From d34242c6b7a79ab1b09b3cb5021b04927a3ddef3 Mon Sep 17 00:00:00 2001 From: HenrikBengtsson Date: Fri, 1 Mar 2024 07:43:18 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20seguid/s?= =?UTF-8?q?eguid-python@abc745cf72b76f813735ce8518646df08da7e6dc=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- _modules/index.html | 5 +- _modules/seguid/chksum.html | 41 +++--- _modules/seguid/config.html | 2 +- _modules/seguid/reprutils.html | 2 +- genindex.html | 102 +++----------- index.html | 246 +++++++++++++++------------------ objects.inv | Bin 445 -> 369 bytes py-modindex.html | 15 -- searchindex.js | 2 +- 9 files changed, 158 insertions(+), 257 deletions(-) diff --git a/_modules/index.html b/_modules/index.html index d8b8703..b8f91fa 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -30,12 +30,9 @@

All modules for which code is available

-
diff --git a/_modules/seguid/chksum.html b/_modules/seguid/chksum.html index 74a10b0..7519899 100644 --- a/_modules/seguid/chksum.html +++ b/_modules/seguid/chksum.html @@ -53,13 +53,13 @@

Source code for seguid.chksum

 import hashlib
 import base64
 
-from seguid.manip import reverse
-from seguid.manip import rotate
-from seguid.manip import rotate_to_min
+from seguid._manip import reverse
+from seguid._manip import rotate
+from seguid._manip import rotate_to_min
 
-from seguid.tables import tablefactory
-from seguid.asserts import assert_in_alphabet
-from seguid.asserts import assert_complementary
+from seguid._tables import tablefactory
+from seguid._asserts import assert_in_alphabet
+from seguid._asserts import assert_complementary
 
 seguid_prefix: str = "seguid="
 lsseguid_prefix: str = "lsseguid="
@@ -183,9 +183,6 @@ 
Source code for seguid.chksum
 
     Only defined for circular sequences.
 
-    The srfun argument has to take a string as an argument and
-    return another string.
-
     The checksum is prefixed with "csseguid="
 
     Examples
@@ -217,35 +214,35 @@ 
Source code for seguid.chksum
     r"""SEGUID checksum for double stranded linear DNA (ldSEGUID).
 
     Calculates the ldSEGUID checksum for a dsDNA sequence defined by two
-    strings representing the upper (Watson) and lower (Crick) strand
-    complementary DNA strands and an integer value describing the stagger
-    between the two strands in the 5' (left) end of the molecule.
+    strings representing the upper (Watson) and the complementary (Crick) DNA strands.
+    Optional ssDNA regions in the ends are indicated by a dash "-" in eather strand.
+    Watson and Crick strands are always equal in length.
 
-    The algorithm first selects the lexicographically smallest
-    of the top or bottom strands.
+    The algorithm first selects the lexicographically smallest of the Watson and Crick strands.
 
-    The two string are joined, separated by a line break (ASCII 10) and the
-    lsSEGUID function is used on the resulting string.
+    The two string are joined 5'-3', separated by a semicolon ";" and the lsSEGUID function
+    is used on the resulting string.
 
     ::
+
         dsDNA    ldSEGUID
 
-        -TATGCC  Jv9Z9JJ0IYnG-dTPBGwhDyAqnmU
+        -TATGCC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I
          |||||
         CATACG-
 
-        -GCATAC  Jv9Z9JJ0IYnG-dTPBGwhDyAqnmU
+        -GCATAC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I
          |||||
         CCGTAT-
 
-    For the linear dsDNA sequence defined by watson = "-TATGCC", crick ="-gcatac"
-    (see figures above), The "-gcatac" strand is selected as
-    "-gcatac" < "-TATGCC".
+    For the linear dsDNA sequence defined by watson = "-TATGCC", crick ="-GCATAC"
+    (see figures above), The "-GCATAC" strand is selected since lexicographically,
+    "-GCATAC" < "-TATGCC".
 
