field delimiter uses any char as to declare a new field instead of full string

Hi all,

I've been having a problem with function strread (I also tried it with textscan, but the problem still).

Assume I have this line: str= 'Name=conserved hypothetical protein;description=null;locus=gene3654c'

I want to use as field delimiter 'locus='

Then, I would have as last field gene3654c.

I've been trying the following (and some variations): id = strread(str,'%s', 'delimiter', 'locus=')

However, the output of id becomes: id =

    'Name'
    ''
    ''
    'n'
    'erved hyp'
    'theti'
    'a'
    'pr'
    'tein;de'
    ''
    'ripti'
    'n'
    'n'
    ''
    ''
    ';'
    ''
    ''
    ''
    ''
    ''
    'gene3654'

And it cuts the "c" of gene3654. But I don't want it.

I could solve this problem changing the way I parse my string. However, a question is still in my mind:

How do I use as full string as field delimiter? i.e., using as delimiter 'locus=', it should return: id = 'Name=conserved hypothetical protein;description=null;' 'gene3654c'

Answer 1

[Jiro Doke]

Use Regular Expressions, such as regexp:

id = regexp(str, '(locus=)', 'split')

[Oleg Komarov]

+1

[Antonio]

Thanks! I knew it should have a way to solve this problem.

Answer 2

[Matt Fig]

Just so you understand what happened when you set the delimiter to 'locus=', MATLAB interprets the delimiter property as a list of individual characters to use as delimiters. Thus each character in 'locus=' was used as a delimiter. Jiro showed you how to use REGEXP to specify 'locus=' as a delimiter. You could also get just the string following 'locus=' by using REGEXP:

regexp(str,'(?<=locus\=).*','match')

I am not sure what you mean by, "Then, I would have as last field Rv3654c." Where does the Rv come from?

[Jiro Doke]

Ah, good explanation about why it didn't work for strread.

I assumed "Rv" was a typo. At the end of the question, he has "gene3654c".

[Antonio]

Thanks!

Yes, Rv was a typo. Sorry about that.