updated .travis.yml and fixed genda.plotting.plotting_utils.coverage_…

…hist to accurately account for introns

.gitignore

@@ -7,6 +7,7 @@
 *.lock
 *.DS_Store
 *.swp
+*.swo
 *.out
 *.c
 *.o

.travis.yml

@@ -1,11 +1,31 @@
+# Ideas taken from: https://gist.github.com/dan-blanchard/7045057
+
 language: python
 
 python: 
   - 2.7
 
-install: "pip install -r requirements.txt"
+
+
+before_install:
+  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - chomd +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/miniconda/bin:$PATH
+  - conda update --yes conda
+
+
+install: 
+  - conda install --yes python=$TRAVIS_PYTHON_VERSION atlas numpy scipy nose dateutil pandas statsmodels matplotlib requests cython biopython
+  - conda install --yes -c bioconda pysam bx-python
+  - python setup.py install
+
+
+
+
+
 env: 
   global:
-    - NOSE_ARGS="not slow"
+  - NOSE_ARGS="not slow"
 
 

genda/plotting/plotting_utils.py

@@ -204,7 +204,8 @@ def coverage_hist(read, hist_array, start):
             hist_array[ii + cont:ii+cont+j] +=1
             cont += j
         elif i==3:
-            pass
+            # cigar is always ordered
+            cont += j
 
 
 def create_gene_path(gtf_iter, gene, x_scale):

genda/transcripts/transcripts_utils.py

@@ -1,4 +1,5 @@
 from itertools import tee, izip
+import requests
 # Requires bx python
 from bx.intervals.intersection import Intersecter, Interval
 
@@ -24,6 +25,26 @@ def __init__(self, region, start, end):
 
 
 
+def get_transcript_ids(gene):
+    """ Get transcript ids from Ensembl REST api
+    Returns a list of transcripts,
+
+    :TODO make out_transcripts a list of transcript class
+    """
+    server = "http://rest.ensembl.org"
+    ext = "/lookup/id/{0}?species=homo_sapiens;expand=1"
+    r = requests.get(server+ext.format(gene), headers={ "Content-Type" :
+        "application/json"})
+    out_transcripts = []
+    decoded = r.json()
+    for i in decoded['Transcript']:
+        out_transcripts.append(i['id'])
+    return(out_transcripts, 
+            decoded['display_name'],
+            decoded['seq_region_name'], 
+            (int(decoded['start']), int(decoded['end'])))
+
+
 class Transcript(object):
     """ A collection of exons
     """
@@ -120,6 +141,7 @@ def compare_two_transcripts(trans1, trans2, transcript_dict):
     Returns:
     5' upstream exons - 
     3' downstram exons - 
+
     """
     t1 = transcript_dict[trans1]
     t2 = transcript_dict[trans2]