[mira_talk] Re: convert_project: fasta to fastq
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 24 Apr 2011 00:05:20 +0200
On Apr 23, 2011, at 23:49 , Stephanie Pearl wrote:
> I would like to convert_project to convert my fasta files into a fastq file,
> but I'm not sure what my input should be. I saw the examples on how to
> convert one file into another file type, but I would like to combine my
> separate .fna and .qual files (in fasta format) into a single fastq file. Any
> suggestions on this?
How convenient that I just started writing a man page for convert_project.
Back to your problem.
convert_project does not have a mode to convert multiple files at once ... or
to append to existing files (but maybe I should think of that). The only way to
do what you want is to successively convert and then concatenate. As in:
convert_project -f fasta -t fastq in1.fasta out1
convert_project -f fasta -t fastq in2.fasta out2
convert_project -f fasta -t fastq in3.fasta out3
...
cat out1.fastq out2.fastq out3.fastq ... >mynewfile.fastq
Agreed, not the most effective way to handle things like these, but it works
good enough most of the time.
B.
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