skip stop script execution when encountering invalid input

bin/transvar

@@ -16,7 +16,7 @@ from transvar.localdb import add_parser_index
 if __name__ == '__main__':
 
     import sys
-    if sys.argv[1] in ['-version', '--version']:
+    if len([a for a in sys.argv if a in ['-version', '--version']]) > 0:
         import transvar
         sys.stderr.write("TransVar Version %s\n" % transvar.__version__)
         sys.exit(1)

test/test.py

@@ -43,47 +43,93 @@ def wrap(line):
         yield ' '*3+line[:k]
         line = line[k:]
 
-fh = open(sys.argv[2], 'w') # open('README.md.temp', 'w')
+indir = sys.argv[1]
+outdir = sys.argv[2]
+
+if not os.path.exists(outdir):
+    os.mkdir(outdir)
+# outdir = open(sys.argv[2], 'w') # open('README.md.temp', 'w')
 
 import transvar
 
-result = ''
-for line in open(sys.argv[1]):
+for ifn in os.listdir(indir):
+    if not ifn.endswith(".md"):
+        continue
 
-    line = line.replace('@VERSION', transvar.__version__)
+    ifh = open(os.path.join(indir, ifn))
 
-    if line.startswith('$'):    # exexcute sentinel
+    ofn = os.path.join(outdir, ifn)
+    ofh = open(ofn, "w")
 
-        fh.write(line)
-        line = line[2:].strip()
-        ar = re.split(r'[\'"]', line.strip())
+    result = ''
+    tofill = False
+    infill = False
+    for line in ifh:
 
-        B = []
-        for i, e in enumerate(ar):
-            if i % 2 == 0:
-                if len(e.strip())>0:
-                    B.extend(e.strip().split())
-            else:
-                B.append(e.strip())
+        line = line.replace('@VERSION', transvar.__version__)
+
+        if line.startswith('$'):    # exexcute sentinel
+
+            ofh.write(line)
+            line = line[2:].strip()
+            ar = re.split(r'[\'"]', line.strip())
+
+            B = []
+            for i, e in enumerate(ar):
+                if i % 2 == 0:
+                    if len(e.strip())>0:
+                        B.extend(e.strip().split())
+                else:
+                    B.append(e.strip())
+
+            p = Popen(B, stdin=PIPE, stdout=PIPE, stderr=PIPE)
+            result, err = p.communicate()
+            result = result.strip()
 
-        p = Popen(B, stdin=PIPE, stdout=PIPE, stderr=PIPE)
-        result, err = p.communicate()
-        result = result.strip()
+            print
+            print '======'+line+'======'
+            print result
+            print '\n'.join([rr for rr in result.split('\n') if not (len(rr.strip()) == 0 or rr.startswith('[') or rr.startswith('input'))])
+            tofill = True
+            infill = False
+            oldfill = ''
 
-        print
-        print '======'+line+'======'
-        print '\n'.join([rr for rr in result.split('\n') if not (len(rr.strip()) == 0 or rr.startswith('[') or rr.startswith('input'))])
+        elif line.startswith('```text') and tofill:
+            infill = True
+            tofill = False
+            ofh.write(line)
+
+        elif line.startswith('```') and infill:
+
+            newfill = ''
+            for rr in result.split('\n'):
+
+                if len(rr.strip()) == 0 or rr.startswith('[') or rr.startswith('input'):
+                    continue
+
+                for r in wrap(rr):
+                    newfill += r+'\n'
+
+            if newfill != oldfill:
+                print '\n+++ NEW +++'
+                print newfill
+                print '\n+++ OLD +++'
+                print oldfill
+                raw_input("Difference ...")
+            else:
+                print "\nSame!\n"
 
-    elif line.startswith('@'):
+            ofh.write(newfill)
+            ofh.write('```\n')
 
-        for rr in result.split('\n'):
+            infill = False
 
-            if len(rr.strip()) == 0 or rr.startswith('[') or rr.startswith('input'):
-                continue
+        elif infill:
+            oldfill += line
 
-            for r in wrap(rr):
-                fh.write(r+'\n')
+        else:
 
-    else:
+            ofh.write(line)
 
-        fh.write(line)
+    ifh.close()
+    ofh.close()

transvar/mutation.py

@@ -395,7 +395,9 @@ def vcf_parse_mutation(args, at='g'):
                 q.refseq = ref.upper()
                 q.altseq = alt.upper()
             else:
-                err_raise(InvalidInputError, 'invalid VCF line: %s' % line)
+                q = Query()
+                q.msg = "InvalidVCFLine%s" % line
+                err_warn("Invalid VCF Line: %s" % line)
 
             q.op = line.strip()
 

transvar/record.py

@@ -282,6 +282,8 @@ def __init__(self):
         self.is_codon = True
         self.gn_name = None
         self.tpt = ''
+        self.msg = ''
+        self.tok = None         # by default, is a failed query
 
     def set_pos(self, pos_str):