networkx fix, bugfix for BAM files with no reads, version bump

pita/annotationdb.py

@@ -570,6 +570,7 @@ def splice_stats(self, exon1, exon2, identifier):
     def nreads(self, identifier):
         q = self.session.query(ReadSource)
         q = q.filter(ReadSource.name == identifier)
+
         return sum([s.nreads for s in q.all()])
 
     def get_splice_count(self, e1, e2):

pita/collection.py

@@ -9,7 +9,7 @@
 from networkx.algorithms.components.connected import connected_components
 import networkx as nx 
 from networkx.algorithms.connectivity import minimum_st_node_cut
-from networkx.algorithms.flow import ford_fulkerson
+from networkx.algorithms.flow import edmonds_karp
 from itertools import izip, count
 from gimmemotifs.genome_index import GenomeIndex
 
@@ -151,10 +151,10 @@ def get_connected_models(self):
     def get_node_cuts(self, model):
 
         node_cuts = []
-        cuts = list(minimum_st_node_cut(self.graph, model[0], model[-1], flow_func=ford_fulkerson))
+        cuts = list(minimum_st_node_cut(self.graph, model[0], model[-1], flow_func=edmonds_karp))
         while len(cuts) == 1:
             node_cuts = cuts + node_cuts
-            cuts = list(minimum_st_node_cut(self.graph, model[0], cuts[0], flow_func=ford_fulkerson))
+            cuts = list(minimum_st_node_cut(self.graph, model[0], cuts[0], flow_func=edmonds_karp))
         return node_cuts
 
     def get_best_variant(self, model, weight):

pita/config.py

@@ -21,6 +21,7 @@ def __init__(self):
         """ fname: name of yaml configuration file
         """
         self.logger = logging.getLogger("pita")
+
         self.maxentpath = ""
 
     def load(self, fname,  reannotate=False):

pita/db_backend.py

@@ -78,7 +78,7 @@ class ReadSource(Base):
     id = Column(Integer, primary_key=True)
     name = Column(String(250))
     source = Column(String(250))
-    nreads = Column(Integer)
+    nreads = Column(Integer, default=0)
 
 class FeatureReadCount(Base):
     __tablename__ = "read_count"

pita/dbcollection.py

@@ -9,15 +9,14 @@
 from networkx.algorithms.components.connected import connected_components
 import networkx as nx 
 from networkx.algorithms.connectivity import minimum_st_node_cut
-from networkx.algorithms.flow import ford_fulkerson
+from networkx.algorithms.flow import edmonds_karp
 from itertools import izip, count
 from gimmemotifs.genome_index import GenomeIndex
 import random
 
 def connected_models(graph):
     for u, v in graph.edges():
         graph[u][v]['weight'] = -1
-
     for c in nx.weakly_connected_components(graph):
         starts =  [k for k,v in graph.in_degree(c).items() if v == 0]
         ends = [k for k,v in graph.out_degree(c).items() if v == 0]
@@ -71,7 +70,8 @@ def __init__(self, db, chrom=None):
 
         self.logger.debug("Loading introns in graph")
         n = 0
-        for junction in self.db.get_splice_junctions(chrom, ev_count=1, read_count=20):
+        #for junction in self.db.get_splice_junctions(chrom, ev_count=1, read_count=20):
+        for junction in self.db.get_splice_junctions(chrom, ev_count=0, read_count=1):
         #for junction in self.db.get_splice_junctions(chrom):
             #print junction
             n += 1
@@ -118,10 +118,10 @@ def get_connected_models(self):
 
     def get_node_cuts(self, model):
         node_cuts = []
-        cuts = list(minimum_st_node_cut(self.graph, model[0], model[-1], flow_func=ford_fulkerson))
+        cuts = list(minimum_st_node_cut(self.graph, model[0], model[-1], flow_func=edmonds_karp))
         while len(cuts) == 1:
             node_cuts = cuts + node_cuts
-            cuts = list(minimum_st_node_cut(self.graph, model[0], cuts[0], flow_func=ford_fulkerson))
+            cuts = list(minimum_st_node_cut(self.graph, model[0], cuts[0], flow_func=edmonds_karp))
         return node_cuts
 
     def get_best_variant(self, model, weight):

setup.py

@@ -2,7 +2,7 @@
 from setuptools.command.test import test as TestCommand
 import sys
 
-VERSION = "1.72"
+VERSION = "1.73"
 DESCRIPTION = """
 pita - pita improves transcript annotation
 """
@@ -43,12 +43,12 @@ def run_tests(self):
         install_requires=[
                         "SQLAlchemy",
                         "gimmemotifs > 0.8.6",
-                        "pysam < 0.8",
+                        "pysam >= 0.9",
                         "pyyaml",
                         "HTSeq",
                         "bcbio-gff",
                         "biopython",
-                        "networkx ==1.9",
+                        "networkx >= 1.10",
                         "numpy",
                         ],
         cmdclass = {'test': PyTest},

tests/test_db.py

@@ -1,4 +1,8 @@
+import os
 import pytest
+from pita.config import config
+
+config.maxentpath = os.environ["MAXENT"]
 
 @pytest.fixture
 def three_exons():