[EMBOSS] Conservation of FASTQ scores by the EMBOSS tools.

Charles Plessy charles-listes-emboss at plessy.org
Thu Sep 17 06:36:59 UTC 2009

Le Wed, Sep 16, 2009 at 10:12:16AM +0100, Mahmut Uludag a écrit :
> seqret returns quality scores if the input sequence format is explicitly
> defined on the command line, such as -sformat=fastq-sanger.
> The following patch looks like fixes the vectorstrip problem.

Le Wed, Sep 16, 2009 at 10:31:22AM +0100, Peter a écrit :
> You need to use "fastq-sanger" (or the other variants), since in
> EMBOSS, "fastq" currently means FASTQ ignoring the qualities.

Hi Mahmut and Peter, and thank you very much for your answers!

I would also like if the qualities were kept by default. I actually had tried
to force the fastq-sanger format before, but by adding its name to the USAs,
like in ‘seqret fastq-sanger::stdin fastq-sanger::stdout’. Unfortunately it did
not work; I do not know if it is by design or because of the dash in the format
name. Nevertheless -sformat=fastq-sanger and -osformat=fastq-sanger worked very
well after I applied Mahmut's patch.

I am tempted to apply it also to the Debian EMBOSS package, but maybe it is too
prematurate. In particular, I have the following warning each time the quality
is encoded by an equal sign:

  Warning: Illegal character '='
  Warning: Illegal pattern: =

By the way, I think I found a bug in revseq: it seems that it does not reverse
the qualities:

  $ echo -e "@toto\nACTG\n+toto\n12/3" | seqret -filter -sformat=fastq-sanger -osformat=fastq-sanger
  $ echo -e "@toto\nACTG\n+toto\n12/3" | revseq -filter -sformat=fastq-sanger -osformat=fastq-sanger
  @toto Reversed:

Also, in contrary to what the documentation predicts, using the fastq format
for the output does not ignore the quality scores. (Not that would be
particularly useful, but…)

  $ echo -e "@toto\nACTG\n+toto\nACTG" | revseq -filter -sformat=fastq-sanger -osformat=fastq
  @toto Reversed:

Have a nice day,

Charles Plessy
Tsurumi, Kanagawa, Japan

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