#81 Major: moved www-data/dnadata/ to /results/.

.gitignore

@@ -7,8 +7,7 @@ env/
 env365/
 install_test/
 release/
-www-data/to_process
-www-data/dnadata
+DDV/results/
 release.bat
 scraps/
 env_fresh/

DDV/AnnotatedAlignment.py

@@ -160,7 +160,7 @@ def markup_annotation_differences(self):
 
 if __name__ == '__main__':
     output_name = 'hg38_panTro4_annotated_'
-    base_path = os.path.join('.', 'www-data', 'dnadata', output_name)
+    base_path = os.path.join('.', 'results', output_name)
     chimp_annotation = r'data\PanTro_refseq2.1.4_genes.gtf'
     human_anno = r'data\Hg38_genes.gtf'
     aligner = AnnotatedAlignment('hg38ToPanTro4.over.chain', 'hg38.fa', human_anno, 'panTro4.fa', chimp_annotation, base_path)

DDV/DDVUtils.py

@@ -104,7 +104,7 @@ def execution_dir():
 
 def base_directories(output_name):
     BASE_DIR = execution_dir()
-    SERVER_HOME = os.path.join(BASE_DIR, 'www-data', 'dnadata')
+    SERVER_HOME = os.path.join(BASE_DIR, 'results')
     base_path = os.path.join(SERVER_HOME, output_name) if output_name else SERVER_HOME
     return SERVER_HOME, base_path
 

DDV/Ideogram.py

@@ -214,7 +214,7 @@ def process_file(self, input_file_path, output_folder, output_file_name,
     #     self.palette['T'] = hex_to_rgb('A19E3D')  # light green
     #     self.palette['A'] = hex_to_rgb('6D772F')  # Dark Green
 
-    def draw_nucleotides(self):
+    def draw_nucleotides(self, verbose=True):
         # points_file_name = os.path.join(self.final_output_location, "test_ideogram_points.txt")
         # points_file = None # open(points_file_name, 'w')
         # if points_file:
@@ -293,18 +293,6 @@ def increment(digits, radices, place):
 
 
 if __name__ == "__main__":
-    # layout = Ideogram([3,3,3,63], [5,5,3,3,21])
-    # layout.process_file("example_data/hg38_chr19_sample.fa", 'www-data/dnadata/test ideogram', 'ideogram-padding2')
-
-    # layout = Ideogram([3,3,3,63], [5,5,3,3,21], 2, 2)
-    # layout.process_file("example_data/hg38_chr19_sample.fa", 'www-data/dnadata/test ideogram', 'ideogram-sparse')
-    # layout = Ideogram(([5,5,5,5,11],  # thick, local
-    #                    [5,5,5,5,5 ,53], 1, 1))
-    ## thin layout layout = Ideogram([3,3,3,3,3,27], [3,3,3,3,3,3 ,53], 1, 1)
-    #                               ([5,5,5,5,5,27], [3,3,3,3,3,3 ,53], 1, 1)
-    # 3*3*3*3*3*27*
-    # 3*3*3*3*3 = 1,594,323 bp per fiber row
-
     radix_settings = eval(sys.argv[2])
     assert len(radix_settings) == 4 and \
             type(radix_settings[0]) == type(radix_settings[1]) == type([]) and \

README.md

@@ -15,9 +15,12 @@ You can start using FluentDNA:
  1. Downloading and unzipping the [Latest Release](https://github.com/josiahseaman/FluentDNA/releases) (Mac and Windows only).
  2. Open a terminal (command line) in the same folder you unzipped FluentDNA.
  3. Run the command `./fluentdna --fasta="DDV/example_data/Human selenoproteins.fa" --runserver`
- 4. Once your private server has started, all your results available at [http://127.0.0.1:8000](http://127.0.0.1:8000).  Note that this server is not actually using the internet at all, it's just using your browser as a file viewer.
-
-To use FluentDNA as a python module (required for Linux), follow the [pip install instructions](https://github.com/josiahseaman/FluentDNA/blob/python-master/docs/installation.md).
+ 4. Your result files will be placed in the FluentDNA directory `DDV/results/`.  Once your private server has started, 
+ all your results are viewable at [http://localhost:8000](http://127.0.0.1:8000).  
+
+To use FluentDNA as a python module (required for Linux), follow the [pip install instructions](https://github.com/josiahseaman/FluentDNA/blob/python-master/docs/installation.md).  
+**Locating Results:** You will need to be using the same computer the server is running on.  The server will not be visible 
+over network or internet unless your administrator opens the port.  
 
 ***
 
@@ -45,7 +48,7 @@ This generates an image pyramid with the standard legend (insert image of legend
 * FA File: [DDV/example_data/hg38_chr19_sample.fa](https://github.com/josiahseaman/FluentDNA/blob/python-master/DDV/example_data/hg38_chr19_sample.fa)
 
 **Result:** [Hg38 chr19 sample](https://dnaskittle.com/ddvresults/dnadata/Test%20Simple/)
-![Example FluentDNA output of Human Chr19 2MBp](https://dnaskittle.com/ddvresults/dnadata/Test%20Simple/Test%20Simple.png)
+![Example FluentDNA output of Human Chr19 2MBp](https://dnaskittle.com/ddvresults/dnadata/Test%20Simple/sources/Test%20Simple.png)
 
 It is also possible to generate an image file only that can be accessed with an image viewer using `--no_webpage`.
 

setup.py

@@ -5,11 +5,11 @@
 setup(
     name='DDV',
     version=VERSION,
-    description='Visualization tool for fasta files.  Supports whole genome alignment and multiple sequence alignment.',
+    description='Visualization tool for bare fasta files.  Supports whole genome alignment and multiple sequence alignment.',
     author='Josiah Seaman, Bryan Hurst',
     author_email='josiah.seaman@gmail.com',
     license='BSD',
-    packages=find_packages(exclude=('build', 'obj', 'www-data')),
+    packages=find_packages(exclude=('build', 'obj', 'results')),
     include_package_data=True,
     package_data={'DDV': ['html_template/*', 'example_data/*',
                           'html_template/img/*', 'example_data/alignments/*',]},
@@ -31,7 +31,7 @@
     zip_safe=False,
     url='https://github.com/josiahseaman/FluentDNA',
     download_url='https://github.com/josiahseaman/FluentDNA',  # TODO: post a tarball
-    keywords=['bioinformatics', 'dna', 'fasta', 'chain', 'alignment'],
+    keywords=['bioinformatics', 'dna', 'fasta', 'chain', 'alignment', 'species diversity'],
     classifiers=[
         'Development Status :: 4 - Beta',  # 5 - Production/Stable
         'Intended Audience :: Developers',