator_exit.html
index b6f75702..dd2a36a6 100644
--- a/_modules/pydna/threading_timer_decorator_exit.html
+++ b/_modules/pydna/threading_timer_decorator_exit.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.threading_timer_decorator_exit — pydna 0.0.0.post1+fd8577c documentation
+  pydna.threading_timer_decorator_exit — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/tm.html b/_modules/pydna/tm.html
index 55e00fb3..a14ee6c9 100644
--- a/_modules/pydna/tm.html
+++ b/_modules/pydna/tm.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.tm — pydna 0.0.0.post1+fd8577c documentation
+  pydna.tm — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_modules/pydna/utils.html b/_modules/pydna/utils.html
index 133d11ed..967e287e 100644
--- a/_modules/pydna/utils.html
+++ b/_modules/pydna/utils.html
@@ -5,14 +5,14 @@
 
   
   
-  pydna.utils — pydna 0.0.0.post1+fd8577c documentation
+  pydna.utils — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/_static/assembly_fragment_slide_circular.png b/_static/assembly_fragment_slide_circular.png
new file mode 100644
index 00000000..fca398b6
Binary files /dev/null and b/_static/assembly_fragment_slide_circular.png differ
diff --git a/_static/assembly_fragment_slide_linear.png b/_static/assembly_fragment_slide_linear.png
new file mode 100644
index 00000000..a0091a08
Binary files /dev/null and b/_static/assembly_fragment_slide_linear.png differ
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
index 59078648..0a57c56b 100644
--- a/_static/documentation_options.js
+++ b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.0.0.post1+fd8577c',
+    VERSION: '0.0.0.post1+0f15ccd',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/genindex.html b/genindex.html
index b65dd0bb..c38815f4 100644
--- a/genindex.html
+++ b/genindex.html
@@ -5,14 +5,14 @@
 
   
   
-  Index — pydna 0.0.0.post1+fd8577c documentation
+  Index — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/index.html b/index.html
index 6a4a134c..d1ac1953 100644
--- a/index.html
+++ b/index.html
@@ -6,14 +6,14 @@
   
 
   
-  Welcome to pydna’s documentation! — pydna 0.0.0.post1+fd8577c documentation
+  Welcome to pydna’s documentation! — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
@@ -3150,7 +3150,7 @@ 
Examples of pydna in use
 

-pydna.design.assembly_fragments(f, overlap=35, maxlink=40)[source]

+pydna.design.assembly_fragments(f, overlap=35, maxlink=40, circular=False)[source]
 
This function return a list of pydna.amplicon.Amplicon objects where
 primers have been modified with tails so that the fragments can be fused in
 the order they appear in the list by for example Gibson assembly or homologous
@@ -3419,6 +3419,7 @@ 
Examples of pydna in usepydna.amplicon.Amplicon and other Dseqrecord like objects) – list Amplicon and Dseqrecord object for which fusion primers should be constructed.

 
  • overlap (int, optional) – Length of required overlap between fragments.
    • 
 
  • maxlink (int, optional) – Maximum length of spacer sequences that may be present in f. These will be included in tails for designed primers.
    • 
+
  • circular (bool, optional) – If True, the assembly is circular. If False, the assembly is linear.
    • 
 
 
    
 
    Returns:
    
@@ -3483,7 +3484,9 @@ 
    Examples of pydna in use
 
    
 pydna.design.circular_assembly_fragments(f, overlap=35, maxlink=40)[source]
    
-
    
+
    Equivalent to assembly_fragments with circular=True.
    
+
    Deprecated, kept for backward compatibility. Use assembly_fragments with circular=True instead.
    
+
    
 
 
 
    
diff --git a/py-modindex.html b/py-modindex.html
index cb839e21..c4aa904d 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -5,14 +5,14 @@
 
   
   
-  Python Module Index — pydna 0.0.0.post1+fd8577c documentation
+  Python Module Index — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
   
       
       
-      
+      
       
       
     
diff --git a/search.html b/search.html
index 2a0e5361..3d86d461 100644
--- a/search.html
+++ b/search.html
@@ -5,7 +5,7 @@
 
   
   
-  Search — pydna 0.0.0.post1+fd8577c documentation
+  Search — pydna 0.0.0.post1+0f15ccd documentation
       
       
 
@@ -13,7 +13,7 @@
     
       
       
-      
+      
       
       
     
diff --git a/searchindex.js b/searchindex.js
index 979729e4..5b463542 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"Examples of pydna in use": [[0, "examples-of-pydna-in-use"]], "How to get more help": [[0, "how-to-get-more-help"]], "How to use the documentation": [[0, "how-to-use-the-documentation"]], "Indices and tables": [[0, "indices-and-tables"]], "Module contents": [[0, "module-pydna"]], "Welcome to pydna\u2019s documentation!": [[0, null]], "pydna": [[0, "pydna"]], "pydna package layout": [[0, "pydna-package-layout"]], "pydna source code": [[0, "pydna-source-code"]], "pydna.amplicon module": [[0, "module-pydna.amplicon"]], "pydna.amplify module": [[0, "module-pydna.amplify"]], "pydna.assembly module": [[0, "module-pydna.assembly"]], "pydna.common_sub_strings module": [[0, "module-pydna.common_sub_strings"]], "pydna.contig module": [[0, "module-pydna.contig"]], "pydna.design module": [[0, "module-pydna.design"]], "pydna.download module": [[0, "module-pydna.download"]], "pydna.dseq module": [[0, "module-pydna.dseq"]], "pydna.dseqrecord module": [[0, "module-pydna.dseqrecord"]], "pydna.editor module": [[0, "module-pydna.editor"]], "pydna.gel module": [[0, "module-pydna.gel"]], "pydna.genbank module": [[0, "module-pydna.genbank"]], "pydna.genbankfile module": [[0, "module-pydna.genbankfile"]], "pydna.genbankfixer module": [[0, "module-pydna.genbankfixer"]], "pydna.genbankrecord module": [[0, "module-pydna.genbankrecord"]], "pydna.myprimers module": [[0, "module-pydna.myprimers"]], "pydna.parsers module": [[0, "module-pydna.parsers"]], "pydna.primer module": [[0, "module-pydna.primer"]], "pydna.readers module": [[0, "module-pydna.readers"]], "pydna.seqrecord module": [[0, "module-pydna.seqrecord"]], "pydna.tm module": [[0, "module-pydna.tm"]], "pydna.utils module": [[0, "module-pydna.utils"]]}, "docnames": ["index"], "envversion": {"sphinx": 63, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 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