Single or double quotation mark in descr file matters

[qifei9]

When single quotation mark is used for the seq parameters in the descr files, the behavior is weird.

Tested on sequence:

>t
TTTT

When single quotation marks are used in descr file, for example:

descr
ss(seq='^TT')

no motif could be found. Also seq='^UU' and seq='^uu' result in no motif found. Only seq='^tt' could find the motif.

However, when double quotation marks are used, all of seq="^TT", "^tt", "^UU", "^uu" could find the motif.

Is this the designed behavior or a bug?

[dacase]

On Tue, Dec 14, 2021, qifei9 wrote: When single quotation mark is used for the `seq` parameters in the descr files, the behavior is weird.

Thanks for the report. It's been a long time since this code was written, and not by me. I'll cc- this to Tom Macke. All of the examples in the documentation use double quotes, so this is clearly the intended use case, and the one that has been tested. But the rmlex.l parser appears to treat single and double-quoted strings the same -- compare line 103ff with 121ff. So I don't immediately see the source of the problem. Maybe Tom will remember something here. ....regards...dac

[dacase]

Here is the reply from Tom Macke:

seq="gnra" with double quotes considers the letters to be IUPAC base codes, so n
= [acgt] and r = [ag]
seq='gnra' with single quotes considers the letters to be letters, so n = n and r
= r.
Both 'xxx' and "xxx" are strings. But in the case of "xxx", the xxx is passed to
RM_str2seq() and any letters that are IUPAC codes are converted to char classes
in the stored string value.. In the case of 'xxx' the string value is xxx.
RM_str2seq() is at line 117 of rmlex.l in the code for processing "" strings. but
it is not used in the code for processing '' strings.
I'm pretty sure this is in the doc as I remember the Isis people thought the two
types of strings were pretty cool.
Hope this helps, if not ask more questions and I'll try again.

I'm embarassed (but not surprised) that I missed the difference in rmlex.l between single and double quoted strings. Plus, the distinction between single and double quotes is explained in the middle of p. 15 of rnamotif.pdf. But we should probably have a cross-reference to this explanation earlier in the document -- I'll work on that.

[qifei9]

Thank you very much for this software and for the reply. Sorry that I missed that part in the manual.

Is it OK to report/ask more issue/question in this repo? Perhaps it would also be misreading of manual...

[dacase]

On Thu, Dec 16, 2021, qifei9 wrote: Is it OK to report/ask more issue/question in this repo? Perhaps it would also be misreading of manual...

By all means...please create issues as questions arise. The info about single and double quotes was pretty well hidden in the manual, so your question was a good one.

[dacase]

Reopening this issue so I don't forget my promise to update the Reference Manual.