Working

.gitignore

@@ -8,3 +8,11 @@ tests/tneedlemanWunsch
 tests/test_utils
 
 tests/test_deBruijn
+
+src/bionim/utils
+
+src/bionim/smithWaterman
+
+src/bionim/deBruijn
+
+tests/test_needlemanWunsch

README.md

@@ -19,19 +19,6 @@ To run test just run `nimble test` in the bionim directory
 
 
 Currently implemented alogrithms and data structures
-# Alignment
-Algorithms and data structures usefull in the alignment of genomic and protein based sequences.
- ## Algorithms
- * [Needleman-Wunsch](https://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm "Wikipedia page of the Needleman-Wunsch algorithm") Basic algorithm used for global alignment
- * [Smith-Waterman](https://en.wikipedia.org/wiki/Smith-Waterman_algorithm) Basic algorithm used for local alignment.
-
-# Phylogenetics
- * Fitch's algorithm for constructing phylogenetic trees from aligned sequences.
-
-# Assembly
- * DeBruijn Graph building
-
-# Credits
 In this section are all packages listed on which bionim depends and which were not created by me.
  * [PhylogeNi](https://github.com/kerrycobb/PhylogeNi) A library for working with phylogenetic trees
 
@@ -42,11 +29,3 @@ Also I am always happy if someone suggest code improvements and stuff like that.
 # Contact 
 If you have any questions or just want to contact me regarding this package. Please write to
 [email protected]
-# Todo
-## Parsing
- * FASTA and FASTQ parsing
-## Alignment
- * Calculation of all possible optimal alignment for Needleman-Wunsch
- * Usage of similiarity matrices in Needleman-Wunsch
-     * Customizable gap penalties for Needleman-Wunsch
-## Minimum skew problem

bionim.nimble

@@ -5,10 +5,9 @@ author        = "Thomas Dost"
 description   = "A collection of useful algorithms and data structures for bioinformatics"
 license       = "MIT"
 srcDir        = "src"
-binDir        = "bin"
 installExt    = @["nim"]
 
 
 # Dependencies
 
-requires "nim >= 1.4.4", "phylogeni >= 0.0.2", "bio_seq >= 0.0.5"
+requires "nim >= 1.4.4", "phylogeni >= 0.0.2", "bio_seq >= 0.0.7"

src/bionim.nim

@@ -1,6 +1,3 @@
-import src/needlemanWunsch
-import src/smithWaterman
-import src/utils
-import src/deBruijn
+import bionim/utils
 import phylogeni