update to message print

setup.cfg

@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.md

setup.py

@@ -133,7 +133,8 @@ def main():
         name = "TransVar",
         version = __version__,
         description = "Transcript-based Variant annotator",
-        url = "https://bitbucket.org/wanding/transvar",
+        url = "https://github.com/zwdzwd/transvar",
+        download_url = "https://github.com/zwdzwd/transvar/releases/latest",
         author = "Wanding Zhou",
         author_email = "[email protected]",
         license = "MIT",

test/test.sh

@@ -14,6 +14,10 @@ transvar canno -l data/cosmic/cosmic_canno_snv -g 1 -m 3 --ccds | tee testout/ca
 transvar canno -l data/cosmic/cosmic_canno_deletion -g 1 -m 3 --ccds | tee testout/canno_cosmic_deletion
 
 transvar canno -l data/cosmic/cosmic_canno_insertion -g 1 -m 3 --ccds | tee testout/canno_cosmic_insertion
+colordiff testout/canno_cosmic_insertion golden/canno_cosmic_insertion
 
 transvar panno -l data/tamborero_data/transvar_revprotein_input.txt_ens --ensembl --seqmax -1 | tee testout/panno_tamborero
+colordiff testout/panno_tamborero golden/panno_tamborero
 
+transvar ganno --vcf data/tamborero_data/docm_variants_mar_2016.vcf --ensembl | tee testout/ganno_tamborero.vcf
+colordiff testout/ganno_tamborero.vcf

transvar/err.py

@@ -60,7 +60,7 @@ def err_die(msg):
 
 def err_warn(msg):
     fn = inspect.stack()[1][3]
-    sys.stderr.write('[%s] warning: %s\n' % (fn, msg))
+    sys.stderr.write('\r[%s] warning: %s\n' % (fn, msg))
 
 def err_raise(cls, msg):
     fn = inspect.stack()[1][3]

transvar/mutation.py

@@ -426,6 +426,8 @@ def vcf_parse_mutation(args, at='g'):
 
             yield q, line
 
+    sys.stderr.write("\nProcessed %d records\033[K\n" % nrec)
+
 def list_parse_mutation(args, muttype):
 
     indices = parse_indices(args.o)

transvar/snv.py

@@ -37,6 +37,7 @@ def annotate_snv_cdna(args, q, tpts, db):
 
     found = False
     rs = []
+    gene_name = ""
     for t in tpts:
         try:
             if q.tpt and t.name != q.tpt:
@@ -53,6 +54,7 @@ def annotate_snv_cdna(args, q, tpts, db):
             r.chrm = t.chrm
             r.tname = t.format()
             r.gene = t.gene_name
+            gene_name = t.gene_name
             r.strand = t.strand
 
             r.gnuc_pos = t.tnuc2gnuc(q.pos)
@@ -109,7 +111,7 @@ def annotate_snv_cdna(args, q, tpts, db):
     format_all(rs, q, args)
 
     if not found:
-        wrap_exception(Exception('no_valid_transcript_found_(from_%s_candidates)' % len(tpts)), q, args)
+        wrap_exception(Exception('no_valid_transcript_found_(from_%s_candidates)_%s' % (len(tpts),gene_name)), q, args)
 
     return