Allow .fq extension about cutadapt HOT 5 CLOSED

From [email protected] on March 17, 2011 01:17:51

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.

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From [email protected] on April 12, 2011 10:43:56

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).

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From [email protected] on May 17, 2011 06:07:43

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.

Status: Fixed

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From [email protected] on June 10, 2011 16:55:52

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.

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From [email protected] on June 14, 2011 00:32:09

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

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