[EMBOSS] pasteseq

pmr at ebi.ac.uk pmr at ebi.ac.uk
Tue Dec 13 08:46:00 UTC 2005

Dear Amit,

> I'm an EMBOSS newbie but have a simple question. For the pasteseq
> program I'm trying to paste in the character '-' into my sequence:
>> pasteseq -asequence foo.fa -bsequence insert.fa -pos 1 -outseq temp.fa
> But my sequence is unchanged after I run the above command. However if
> I change insert.fa to be the sequence NN it works fine. Is there
> anyway I can insert the '-' character

Ah ... it seems we have no program that does this easily. pasteseq is
really for merging two sequences, rather than sequence editing.

However, the reason pasteseq rejects your gaps is because both inputs are
of type sequence and have no gaps.

It makes sense to allow them. Change emboss/acd/pasteseq.acd to have the
sequence input definitions below (only the types have changed) and "make
install" again - or, simply copy the pasteseq.acd file to overwrite the
installed one in (by default) /usr/local/share/EMBOSS/acd/pasteseq.acd

We will make this change in the next release.

Hope that helps,



section: input [
  information: "Input section"
  type: "page"

  sequence: asequence  [
    parameter: "Y"
    type: "gapany"

  sequence: bsequence  [
    parameter: "Y"
    information: "Sequence to insert"
    type: "@($(acdprotein) ? gapstopprotein : gapnucleotide)"

endsection: input

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