Merge branch 'release/0.1.31'

churchill-lab · Feb 17, 2017 · 57c3dde · 57c3dde
2 parents 10547e9 + be92826
commit 57c3dde
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Showing 3 changed files with 33 additions and 12 deletions.
diff --git a/g2gtools/__init__.py b/g2gtools/__init__.py
@@ -14,7 +14,7 @@
 from .bins import bins
 
 
-__version__ = '0.1.29'
+__version__ = '0.1.31'
 __author__ = 'Matthew Vincent, The Jackson Laboratory'
 __email__ = 'matt.vincent@jax.org'
 

diff --git a/g2gtools/fasta_patch.py b/g2gtools/fasta_patch.py
@@ -69,6 +69,21 @@ def get_pos(fai, chromosome, start, end):
     byte_end = fai_entry_offset + newlines_total + fai_entry_length
     return byte_start, byte_end, byte_len_seq
 
+def _show_error():
+    import traceback, sys
+    """
+    show system errors
+    """
+    et, ev, tb = sys.exc_info()
+
+    print "Error Type: %s" % et
+    print "Error Value: %s" % ev
+    while tb :
+        co = tb.tb_frame.f_code
+        filename = str(co.co_filename)
+        line_no = str(traceback.tb_lineno(tb))
+        print '    %s:%s' % (filename, line_no)
+        tb = tb.tb_next
 
 def process_piece(filename_vcf, chrom, start, end, sample_index, diploid, pass_only, quality):
     """
@@ -109,11 +124,8 @@ def process_piece(filename_vcf, chrom, start, end, sample_index, diploid, pass_o
             byte_start, byte_end, byte_len_seq = get_pos(fasta_index, rec.CHROM, rec.POS-1, rec.POS)
             gt = parse_gt(rec, sample_index)
 
-            #LOG.debug(rec)
-            #LOG.debug(gt)
-
             # FI : Whether a sample was a Pass(1) or fail (0) based on FILTER values
-            if quality and gt.fi == '0':
+            if quality and gt.fi is not None and gt.fi == '0':
                 continue
 
             global mm_l

diff --git a/g2gtools/vcf.py b/g2gtools/vcf.py
@@ -6,6 +6,7 @@
 # 1 based
 
 
+from collections import namedtuple
 from collections import namedtuple
 
 from .g2g_utils import get_logger
@@ -149,7 +150,11 @@ def parse_gt(vcf_record, sample_index):
 
     if sample_data != '.':
         gt_index = vcf_record.FORMAT.split(':').index('GT')
-        fi_index = vcf_record.FORMAT.split(':').index('FI')
+
+        try:
+            fi_index = vcf_record.FORMAT.split(':').index('FI')
+        except:
+            fi_index = None
 
         try:
             # parse the GT field
@@ -181,12 +186,16 @@ def parse_gt(vcf_record, sample_index):
             LOG.debug(ve)
         except IndexError, ie:
             LOG.debug(ie)
-        try:
-            fi = sample_data.split(':')[fi_index]
-        except ValueError, ve:
-            LOG.debug(ve)
-        except IndexError, ie:
-            LOG.debug(ie)
+
+        if fi_index is not None:
+            try:
+                fi = sample_data.split(':')[fi_index]
+            except ValueError, ve:
+                LOG.debug(ve)
+            except IndexError, ie:
+                LOG.debug(ie)
+        else:
+            fi = None
 
     return GTData(vcf_record.REF, left, right, gt, fi, phase)