smoothing out

README.md

@@ -12,7 +12,49 @@ cd ~/circos-py
 python make_circos_plots.py example_input_data.csv
 ```
 
-## Install Circos-Py
+## Install
+### Quick-Guide
+Just a quick gerneral guide for Mac users: if you do not actively use Python, Perl, or Circos already I would recommend installing [Anaconda3](https://www.anaconda.com/download/), then installing Perl via conda:
+
+```
+conda install -c anaconda perl
+```
+
+Then install [Circos](http://circos.ca/software/download/), unzip, and symlink to usr/local/bin:
+
+```
+cd ~/Desktop
+wget http://circos.ca/distribution/circos-0.69-6.tgz
+tar xvfz circos-0.69-6.tgz
+ln -s ~/Desktop/circos-0.69-6/bin/circos /usr/local/bin/circos
+```
+
+You should now be able to run circos from the command line.  Check this by running the following from the terminal:
+
+`$ circos -v`
+
+And you should see something similar to:
+
+`circos | v 0.69-6 | 31 July 2017 | Perl 5.022000`
+
+Now it's time to check what Perl modules are needed to run Circos: `circos -module`
+
+A list of modules should sputter forth.  Use the below snippet to install all Circos Perl modules with CPAN:
+
+```
+cpan Carp Clone Config::General Cwd Data::Dumper Digest::MD5 File::Basename File::Spec::Functions File::Temp FindBin Font::TTF::Font GD GF::Polyline Getopt::Long IO::File List::MoreUtils List::Util Math::Bezier Math::BigFloat Math::Round Math::VecStat Memoize POSIX Params::Validate Pod::Usage Readonly Regexp::Common SVG Set::IntSpan Statistics::Basic Storable Sys::Hostname Text::Balanced Text::Format Time::HiRes
+```
+
+Last thing is to clone this repository:
+
+```
+git clone [email protected]:greenkidneybean/circos-py.git
+```
+
+### Circos
+Unfortunately Circos takes a bit of effort to get up and running.  If you're on a Mac I'd recommend [installing via Homebrew](http://circos.ca/tutorials/lessons/configuration/distribution_and_installation/).  
+### Circos-Py
+
 
 ## Setup
 ### Add Circos Binary to Your Shell Path

circos.py

@@ -200,13 +200,14 @@ def generate_circos_links(input_dataframe, spec_dict):
     final_links=final_links.rename(columns={'circos_time':'#ciros_time'})
 
     # write link files
+    # this can be changed
     final_links.to_csv(f'links_{output_file_name}.txt', sep='\t', index=False, header=True)
 
     # this is dangerous because it will layer the links.txt with each iteration
-    if os.path.isfile('links.txt') is False:
-        final_links.to_csv('links.txt', sep='\t', index=False, header=True)
+    if os.path.isfile('links_all-data.txt') is False:
+        final_links.to_csv('links_all-data.txt', sep='\t', index=False, header=True)
     else:
-        with open('links.txt', 'a') as f:
+        with open('links_all-data.txt', 'a') as f:
             final_links.to_csv(f, sep='\t', index=False)
 
     return final_links

circos_conf/circos.conf

@@ -133,7 +133,7 @@ format         = %d
 <links>
 
 <link>
-file          = links.txt
+file          = links_all-data.txt
 ribbon        = yes
 flat = yes
 radius        = .99r

circos_conf/circos_h7.conf

@@ -132,7 +132,7 @@ format         = %d
 <links>
 
 <link>
-file          = links_h7.txt
+file          = links_spec_1.txt
 ribbon        = yes
 flat = yes
 radius        = .99r

circos_conf/circos_stem.conf

@@ -132,7 +132,7 @@ format         = %d
 <links>
 
 <link>
-file          = links_stem.txt
+file          = links_spec_2.txt
 ribbon        = yes
 flat = yes
 radius        = .99r

make_circos_plots.py

@@ -12,7 +12,6 @@
 
 '''
 TODO:
-dump all images into generated project folder
 better names for files
 handle .csv and .xls file input
 easily replicate environment (Docker?)
