input from STDIN stops working when -f option given

[marcelm]

From pat...@gmail.com on August 18, 2011 01:35:31

If I run cutadapt on very simple fasta input, I get an error when taking input from STDIN and using the -f fasta option. When reading input from a file, or not using -f, everything works correctly.

My test input file (test0.fa) contains the following:

perfect
TTTGGGGGGG

I want to test cutadapt taking input from STDIN. With no -f option, it works as expected:

$ cat test0.fa | cutadapt -a GGGGGGGGGGGGGGG -

perfect
TTT
cutadapt version 0.9.4
Command line parameters: -a GGGGGGGGGGGGGGG -
Maximum error rate: 10.00%
Processed reads: 1
Trimmed reads: 1 (100.0%)
Too short reads: 0 ( 0.0% of processed reads)
Too long reads: 0 ( 0.0% of processed reads)
Total time: 0.00 s
Time per read: 0.00 ms

=== Adapter 1 ===

Adapter 'GGGGGGGGGGGGGGG', length 15, was trimmed 1 times.

Histogram of adapter lengths
length count
7 1

However, if I add -f fasta to the options, it stops working:

$ cat test0.fa | cutadapt -f fasta -a GGGGGGGGGGGGGGG -
Traceback (most recent call last):
File "/home/weronika/programs/work_software/cutadapt", line 5, in
pkg_resources.run_script('cutadapt==0.9.4', 'cutadapt')
File "/usr/lib/python2.6/dist-packages/pkg_resources.py", line 461, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python2.6/dist-packages/pkg_resources.py", line 1194, in run_script
execfile(script_filename, namespace, namespace)
File "/home/weronika/programs/work_software/cutadapt-0.9.4-py2.6-linux-x86_64.egg/EGG-INFO/scripts/cutadapt", line 595, in
sys.exit(main())
File "/home/weronika/programs/work_software/cutadapt-0.9.4-py2.6-linux-x86_64.egg/EGG-INFO/scripts/cutadapt", line 546, in main
for desc, seq, qualities in reader:
File "/home/weronika/programs/work_software/cutadapt-0.9.4-py2.6-linux-x86_64.egg/cutadapt/seqio.py", line 154, in _streaming_iter
for line in self.fp:
IOError: File not open for reading

Just to make sure, if I run it with the -f option but reading input from a file instead of STDIN, it also works as expected:

$ cutadapt -f fasta -a GGGGGGGGGGGGGGG test0.fa

perfect
TTT
cutadapt version 0.9.4
Command line parameters: -f fasta -a GGGGGGGGGGGGGGG test0.fa
Maximum error rate: 10.00%
Processed reads: 1
Trimmed reads: 1 (100.0%)
Too short reads: 0 ( 0.0% of processed reads)
Too long reads: 0 ( 0.0% of processed reads)
Total time: 0.01 s
Time per read: 10.00 ms

=== Adapter 1 ===

Adapter 'GGGGGGGGGGGGGGG', length 15, was trimmed 1 times.

Histogram of adapter lengths
length count
7 1

Cutadapt version: cutadapt-0.9.4-py2.6-linux-x86_64.egg

Operating system: Linux, Ubuntu 10.04, 64-bit.
$ uname -a
Linux bleen 2.6.32-32-generic #62-Ubuntu SMP Wed Apr 20 21:52:38 UTC 2011 x86_64 GNU/Linux

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=28

[marcelm]

From marcel.m...@tu-dortmund.de on August 24, 2011 07:08:54

Hi, thanks for the report and sorry for the late reply (due to vacation).

It seems you've stumbled upon an error that I have fixed in the most recent cutadapt version (without putting a note about this in the changelog, sorry).

Please either upgrade to cutadapt 0.9.5 or fix the problem by changing within your file /home/weronika/programs/work_software/cutadapt-0.9.4-py2.6-linux-x86_64.egg/cutadapt/xopen.py the line

return sys.stdout if 'r' in mode else sys.stdin
to
return sys.stdin if 'r' in mode else sys.stdout

Regards,
Marcel

[marcelm]

From pat...@gmail.com on August 25, 2011 17:57:29

Thanks for the very helpful answer! I made the line change, it works now.

[marcelm]

From marcel.m...@tu-dortmund.de on October 07, 2011 05:36:25

Status: Fixed