Merge pull request #11 from domenico-somma/SOLID

v 0.1.1

.gitignore

@@ -6,3 +6,9 @@
 
 # Python egg metadata, regenerated from source files by setuptools.
 /*.egg-info
+
+#check list
+check_list.txt
+
+#images
+*.png

AUTHORS.md

@@ -6,3 +6,5 @@ Contributors:
 
 * Emma Smith: e.smith.4@research.gla.ac.uk
   * for suggestions and Beta testing
+
+Thanks to "riko" and python-it.org's guys for tips and suggestions.

CHANGE.txt

@@ -1,3 +1,6 @@
+v 0.1.1, 21-01-18 -- Minor changes: 
+add python 3 restriction, add the function to load directly the cuffdiff files, changed function names: self.read_db() -> self.read_folder() and self.plot() -> self.lineplot(),improved code quality (tried to follow the single responsibility principle), removed some potential bugs. 
+
 v 0.1.0, 09-01-18 -- Minor changes: improved code quality
 v 0.0.9, 05-01-18 -- Minor changes: in MANIFEST.in to include license and test_files. Compatible with conda forge
 v 0.0.8, 03-01-18 -- Minor changes: improved test coverage, now papillon.py is a module and not a package

MANIFEST.in

@@ -2,6 +2,7 @@ include docs/*.*
 include test/*.py
 include test/Test_files/*.*
 include test/Test_files/Papillon/*.list
+include test/Test_files/galaxy/*.*
 include AUTHORS.md
 include CHANGE.txt
 include CONTRIBUTING.md

README.md

@@ -1,5 +1,5 @@
 # Papillon
-A python alternative to [cummeRbund](http://compbio.mit.edu/cummeRbund/) to read and plot [Galaxy](https://usegalaxy.org/) RNA-seq data 
+A python alternative to [cummeRbund](http://compbio.mit.edu/cummeRbund/) to read and plot [Galaxy](https://usegalaxy.org/)/cuffdiff RNA-seq data 
 
 ![Preview](https://user-images.githubusercontent.com/34346930/34152979-4c3dae42-e4a8-11e7-9259-005a016edb53.png)
 

TO DO.txt

@@ -7,7 +7,6 @@
 
 * Move plots functions in another py file?
 * Wondering if z_score calc, fusion_gene_id and only_FPKM should be only one function?
-* Change self.plot() name to self.lineplot()?
 
 * Add Volcano plot
 

docs/manual.rst

@@ -35,7 +35,7 @@ Commands
 Functions:
 ----------
 
-``read_db(path, drop_comparison=[])``
+``read_folder(path, drop_comparison=[])``
 
 Read the cuffdiff/cummeRbund files. Return a class papillon.
 
@@ -53,7 +53,41 @@ i.e.:
 
      import papillon as pl
 
-     MyExp=pl.read_db("My Experiment", drop_comparison=["Sample 1_vs_Sample 2","Sample 3_vs_Sample 4"])
+     MyExp=pl.read_folder("My Experiment", drop_comparison=["Sample 1_vs_Sample 2","Sample 3_vs_Sample 4"])
+
+--------------
+
+
+``read_files(files, path=None, drop_comparison=None)``
+
+Accept cuffdiff/cummeRbund files as iterable. Return a class papillon.
+
+**files**: *iterable*
+
+iterable with cuffdiff files
+
+**path**: *str*
+
+folder path where export Papillon generated files
+
+**drop\_comparison**: *str or iterable*
+
+what comparison do not import
+
+i.e.:
+
+::
+
+     import papillon as pl
+
+     MyExp=pl.read_files(["file1.tab","file2.tab","file3.tab","file4.tab",],"My Experiment")
+
+--------------
+
+
+``read_db`` is deprecated
+
+--------------
 
 
 Class:
@@ -321,7 +355,7 @@ i.e.:
 
 --------------
 
-**self.plot(self, title="", legend=True, z_score=False, export=False, df=None, size=10, **option)**
+**self.lineplot(self, title="", legend=True, z_score=False, export=False, df=None, size=10, **option)**
 
 Create a lineplot with self.selected. Max number of genes/isoforms is
 200.
@@ -368,11 +402,15 @@ i.e.:
 
      MyExp.get_isoform()
 
-     MyExp.plot()
+     MyExp.lineplot()
 
-     MyExp.plot(title="My genes", legend=False)
+     MyExp.lineplot(title="My genes", legend=False)
+
+     MyExp.lineplot(z_score=True, export=True)
+
+--------------
 
-     MyExp.heatmap(z_score=True, export=True)
+**self.plot** is deprecated
 
 --------------