# HG changeset patch
# User petr-novak
# Date 1567593918 14400
# Node ID 0e820310d4dc234c5d4953853f59b1786431d833
# Parent  3151a72a667155298e2375287133b4656b2010ed
Uploaded

diff -r 3151a72a6671 -r 0e820310d4dc coverage2gff.py
--- a/coverage2gff.py	Tue Sep 03 05:20:02 2019 -0400
+++ b/coverage2gff.py	Wed Sep 04 06:45:18 2019 -0400
@@ -36,7 +36,6 @@
         d = {}
         for name, prof in zip(p, p):
             d[name[1:].strip()] = [int(i) for i in prof.split()]
-    print(d, file=sys.stderr)
     return d
 
 
diff -r 3151a72a6671 -r 0e820310d4dc parse_aln.py
--- a/parse_aln.py	Tue Sep 03 05:20:02 2019 -0400
+++ b/parse_aln.py	Wed Sep 04 06:45:18 2019 -0400
@@ -41,7 +41,7 @@
 
 
 def get_header(f):
-    aln_header = ".    :    .    :    .    :    .    :    .    :    .    :"
+    aln_header = "    .    :    .    :    .    :    .    :    .    :    .    :"
     contig_lead = "******************"
     aln_start = -1
     while True:
@@ -63,7 +63,7 @@
     pos = f.tell()
     line = f.readline()
     # detect next contig or end of file
-    if "********" in line or line == "":
+    if "********" in line or line == "" or "Number of segment pairs = " in line:
         segment = False
     else:
         segment = True
diff -r 3151a72a6671 -r 0e820310d4dc test-data/toolshed.g2.bx.psu.edu_repos_petr-novak_dante_dante_1.0.0.tgz
Binary file test-data/toolshed.g2.bx.psu.edu_repos_petr-novak_dante_dante_1.0.0.tgz has changed