     A string is constructed like so:
     ::
 
-        "-gcatac" + chr(10) + "CCGTAT-"
+        "-GCATAC" + ";" + "-TATGCC"
 
     The checksum is prefixed with "ldseguid="
 
diff --git a/_modules/seguid/config.html b/_modules/seguid/config.html
index e03133b..0284fac 100644
--- a/_modules/seguid/config.html
+++ b/_modules/seguid/config.html
@@ -34,7 +34,7 @@ 
Source code for seguid.config
 # -*- coding: utf-8 -*-
 
 import warnings
-from seguid.manip import min_rotation_py
+from seguid._manip import min_rotation_py
 
 ## The min_rotation() function
 _min_rotation = min_rotation_py
diff --git a/_modules/seguid/reprutils.html b/_modules/seguid/reprutils.html
index 46b9dd9..3df0f00 100644
--- a/_modules/seguid/reprutils.html
+++ b/_modules/seguid/reprutils.html
@@ -30,7 +30,7 @@
           

             
   
Source code for seguid.reprutils
-from seguid.manip import reverse
+from seguid._manip import reverse
 import re
 
 
diff --git a/genindex.html b/genindex.html
index 7b8befb..ea63aae 100644
--- a/genindex.html
+++ b/genindex.html
@@ -33,41 +33,32 @@
 
Index

 
 

- A
- | C
+ C
  | E
  | I
  | L
  | M
  | P
- | R
  | S
- | T
  
 

-
A

-
-  
-  
-

-
 
C

 

   
   
 

 
@@ -90,37 +81,37 @@ 
I

 
L

 

   
   
 

 
 
M

 
@@ -134,24 +125,6 @@ 
P

   
   
 

 
-
R

-
-  
-  
-

-
 
S

 

   
   
 

 
-
T

-
-  
-

-
 
 
           

diff --git a/index.html b/index.html
index 2d23fc4..0eac241 100644
--- a/index.html
+++ b/index.html
@@ -32,30 +32,9 @@
             
   

 
seguid package

-

-
Submodules

-

-

-seguid.asserts.assert_in_alphabet(seq: str, alphabet: set)[source]

-

-
-

-

-seguid.asserts.assert_alphabet(alphabet: dict)[source]

-

-
-

-

-seguid.asserts.reverse(seq) → str[source]

-
Reverses a DNA sequence

-

-
-

-

-seguid.asserts.assert_complementary(watson: str, crick: str, alphabet: dict)[source]

-

-
-
seguid.

+

+
Submodules

+
seguid.

 
The seguid module provides four functions for calculations of SEGUID checksums
 for biological sequences with varying topologies

 
lsseguid (l)inear   (s)ingle-stranded SEGUID
@@ -121,8 +100,6 @@ 
seguid packageExamples

 
>>> csseguid("ATTT")
@@ -142,32 +119,28 @@ 
seguid packageseguid.chksum.ldseguid(watson: str, crick: str, alphabet: str = '{DNA}', form: str = 'long') → str[source]
 
SEGUID checksum for double stranded linear DNA (ldSEGUID).

 
Calculates the ldSEGUID checksum for a dsDNA sequence defined by two
-strings representing the upper (Watson) and lower (Crick) strand
-complementary DNA strands and an integer value describing the stagger
-between the two strands in the 5’ (left) end of the molecule.

-
The algorithm first selects the lexicographically smallest
-of the top or bottom strands.

-
The two string are joined, separated by a line break (ASCII 10) and the
-lsSEGUID function is used on the resulting string.

-

-
::
dsDNA    ldSEGUID

-

-
-TATGCC

-

-

-
CATACG-

-

-
-GCATAC

-

-

-
CCGTAT-

-

-

-
For the linear dsDNA sequence defined by watson = “-TATGCC”, crick =”-gcatac”
-(see figures above), The “-gcatac” strand is selected as
-“-gcatac” < “-TATGCC”.

+strings representing the upper (Watson) and the complementary (Crick) DNA strands.
+Optional ssDNA regions in the ends are indicated by a dash “-” in eather strand.
+Watson and Crick strands are always equal in length.

+
The algorithm first selects the lexicographically smallest of the Watson and Crick strands.

+
The two string are joined 5’-3’, separated by a semicolon “;” and the lsSEGUID function
+is used on the resulting string.