@@ -21,6 +20,8 @@
 function to make file paths
 option for all images or specific color layer
 specify full path to project folder if saving somewhere else
+run circos and specify links file rather than specific circos.conf?
+run circos once if current_spec is "all-data"
 '''
 
 # imports may not be necessary with the circos module imported
@@ -42,19 +43,19 @@
 args = parser.parse_args()
 
 # setup sample dictionaries
+# includes circos.conf files to be used (call different link files)
 
-all_spec_dict = {'output_file_name':'h7-stem',
+all_spec_dict = {'output_file_name':'all-data',
                  'circos_conf_file':'circos.conf'}
-h7_spec_dict = {'output_file_name':'h7',
-                'spec_list':['H7 sp', 'spec_2'],
+spec_dict_1 = {'output_file_name':'spec_1',
+                'spec_list':['H7 sp', 'spec_1'], # feature #1 in "spec" column
                 'color':'red_orange',
                 'circos_conf_file':'circos_h7.conf'}
-stem_spec_dict = {'output_file_name':'stem',
-                  'spec_list':['H7 dp', 'spec_1'],
+spec_dict_2 = {'output_file_name':'spec_2',
+                  'spec_list':['H7 dp', 'spec_2'], # feature #2 in "spec" column
                   'color':'blue',
                   'circos_conf_file':'circos_stem.conf'}
-dict_list = [all_spec_dict, h7_spec_dict, stem_spec_dict]
-
+dict_list = [all_spec_dict, spec_dict_1, spec_dict_2]
 
 # assign variables
 input_file = args.input_excel
@@ -72,6 +73,8 @@
 os.makedirs(input_files_folder, exist_ok=True)
 os.makedirs(samples_dir, exist_ok=True)
 
+### run a test to check for .csv or .xlsx file and generate sheet
+
 # identify all sheets in Excel input file
 x1 = pd.ExcelFile(input_file)
 sheets = x1.sheet_names
@@ -111,11 +114,11 @@
         os.chdir(sample_dir)
         # make directories
         img_fld = sample_image_dir + '/' + i['output_file_name']
-        current_folder_name = i['output_file_name']
-        os.makedirs(current_folder_name, exist_ok=True)
+        current_spec = i['output_file_name']
+        os.makedirs(current_spec, exist_ok=True)
         os.makedirs(img_fld, exist_ok=True)
         # go to directory
-        os.chdir(current_folder_name)
+        os.chdir(current_spec)
         # make circos files
         #df = circos_input_file(sample_input_file, i) # spits out sorted file
         df = format_dataframe(start_df, i)
@@ -124,17 +127,21 @@
         for a in dict_list[1:]:
             generate_circos_links(df, a)
 
-    # run circos
+        # run circos
         for i in dict_list:
-            circos_conf = circos_conf_dir + '/' + i['circos_conf_file']
-            circos_plot_name = sample_id + '_' + i['output_file_name']
+            #circos_conf = circos_conf_dir + '/' + i['circos_conf_file']
+            current_circos_spec =  i['output_file_name']
+            circos_conf = f'{circos_conf_dir}/circos.conf'
+            circos_plot_name = f'{sample_id}_{current_circos_spec}'
+
+            link_file=f'links_{current_circos_spec}.txt'
             print()
             print('---')
             print('Running Circos')
             print(f'Circos configuration file path: {circos_conf}')
             print(f'Output plot name: {circos_plot_name}')
             print('---')
-            subprocess.run('circos -conf {0} -outputfile {1}'.format(circos_conf, circos_plot_name), shell=True)
+            subprocess.run('circos -conf {0} -outputfile {1} -param links/link/file={2}'.format(circos_conf, circos_plot_name, link_file), shell=True)
 
         # copy images to main image folder
         print()