From 68dcae74440b7abdcfede6252f3aa73d36fc60ac Mon Sep 17 00:00:00 2001
From: dmnfarrell <farrell.damien@gmail.com>
Date: Fri, 6 Jul 2018 14:30:33 +0100
Subject: [PATCH] setup.py fix

---
 setup.py             |  2 +-
 smallrnaseq/novel.py |  9 +++++++--
 smallrnaseq/utils.py | 11 ++++++++---
 snap/snapcraft.yaml  |  4 +++-
 4 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/setup.py b/setup.py
index 3b1ddd3..25c6fbe 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@
                     'pysam>=0.10.0',
                     'HTSeq>=0.6',
                     'bx-python>=0.5',
-                    'forgi>=0.4']
+                    'forgi==0.20']
 
 major, minor, micro = sys.version_info[:3]
 if major == '2':
diff --git a/smallrnaseq/novel.py b/smallrnaseq/novel.py
index 5cb47fa..fed7689 100644
--- a/smallrnaseq/novel.py
+++ b/smallrnaseq/novel.py
@@ -176,6 +176,8 @@ def check_mature(seq, struct, mature):
     """Check if the mature sequence is not in hairpin loop and inside stem"""
 
     bg = utils.get_bg(seq, struct)
+    if bg is None:
+        return
     start = utils.find_subseq(seq, mature)+1
     end = start + len(mature)
     loops = list(bg.hloop_iterator())
@@ -424,7 +426,8 @@ def generate_precursors(ref_fasta, coords, mature=None, step=5):
         struct,sc = utils.rnafold(prseq)
         #prseq, struct = check_hairpin(prseq, struct)
         mstatus = check_mature(prseq, struct, mature)
-        #print (mstatus)
+        if mstatus is None:
+            continue
         #print (i)
         #print (prseq)
         #print (struct)
@@ -442,6 +445,8 @@ def generate_precursors(ref_fasta, coords, mature=None, step=5):
         struct,sc = utils.rnafold(prseq)
         #prseq, struct = check_hairpin(prseq, struct)
         mstatus = check_mature(prseq, struct, mature)
+        if mstatus is None:
+            continue
         N.append({'precursor':prseq,'struct':struct,'score':sc,
                   'chrom':chrom,'start':start3,'end':end3,
                   'mature':mature,'strand':strand,'mature_check': mstatus})
@@ -611,7 +616,7 @@ def find_mirnas(reads, ref_fasta, score_cutoff=.8, read_cutoff=50, species='',
         m['mature'] = True
         X.append(m)
         #remainder of reads assigned as non-mature
-        o = df.loc[-df.index.isin(m.index)].copy()
+        o = df.loc[~df.index.isin(m.index)].copy()
         o['mature'] = False
         X.append(o)
 
diff --git a/smallrnaseq/utils.py b/smallrnaseq/utils.py
index 16f6d78..1f7714a 100644
--- a/smallrnaseq/utils.py
+++ b/smallrnaseq/utils.py
@@ -705,8 +705,13 @@ def get_bg(seq, struct=None):
 
     import forgi.graph.bulge_graph as cgb
     if struct == None:
-        struct,sc = utils.rnafold(seq)
+        struct,sc = rnafold(seq)
     bg = cgb.BulgeGraph()
     bg.from_dotbracket(struct)
-    bg.seq = seq
-    return bg
+    #print (bg.struct)
+    try:
+        bg.seq = seq
+        return bg
+    except Exception as e:
+        print (e)
+        return
diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
index 1be6a7e..94fd9a0 100644
--- a/snap/snapcraft.yaml
+++ b/snap/snapcraft.yaml
@@ -19,8 +19,10 @@ parts:
   part1:
     plugin: python
     python-version: python2
+    python-packages:
+      [numpy]
     stage-packages:
-      [python-numpy,libblas3,libopenblas-dev]
+      [libblas3,libopenblas-dev]
   smallrnaseq:
     plugin: python
     python-version: python2