+
dsDNA    ldSEGUID
+
+-TATGCC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I
+ |||||
+CATACG-
+
+-GCATAC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I
+ |||||
+CCGTAT-
+

+

+
For the linear dsDNA sequence defined by watson = “-TATGCC”, crick =”-GCATAC”
+(see figures above), The “-GCATAC” strand is selected since lexicographically,
+“-GCATAC” < “-TATGCC”.

 
A string is constructed like so:

-
"-gcatac" + chr(10) + "CCGTAT-"
+
"-GCATAC" + ";" + "-TATGCC"
 

 

 
The checksum is prefixed with “ldseguid=”

@@ -195,84 +168,6 @@ 
seguid packageseguid.config.set_min_rotation(which)[source]
 

 
-

-

-seguid.manip.rotate(seq: str, amount: int = 0) → str[source]

-
Rotates a circular, DNA sequence a certain amount.

-
Rotates sequence ‘seq’, ‘amount’ number of symbols to the right.
-A rotation ‘amount’ is the same as a rotation ‘amount + n * len(seq)’
-for any integer ‘n’.

-
Returns the rotated sequence as a string of length ‘len(seq)’.

-
Examples

-
>>> seq = "ABCDEFGH"
->>> rotate(seq, 0)
-'ABCDEFGH'
-

-

-
>>> rotate(seq, +1)
-'BCDEFGHA'
-

-

-
>>> rotate(seq, +7)
-'HABCDEFG'
-

-

-
>>> rotate(seq, -1)
-'HABCDEFG'
-

-

-
>>> rotate(seq, +8)
-'ABCDEFGH'
-

-

-

-
-

-

-seguid.manip.reverse(seq) → str[source]

-
Reverses a DNA sequence

-

-
-

-

-seguid.manip.min_rotation_py(s: str) → int[source]

-
Start position for the smallest rotation of a string s (pure Python).

-
Algorithm described in:

-
Pierre Duval, Jean. 1983. Factorizing Words
-over an Ordered Alphabet. Journal of Algorithms & Computational Technology
-4 (4) (December 1): 363–381. and Algorithms on strings and sequences based
-on Lyndon words, David Eppstein 2011.
-https://gist.github.com/dvberkel/1950267

-
This is a pure python implementation, considerably slower than the
-min_rotation function from pydivsufsort that is imported at the top of
-this script.

-
Should only be used if pydivsufsort.min_rotation can not be used.

-
Note that both functions are case-sensitive and sorts by ASCII-code order
-or “ASCIIbetical” order so:

-
    
-
  • Uppercase come before lowercase letters; for example, “Z” precedes “a”
    • 
-
  • Digits and several punctuation marks come before letters.
    • 
-

-
See the last two examples below for an example of the consequences of this.

-
Examples

-
>>> min_rotation_py("TAAA")
-1
->>> "TAAA"[1:] + "TAAA"[:1]
-'AAAT'
->>> s = "ACAACAAACAACACAAACAAACACAAC"
->>> min_rotation_py(s)
-14
->>> s[14:] + s[:14]
-'AAACAAACACAACACAACAAACAACAC'
-

-

-

-
-

-

-seguid.manip.rotate_to_min(s: str) → int[source]

-

-
 

 

 seguid.reprutils.is_staggered(watson, crick)[source]

@@ -289,14 +184,97 @@ 
seguid package

-

-seguid.tables.tablefactory(argument: str)[source]

-

-
 

 

 
Module contents

+

+

+seguid.lsseguid(seq: str, alphabet: str = '{DNA}', form: str = 'long') → str[source]

+
SEGUID checksum for single stranded linear DNA (slSEGUID).

+
Identical to the seguid function except for that the ‘+’ and ‘/’ characters
+of standard Base64 encoding are replaced by ‘-’ and ‘_’, respectively
+following the standard in RFC 4648 section 5.

+
The base64.urlsafe_b64encode from the Python standard libary is used.

+
This checksum is applicable to single stranded linear DNA sequences.
+Can also be used for protein sequences.

