Allow .fq extension

[GoogleCodeExporter]

Would it be possible to allow .fq as an extension or to have an option to 
specify the input format? I know it's a tiny point but it would avoid me 
renaming or soft linking all the files I currently have.

Original issue reported on code.google.com by n.r.str...@gmail.com on 17 Mar 2011 at 7:46

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

Good point! Since cutadapt can look at the file contents and autodetect the 
file type from that, I guess it also makes sense to ignore the extension 
entirely.

For now, open lib/cutadapt/seqio.py and change the line 75:
                elif ext in ['.fastq']:
into
                elif ext in ['.fastq', '.fq']:

I will leave this issue open until I have implemented a proper solution.

Original comment by marcel.m...@tu-dortmund.de on 17 Mar 2011 at 8:17

[GoogleCodeExporter]

Allowing the user to specify the input format and overriding the extension 
and/or filecheck would be helpful when integrating this tool into workflows 
where the filenames may not be easily changed (e.g. Galaxy).

Original comment by lancepar...@gmail.com on 12 Apr 2011 at 5:43

[GoogleCodeExporter]

The input format can now be specified via the -f or --format command-line 
option. This will be part of cutadapt 0.9.5, to be released soon.

Original comment by marcel.m...@tu-dortmund.de on 17 May 2011 at 1:07

• Changed state: Fixed

[GoogleCodeExporter]

Being able to specify the format is great, but it would still be convenient to 
have .fq as a recognized fastq format extension, since it's fairly common. Same 
for .fa for fasta.

Original comment by pat...@gmail.com on 10 Jun 2011 at 11:55

[GoogleCodeExporter]

Thanks for the reminder, I had intended to do this, but forgotten. I've just 
changed this: .fq is now autodetected as FASTQ.

The following extensions are already recognized as FASTA:
.fasta, .fa, .fna, .csfasta, .csfa

Original comment by marcel.m...@tu-dortmund.de on 14 Jun 2011 at 7:32