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 @toto ACTG + 12/3 $ echo -e "@toto\nACTG\n+toto\n12/3" | revseq -filter -sformat=fastq-sanger -osformat=fastq-sanger @toto Reversed: CAGT + 12/3 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: CAGT + ACTG Have a nice day, -- Charles Plessy http://charles.plessy.org Tsurumi, Kanagawa, Japan _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