+
The checksum is prefixed with “lsseguid=”

+
Examples

+
>>> lsseguid("AT")
+'lsseguid=Ax_RG6hzSrMEEWoCO1IWMGska-4'
+

+

+

+
+

+

+seguid.csseguid(seq: str, alphabet: str = '{DNA}', form: str = 'long') → str[source]

+
SEGUID checksum for single stranded circular DNA (csSEGUID).

+
The csSEGUID is the lsSEGUID checksum calculated for the lexicographically
+smallest string rotation of a ssDNA sequence.

+
Only defined for circular sequences.

+
The checksum is prefixed with “csseguid=”

+
Examples

+
>>> csseguid("ATTT")
+'csseguid=ot6JPLeAeMmfztW1736Kc6DAqlo'
+>>> lsseguid("ATTT")
+'lsseguid=ot6JPLeAeMmfztW1736Kc6DAqlo'
+>>> csseguid("TTTA")
+'csseguid=ot6JPLeAeMmfztW1736Kc6DAqlo'
+>>> lsseguid("TTTA")
+'lsseguid=8zCvKwyQAEsbPtC4yTV-pY0H93Q'
+

+

+

+
+

+

+seguid.ldseguid(watson: str, crick: str, alphabet: str = '{DNA}', form: str = 'long') → str[source]

+
SEGUID checksum for double stranded linear DNA (ldSEGUID).

+
Calculates the ldSEGUID checksum for a dsDNA sequence defined by two
+strings representing the upper (Watson) and the complementary (Crick) DNA strands.
+Optional ssDNA regions in the ends are indicated by a dash “-” in eather strand.
+Watson and Crick strands are always equal in length.

+
The algorithm first selects the lexicographically smallest of the Watson and Crick strands.

+
The two string are joined 5’-3’, separated by a semicolon “;” and the lsSEGUID function
+is used on the resulting string.

+
dsDNA    ldSEGUID
+
+-TATGCC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I
+ |||||
+CATACG-
+
+-GCATAC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I
+ |||||
+CCGTAT-
+

+

+
For the linear dsDNA sequence defined by watson = “-TATGCC”, crick =”-GCATAC”
+(see figures above), The “-GCATAC” strand is selected since lexicographically,
+“-GCATAC” < “-TATGCC”.

+
A string is constructed like so:

+
"-GCATAC" + ";" + "-TATGCC"
+

+

+
The checksum is prefixed with “ldseguid=”

+
Examples

+
>>> ldseguid("-TATGCC", "-GCATAC")
+'ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I'
+>>> ldseguid("-GCATAC", "-TATGCC")
+'ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I'
+

+

+

+
+

+

+seguid.cdseguid(watson: str, crick: str, alphabet: str = '{DNA}', form: str = 'long') → str[source]

+
SEGUID checksum for double stranded circular DNA (dcSEGUID).

+
The dcSEGUID is the slSEGUID checksum calculated for the lexicographically
+smallest string rotation of a dsDNA sequence. Only defined for circular
+sequences.

+
The checksum is prefixed with “cdseguid=”

+

+
 

 

 
diff --git a/objects.inv b/objects.inv
index bd1460acc9ee773669f490875e783a682eedcc93..d9b1e637abb041eefc21ba228cc48986131bf499 100644
GIT binary patch
delta 260
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z8qBkPPX-gz&X^rJW=Bp7;p|1LhQ_jfNr=Ow?GRk#+5f4mmVHy2x@syZpbsf(L(gA*
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zr_oC?!L$9^;(t~K7cDsOB+|6S!1!(X3BDj9R55ZmPython Module Index
        
        seguid
        
-     
-       
-          
-       seguid.asserts
-       
      
        
           
@@ -64,21 +59,11 @@ 
Python Module Index

           
        seguid.config
        
-     
-       
-          
-       seguid.manip
-       
      
        
           
        seguid.reprutils
        
-     
-       
-          
-       seguid.tables
-       
    
 
 
