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Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 25 Jul 2016 14:09:29 +0200
Description: We do not start the scripts at the location where the
executable is hanging around.
--- a/basecall_no_metrichor.py
+++ b/basecall_no_metrichor.py
@@ -156,7 +156,7 @@ def basecall(read_file_name, fo):
if do_2d and "comp_events2" in data and\
len(data["comp_events2"]) <= args.max_2d_length and\
len(data["temp_events2"]) <= args.max_2d_length:
- p = subprocess.Popen("./align_2d", stdin=subprocess.PIPE, stdout=subprocess.PIPE)
+ p = subprocess.Popen("/usr/lib/deepnano/align_2d", stdin=subprocess.PIPE, stdout=subprocess.PIPE)
f2d = p.stdin
print >>f2d, len(o1)+len(o2)
for a, b in zip(o1, o2):
--- a/basecall_no_metrichor_devel.py
+++ b/basecall_no_metrichor_devel.py
@@ -297,7 +297,7 @@ for i, read in enumerate(args.reads):
print >>f2d, " ".join(map(str, a))
print >>f2d, " ".join(map(str, b))
f2d.close()
- os.system("./align_2d <2d.in >2d.out")
+ os.system("/usr/lib/deepnano/align_2d <2d.in >2d.out")
f2do = open("2d.out")
call2d = f2do.next().strip()
print >>fo, ">%d_2d_rnn_simple" % i
--- a/training/train.py
+++ b/training/train.py
@@ -32,7 +32,7 @@ def realign(s):
f.close()
print "s", s
- if os.system("./realign <%stmpb-%s.in >%stmpb-%s.out" % (base_dir, s, base_dir, s)) != 0:
+ if os.system("/usr/lib/deepnano/realign <%stmpb-%s.in >%stmpb-%s.out" % (base_dir, s, base_dir, s)) != 0:
print "watwat", s
sys.exit()
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