actapia
commented
3 years ago I encountered the same error. I believe this is a problem with the cufflinks package from Debian—not the upstream cufflinks. The package maintainers apply a patch to make cuffmerge work with Python 3, but it seems they neglected to change the calls to open. Here's a short patch that should fix it.
--- a/src/cuffmerge
+++ b/src/cuffmerge
@@ -56,6 +56,21 @@
def __init__(self, msg):
self.msg = msg
+# Unbuffered class from Magnus Lycka
+# Wraps a stream so that writes are always flushed.
+# https://mail.python.org/pipermail/tutor/2003-November/026645.html
+class Unbuffered(object):
+ def __init__(self, stream):
+ self.stream = stream
+ def write(self, data):
+ self.stream.write(data)
+ self.stream.flush()
+ def writelines(self, datas):
+ self.stream.writelines(datas)
+ self.stream.flush()
+ def __getattr__(self, attr):
+ return getattr(self.stream, attr)
+
class TestParams:
class SystemParams:
@@ -523,7 +538,7 @@
start_time = datetime.now()
prepare_output_dir()
- run_log = open(logging_dir + "run.log", "w", 0)
+ run_log = Unbuffered(open(logging_dir + "run.log", "w"))
run_cmd = " ".join(argv)
print(run_cmd, file=run_log)
Vermarashi
RahmatAderemi
Hi I was using cuffmerge for merging my transcripts..gtd file. I get the following error Thu May 13 23:19:38 2021] Preparing output location ./merged_asm/ Traceback (most recent call last): File "/usr/bin/cuffmerge", line 580, in
sys.exit(main())
File "/usr/bin/cuffmerge", line 526, in main
run_log = open(logging_dir + "run.log", "w", 0)
ValueError: can't have unbuffered text I/O
Ive tried switching my python version from 3.8 to 2.7... Any suggestions to solve this error would be much appreciated
Thanks in advance