Updated documentation, added reference links.

CONTRIBUTING.rst

@@ -45,7 +45,8 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/jrderuiter/imfusion/issues.
+The best way to send feedback is to file an issue at
+https://github.com/jrderuiter/imfusion/issues.
 
 If you are proposing a feature:
 
@@ -64,23 +65,25 @@ Ready to contribute? Here's how to set up `imfusion` for local development.
 
     $ git clone git@github.com:your_name_here/imfusion.git
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+3. Install your local copy into a virtualenv. Assuming you have v
+irtualenvwrapper installed, this is how you set up your fork for
+local development::
 
     $ mkvirtualenv imfusion
     $ cd imfusion/
-    $ python setup.py develop
+    $ pip install -e .[dev]
 
 4. Create a branch for local development::
 
     $ git checkout -b name-of-your-bugfix-or-feature
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+5. When you're done making changes, check that your changes pass the tests,
+including testing other Python versions with tox::
 
-    $ flake8 imfusion tests
-    $ python setup.py test or py.test
-    $ tox
+    $ make test
+    $ make tox
 
    To get flake8 and tox, just pip install them into your virtualenv.
 
@@ -101,6 +104,6 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
+3. The pull request should work for Python 2.7, 3.4 and 3.5. Check
    https://travis-ci.org/jrderuiter/imfusion/pull_requests
    and make sure that the tests pass for all supported Python versions.

HISTORY.rst

@@ -2,6 +2,15 @@
 History
 =======
 
+0.3.1 (2017-05-09)
+------------------
+
+* Several small fixes for Python 2.7 compatibility.
+* Fixed issue in CTG test that occurs when no insertions are within the
+  gene windows.
+* Replaced usage of deprecated .ix indexer for pandas DataFrames.
+* Updated documentation.
+
 0.3.0 (2017-05-04)
 ------------------
 

docs/getting_started.rst

@@ -50,9 +50,9 @@ more sensitivity in the results.
 
 For building a reference, the following files are required:
 
-    - The reference genome sequence, (Fasta file).
+    - The reference genome sequence, (fasta file).
     - The reference gene features. (GTF file, adhering to Ensembl's GTF format).
-    - The transposon sequence (Fasta file).
+    - The transposon sequence (fasta file).
     - The transposon features file (tab-separated file).
 
 The transposon feature file describes the locations of the splice-donor and
@@ -65,6 +65,16 @@ be either ‘SD’ or ‘SA’ for splice-donor or splice-acceptor sites respect
 The field may also be left empty for other types of features, however these
 features will not be used by IM-Fusion.
 
+Example reference files
+-----------------------
+
+Reference files for various genomes can be downloaded here:
+
+    - mm10 (Ensembl, current): `Fasta <ftp://ftp.ensembl.org//pub/release-88/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz>`_, `GTF <ftp://ftp.ensembl.org//pub/release-88/gtf/mus_musculus/Mus_musculus.GRCm38.88.gtf.gz>`_
+    - mm9 (Ensembl, archive): `Fasta <ftp://ftp.ensembl.org//pub/release-67/fasta/mus_musculus/dna/Mus_musculus.NCBIM37.67.dna.toplevel.fa.gz>`_, `GTF <ftp://ftp.ensembl.org//pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz>`_
+
 Example sequence and feature files for the Sleeping Beauty
-*T2/Onc2* and Piggybac transposons are available in the GitHub `respository
-<https://github.com/jrderuiter/imfusion/tree/develop/data>`_.
+*T2/Onc* and Piggybac transposons are available in our GitHub `respository
+<https://github.com/jrderuiter/imfusion/tree/develop/data>`_. For other
+transposon,s these files need to be created manually using knowledge of the
+transposon sequence and the locations of its splice acceptor/donor sites.

docs/usage.rst

@@ -54,7 +54,7 @@ The command for building a Tophat-Fusion reference is nearly identical:
         --transposon_seq transposon.fa \
         --transposon_features transposon.features.txt \
         --output_dir references/GRCm38.76.t2onc.tophat \
-        --blacklist_genes ENSMUSG00000039095 ENSMUSG00000038402 \
+        --blacklist_genes ENSMUSG00000039095 ENSMUSG00000038402
 
 However, both aligners do have some aligner-specific arguments for building
 their references. See the help of the respective sub-commands for more details.
@@ -76,10 +76,11 @@ The basic command for ``imfusion-insertions`` using the STAR aligner is:
 
 .. code:: bash
 
-    imfusion-insertions star
+    imfusion-insertions star \
         --fastq sample_s1.R1.fastq.gz \
         --reference references/GRCm38.76.t2onc.star \
-        --output_dir output/sample_s1
+        --output_dir output/sample_s1 \
+        --star_threads 4
 
 In this command, the ``--fastq`` argument specifies a path to the fastq
 file containing RNA-seq reads for the given sample. For paired-end samples, the
@@ -98,10 +99,11 @@ The command for using Tophat-Fusion is nearly identical:
 
 .. code:: bash
 
-    imfusion-insertions tophat
+    imfusion-insertions tophat \
         --fastq sample_s1.R1.fastq.gz \
         --reference references/GRCm38.76.t2onc.tophat \
-        --output_dir output/sample_s1
+        --output_dir output/sample_s1 \
+        --tophat_threads 4
 
 However, both aligners do have some aligner-specific arguments concerning the
 alignment. See the help of the respective sub-commands for more details. For