Warning Gumbie Question

grits

OK at the risk of being abused here we go 😉
I am trying to write a script which searches one file with the contents of another file one line at a time. That is the target file is similar to

this line contains info
abcdef abecde
khbibioub
kjbiubiub
jhbviyubiub
more info for the followin data
ugvuiyviyv
uiybiubiub
iuybiubiub
etc
for those of you in science this is a list of FASTA sequences.
I need to search this file with each of the terms in a file containing a list:
first item
second item
third item
etc

I have already loaded the second file into an array so I can just do an itterative loop and step through it. The trouble I am having is getting php to do a text search and to keep the line begining with ">" and all the data after it until the next ">".
Phew hmm not bad for my first post here 😉

Thanx for any help in advance guys

MrAlaska

The 'file' functions will go through a file one line at a time or you can break the file up by splitting it on the '>'. It seems whatever you are trying to do would be done within a nested foreach loop. Perhaps if you post your code and the problems you are having it might be simpler to figure out.

This might help:
http://www.php.net/manual/en/function.preg-split.php

Or exploding the file might be a better alternative:
http://www.php.net/manual/en/function.explode.php

grits

Hmm sorry must have not explained myself well enough. The problem is not so much with the files, it is to do with the search function. The code I have is just putting the search terms into an array. This works fine. I now need to do a search loop, something like:
search for arrayterm[0]
if found print from target file from Line starting with ">" containing match until the next ">".
do it again with arrayterm[1]
until end of searchterms

Does this make it a bit clearer?? I could put the search file into an array split on ">" but how do I then search that array?? I have tried strstr() etc but they don't seem to work ie I get no match when I know there is one.
Thanx

MrAlaska

It makes it a HELL of a lot easier to help with scripting problems if you post the code that is giving you trouble! strstr() should work. I have no idea why it isn't, of course, because I have no idea what you are tring to do with it.

In this example I use stristr() to make the search case insensitve, but it works just the sam with strstr. Give this a try:

<?php
//build the search array
$search=array("khbibioub","kjbiubiub");

//import the file into a variable named $file
$file="
this line contains info
abcdef abecde
khbibioub
kjbiubiub
jhbviyubiub
more info for the followin data
ugvuiyviyv
uiybiubiub
iuybiubiub
etc
";
//parse out the lines of the file
$lines=explode(">",$file);
//go through the lines one at a time
foreach($lines as $line){
	//go through each search word
	foreach($search as $word){
		//check for a match against that word
		if(stristr($line, $word)){
			//print the line if a match exists
			echo $line."<br>";
			//do not check for duplicate matches for this line
			break;
		}
	}
}
?>

grits

Ok
Thanx for the help Mr A
I finally found my problem, it was confusing the File Handle and string variable concept.
A real newbie eh 😉 With your code and some other modified code I can do what I wanted.
Once again thanx for the education
Grits