Format option ignored occasionally in 1.5

[GoogleCodeExporter]

cutadapt --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq 
--adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG 
--adapter=CTCTTCCGATCT  --minimum-length=25 -o 
/v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_f
astq.trimmed.tmp.txt -p 
/v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_f
astq.trimmed.tmp.txt 
/v-data/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt

/v-data/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt

   cutadapt.main()
  File "/home/vagrant/anaconda/envs/bcbio/lib/python2.7/site-packages/cutadapt-1.5-py2.7-linux-x86_64.egg/cutadapt/scripts/cutadapt.py", line 843, in main
    colorspace=options.colorspace, fileformat=options.format)
  File "/home/vagrant/anaconda/envs/bcbio/lib/python2.7/site-packages/cutadapt-1.5-py2.7-linux-x86_64.egg/cutadapt/seqio.py", line 429, in __init__
    self.reader1 = SequenceReader(file1)
  File "/home/vagrant/anaconda/envs/bcbio/lib/python2.7/site-packages/cutadapt-1.5-py2.7-linux-x86_64.egg/cutadapt/seqio.py", line 224, in SequenceReader
    raise UnknownFileType("Could not determine whether this is FASTA or FASTQ: file name extension {0} not recognized".format(ext))
cutadapt.seqio.UnknownFileType: Could not determine whether this is FASTA or 
FASTQ: file name extension .txt not recognized

The same command works fine with 1.4.2.

Thanks for keeping up working on cutadapt; maintaining software is a lot of 
work and not very glamorous. I appreciate all of your work.

Original issue reported on code.google.com by rory.kir...@gmail.com on 15 Aug 2014 at 3:56

[GoogleCodeExporter]

Thanks for the nice words :-).

And you're right, this is a bug. Thanks for reporting it! This happened because 
I slightly changed how paired-end files are read. It's now fixed in the 
repository: 
https://github.com/marcelm/cutadapt/commit/4c39ab4a3bda386858e286d4d5440f2ab1a9a
3e2 .

Original comment by marcel.m...@tu-dortmund.de on 19 Aug 2014 at 12:48

• Changed state: Fixed

[GoogleCodeExporter]

Issue 78 has been merged into this issue.

Original comment by marcel.m...@tu-dortmund.de on 20 Aug 2014 at 8:02