Select query to retrieve text column with hyphen, comma, period and parantheses - php

Question

Thanks for taking time to read my question.
I have created a MySQL table, a HTML form and a program in PHP which connects the form to MySQL table and retrieves sequences for column Annotations which is text data type.
This column has characters and also has one or more of hyphen, comma, parentheses, period or spaces.
Please look at the following code that I used for select query:
$values=mysql_query("SELECT Sequence
FROM oats
WHERE Foldchange = '$Foldchange' AND
RustvsMockPvalue = '$RustvsMockpvalue' AND
Annotations REGEXP '%$Annotation%[-]+'");
Here $Annotation is the form variable which holds the value entered by the user in the form. Annotations is the column name in the MySQL table.
Annotations column has characters A-Z or a-z and one or more of hyphen, comma, space or parentheses like the following.
Sequence is another text column in the MySQL table but does not have ,./().
Example data from Annotations column:
ADP, ATP carrier protein,  mitochondrial precursor (ADP/ATP translocase) (Adenine nucleotide translocator) (ANT).
I am not able to retrieve Sequence column data when I search for any Annotations column data with comma, parentheses, period and slash. It works fine for those records which does not have these ,.()/.
I tried to use LIKE instead of REGEX but it didn't work either.
A record from mysql table:(columns that you see below: contigid,source,genelength,rustmeans, mockmeans,foldchange,pvalue,rustmockteststatistic,Annotations and Sequence)
as_rcr_contig_10002 ORME1 2101 506.33 191 -2.18 2.21E-10 -6.35 Tesmin/TSO1-like, CXC domain containing protein. AACAATTCCCCTCAACCAACCTTTTATTTCATCCCATTTTTATCATCTGTCCGGTTACAGATTTTGCTTCCAGTTAGGTGCCACTTCTTCAAACGCTCAACCCTTACCCACTACCACCCCACCAAAACCAACCCCCCAAGATGCAGTTCATCACTCTCGCCGTTGCTTTTGCTTTCTTTGCTGGTGCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTTTGCTTTCTTTGCTGGTGCCACCTCGTCGCCGGTTTCCATGGACCCCAAAGCCGAGAAGTCCGGCTCCTCGGGATCCGGTGGCGCCCCTCTGGGCACTGCTAGCCCCTATCCCCAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTGGCCCTCAGTCGCCAGGCTCTGGCCAACCCGGTAGGATGCCATGGGGTAGCGACCAATCTGCCTACGGTGGTGGTTTCCCTTATGGATCATTCCCCTCGGTTTCGGGGCAATCCCAATCGACGGCCTATGCTCAAGCTCAATCATCCAGTTTCCCCTCAAACGGTGTCCCGACACACTCCTCGGCCTCCGCCCAAGCGCAATCATCCGGTCCTGGACAAGCTCAGGCAGCCGCTTCTGCCCAGGTTCCCGGCGGCCCCCACGGTCAAGGTTCTAACGGATTTGGCGCACAAGGCCAGTTTGGACAGAACGGGCAGAACGGCCTCTATGGTCAAGACGGCAATGGCTTTAGTGCCCAAGGCCAATTTGGACAGAGTGGACAGAATGGCTTCTATGGTCA
Could someone please help me in the correct syntax of the SELECT syntax? Thank you.

Answer 1

You need to familiarise yourself with regex - it's its ownittke language.
Use REGEXP with the right regex:
WHERE ...
AND Annotations REGEXP '[-A-Za-z(). ]+'
AND Annotations NOT_REGEXP '[A-Za-z]+'
If mysql supported regex look aheads, this could be done in one test.
,

Answer 2

First of all, you are not using REGEXP properly.
You should check the differences between LIKE and REGEXP.
REGEXP use Regular expresions, which have very particular syntax.
LIKE use simple text remplacement with key characters like % or _
Here you are using REGEXP with %, that's why it's not working. % is a key character for LIKE only.
But in REGEXP, . and - are special characters that you need to escape to.
If you want to check several characters, REGEXP is the way to go :
Annotations REGEXP '.*$Annotation.*[\-(),\.]+.*'
This match :
.* : 0 to n characters
$Annotation : Your keyword
.* : 0 to n characters
[\-(),\.]+ : At least 1 character from the list : - ( ) , .
.* : 0 to n characters
Tell us if that match your data.

Answer 3

Since we can't craft a Regular Expression that would work in your case without getting into some crazy matching schemes (orders and so forth), In order to find what you're looking for, you'll need to custom construct the SQL statement and luckily you're using PHP.
Here I'm starting with a simple space delimited entry. Remember that you can't wrap something with parenthesis because the parenthesis might not match up in your result set.
$search_input = 'ADP ANT';
//example of array from a search page full of check boxes or fields
$annSearches = explode(' ',$search_input);
/*annSearches is now and array with ADP,ANT*/
$sql = "SELECT Sequence FROM oats WHERE Foldchange = '$Foldchange' AND RustvsMockPvalue = '$RustvsMockpvalue'";
foreach ($annSearches as $Annotation){
$sql .= " AND Annotations LIKE '%$Annotation%'";
}
The output SQL statement would look like this (wrapped for clarity):
SELECT Sequence FROM oats WHERE
Foldchange = '$Foldchange'
AND RustvsMockPvalue = '$RustvsMockpvalue'
AND Annotations LIKE '%ADP%'
AND Annotations LIKE '%ANT%';
If you do a really long query, this will get slower and slower as MySQL has to run through every record in the database over and over for the results.
FULLTEXT SEARCH OPTION
Another way that you could potentially do this is to enable FULLTEXT search functionality on the Annotations field in the table in the database.
ALTER TABLE oats ADD FULLTEXT(Annotations);
This would allow you to do a search something like this:
Sequence FROM oats WHERE
Foldchange = '$Foldchange'
AND RustvsMockPvalue = '$RustvsMockpvalue'
MATCH(Annotations) AGAINST ('ADP ANT')