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  • Whitespace in FASTA file

    I am making FASTA files from a bowtie index using bowtie-inspect. When I use this file in mirDeep I get the error:

    'Error: Genome file file.fa has not allowed whitespaces in its first identifier'

    I know the whitespace is between the >sequencid and the sequence but for the life of me I cannot figure how to add one that will be recognized.

    I have been trying text editors, vi, emacs to no avail by adding a space or tab and none of these work. A colleague suggested I sed it but I am not sure what I would use to replace the space that is there with white space.

    Any suggestions are appreciated.

  • #2
    You CAN'T have whitespaces in the identifier. Try none.

    Edit: realized you meant after the identifier.
    I would substitute all non-\n whitespace with one \n. In any situation like this, take the first fasta record on it's own (via "head ..." ) and work with it as a separate file.

    This page may be helpful for dealing with whitespace-except-\n: http://stackoverflow.com/questions/3...-newlines-perl

    Comment


    • #3
      Yeah that is where I was confused and I removed all from the identifier and it still did not work, and then I removed all from the whole file and now it works.

      Strange bug but no whitespace at all seems to have resolved it.

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