Incompatible chroms between fasta and annotation

README.md

@@ -7,7 +7,7 @@
 
 Outrigger is a program which uses junction reads from RNA seq data, and a graph database to create a *de novo* alternative splicing annotation with a graph database, and quantify percent spliced-in (Psi) of the events.
 
-* Free software: BSD license
+* Free and open source software: BSD license
 
 ## Features
 
@@ -25,7 +25,6 @@ You'll want to add the [`bioconda`](https://bioconda.github.io/) channel to make
 ```
 conda config --add channels r
 conda config --add channels bioconda
-
 ```
 
 Create an environment called `outrigger-env`. Python 2.7, Python 3.4, and Python 3.5 are supported.

docs/releases/v0.2.9.rst

@@ -0,0 +1,25 @@
+v0.2.9 (...)
+------------
+
+
+
+New features
+~~~~~~~~~~~~
+
+Plotting functions
+~~~~~~~~~~~~~~~~~~
+
+API changes
+~~~~~~~~~~~
+
+
+Bug fixes
+~~~~~~~~~
+
+- Fixed an issue in ``outrigger validate`` when fasta file and genome
+  annotation didn't have overlapping chromosomes and ``outrigger validate``
+  would simply fail rather than gracefully skipping those events.
+
+Miscellaneous
+~~~~~~~~~~~~~
+

outrigger/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = 'Olga Botvinnik'
 __email__ = 'olga.botvinnik@gmail.com'
-__version__ = '0.2.8dev'
+__version__ = '0.2.9dev'
 
 __all__ = ['psi', 'region', 'util', 'io', 'validate', 'index',
            'common']

outrigger/tests/data/simulated/validate_negative_control/chromsizes

@@ -1 +1,2 @@
 simulated	1000
+in_chromsizes   100

outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/events.csv

@@ -1,2 +1,4 @@
 isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+
-isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-
+isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-
+isoform1=junction:nonexistent:100-600:-|isoform2=junction:nonexistent:300-600:-@exon:nonexistent:300-400:-@junction:nonexistent:100-400:-
+isoform1=junction:in_chromsizes:100-600:-|isoform2=junction:in_chromsizes:300-600:-@exon:in_chromsizes:300-400:-@junction:in_chromsizes:100-400:-

outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/exon1.bed

@@ -1,2 +1,4 @@
 simulated	100	150	isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+	.	+
 simulated	500	600	isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-	.	-
+nonexistent	500	600	isoform1=junction:nonexistent:100-600:-|isoform2=junction:nonexistent:300-600:-@exon:nonexistent:300-400:-@junction:nonexistent:100-400:-	.	-
+in_chromsizes	500	600	isoform1=junction:in_chromsizes:100-600:-|isoform2=junction:in_chromsizes:300-600:-@exon:in_chromsizes:300-400:-@junction:in_chromsizes:100-400:-	.	-

outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/exon2.bed

@@ -1,2 +1,4 @@
 simulated	300	400	isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+	.	+
 simulated	300	400	isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-	.	-
+nonexistent	300	400	isoform1=junction:nonexistent:100-600:-|isoform2=junction:nonexistent:300-600:-@exon:nonexistent:300-400:-@junction:nonexistent:100-400:-	.	-
+in_chromsizes	300	400	isoform1=junction:in_chromsizes:100-600:-|isoform2=junction:in_chromsizes:300-600:-@exon:in_chromsizes:300-400:-@junction:in_chromsizes:100-400:-	.	-

outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/exon3.bed

@@ -1,2 +1,4 @@
 simulated	500	600	isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+	.	+
 simulated	100	150	isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-	.	-
+nonexistent	100	150	isoform1=junction:nonexistent:100-600:-|isoform2=junction:nonexistent:300-600:-@exon:nonexistent:300-400:-@junction:nonexistent:100-400:-	.	-
+in_chromsizes	100	150	isoform1=junction:in_chromsizes:100-600:-|isoform2=junction:in_chromsizes:300-600:-@exon:in_chromsizes:300-400:-@junction:in_chromsizes:100-400:-	.	-

outrigger/validate/check_splice_sites.py

@@ -1,10 +1,10 @@
 
 from collections import OrderedDict
 
-from Bio import SeqIO
 import pandas as pd
 import pybedtools
 
+
 NT = 2
 
 MAMMALIAN_SPLICE_SITES = 'GT/AG,AT/AC'
@@ -55,11 +55,10 @@ def read_splice_sites(bed, genome, fasta, direction='upstream'):
         right = NT
 
     flanked = bed.flank(l=left, r=right, s=True, genome=genome)
-    seqs = flanked.sequence(fi=fasta, s=True)
-
-    with open(seqs.seqfn) as f:
-        records = SeqIO.parse(f, 'fasta')
-        records = pd.Series([str(r.seq) for r in records],
-                            index=[b.name for b in bed])
-    # import pdb; pdb.set_trace()
-    return records
+    seqs = flanked.sequence(fi=fasta, s=True, name=True, tab=True)
+
+    splice_sites = pd.read_table(seqs.seqfn, index_col=0, header=None,
+                                 squeeze=True)
+    splice_sites.index = [x.split('::')[0] for x in splice_sites.index]
+    splice_sites.name = None
+    return splice_sites

setup.py

@@ -23,7 +23,7 @@
 
 setup(
     name='outrigger',
-    version='0.2.8dev',
+    version='0.2.9dev',
     description="Outrigger is a tool to de novo annotate splice sites "
                 "and exons",
     long_description=readme + '\n\n' + history,