diff --git a/searchindex.js b/searchindex.js
index 09f3a0e..0754a66 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["index"], "filenames": ["index.rst"], "titles": ["seguid package"], "terms": {"assert": 0, "assert_in_alphabet": 0, "seq": 0, "str": 0, "alphabet": 0, "set": 0, "sourc": 0, "assert_alphabet": 0, "dict": 0, "revers": 0, "dna": 0, "sequenc": 0, "assert_complementari": 0, "watson": 0, "crick": 0, "The": 0, "provid": 0, "four": 0, "function": 0, "calcul": 0, "checksum": 0, "biolog": 0, "vari": 0, "topologi": 0, "lsseguid": 0, "l": 0, "inear": 0, "": 0, "ingl": 0, "strand": 0, "csseguid": 0, "c": 0, "ircular": 0, "ldseguid": 0, "d": 0, "oubl": 0, "sguid": 0, "cdseguid": 0, "some": 0, "auxillari": 0, "ar": 0, "also": 0, "can": 0, "made": 0, "work": 0, "without": 0, "extern": 0, "depend": 0, "consider": 0, "faster": 0, "pydivsufsort": 0, "instal": 0, "chksum": 0, "form": 0, "long": 0, "protein": 0, "singl": 0, "linear": 0, "obsolet": 0, "us": 0, "instead": 0, "given": 0, "nucleotid": 0, "amino": 0, "acid": 0, "return": 0, "string": 0, "contain": 0, "global": 0, "uniqu": 0, "identifi": 0, "option": 0, "encod": 0, "argument": 0, "expect": 0, "accept": 0, "byte": 0, "an": 0, "anoth": 0, "sever": 0, "avail": 0, "from": 0, "standard": 0, "librari": 0, "http": 0, "doc": 0, "python": 0, "org": 0, "3": 0, "base64": 0, "html": 0, "i": 0, "defin": 0, "sha1": 0, "upercas": 0, "trail": 0, "charact": 0, "remov": 0, "thi": 0, "mean": 0, "upper": 0, "lower": 0, "case": 0, "symbol": 0, "do": 0, "affect": 0, "result": 0, "url": 0, "safe": 0, "potenti": 0, "produc": 0, "carri": 0, "special": 0, "uniform": 0, "resourc": 0, "locat": 0, "It": 0, "variabl": 0, "name": 0, "program": 0, "languang": 0, "implement": 0, "follow": 0, "origin": 0, "definit": 0, "babnigg": 0, "et": 0, "al": 0, "2006": 0, "For": 0, "more": 0, "inform": 0, "g": 0, "giometti": 0, "A": 0, "databas": 0, "proteom": 0, "studi": 0, "6": 0, "16": 0, "4514": 0, "4522": 0, "doi": 0, "10": 0, "1002": 0, "pmic": 0, "200600032": 0, "prefix": 0, "exampl": 0, "AT": 0, "ax": 0, "rg6hzsrmeewoco1iwmgska": 0, "4": 0, "slseguid": 0, "ident": 0, "except": 0, "replac": 0, "_": 0, "respect": 0, "rfc": 0, "4648": 0, "section": 0, "5": 0, "urlsafe_b64encod": 0, "libari": 0, "applic": 0, "ax_rg6hzsrmeewoco1iwmgska": 0, "circular": 0, "lexicograph": 0, "smallest": 0, "rotat": 0, "ssdna": 0, "onli": 0, "srfun": 0, "ha": 0, "take": 0, "attt": 0, "ot6jpleaemmfztw1736kc6daqlo": 0, "ttta": 0, "8zcvkwyqaesbptc4ytv": 0, "py0h93q": 0, "doubl": 0, "dsdna": 0, "two": 0, "repres": 0, "complementari": 0, "integ": 0, "valu": 0, "describ": 0, "stagger": 0, "between": 0, "left": 0, "end": 0, "molecul": 0, "algorithm": 0, "first": 0, "select": 0, "top": 0, "bottom": 0, "join": 0, "separ": 0, "line": 0, "break": 0, "ascii": 0, "t": 0, "atgcc": 0, "catacg": 0, "catac": 0, "ccgtat": 0, "tatgcc": 0, "gcatac": 0, "see": 0, "figur": 0, "abov": 0, "construct": 0, "like": 0, "so": 0, "chr": 0, "rr65d6ayup": 0, "cdmavmdw3l9fpt6i": 0, "dcseguid": 0, "config": 0, "set_min_rot": 0, "which": 0, "manip": 0, "amount": 0, 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