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a regular expression inquiry


for an array element $fields[$j] containing:

gb:AF367205.1 DB_XREF=gi:17225988 TID=Os.1005.1 CNT=36 FEA=FLmRNA
TIER=FL+Stack STK=9 UG=Os.1005 DEF=Oryza sativa 1-deoxy-D-xylulose
5-phosphate reductoisomerase precursor, mRNA, complete cds; nuclear gene for
plastid product. PROD=1-deoxy-D-xylulose 5-phosphate
reductoisomeraseprecursor FL=gb:AK059692.1 gb:AK099702.1 gb:AF367205.1
REP_ORG=O. sativa

i try to extract useful content by:

if (preg_match("/PROD=(.+)\s{2}/", $fields[$j], $match ) )
$fields[$j] = $match[1];
else if (preg_match("/UG_TITLE=(.+)\s{2}/", $fields[$j], $match ) )
$fields[$j] = $match[1];
else if (preg_match("/DEF=(.+)\s{2}/", $fields[$j], $match ) )
$fields[$j] = $match[1];
i have confirmed it is 2 spaces (i.e. not tab, linefeed, new line). i just
don't know why sometimes it gives me:

PROD=1-deoxy-D-xylulose 5-phosphate reductoisomeraseprecursor
FL=gb:AK059692.1 gb:AK099702.1 gb:AF367205.1

or more (i.e. run-on matching). i don't know if it deals anything with
matching as much as possible. i also tried:

"/DEF=(.+)\s{2}[A-Z].*/" but it still doesn't work. BTW, because i know
sometimes what i want is at the end, so i also use "/DEF=(.+)$|\s{2}/" but
it also doesn't work.

i really appreciate anybody could help on this. i feel really desperated as
i find difficult to find out relevant documentatoin to explain why this
special case fails. thanks a lot
Jun 9 '06 #1
4 1178
Tim

vito wrote:
for an array element $fields[$j] containing:

gb:AF367205.1 DB_XREF=gi:17225988 TID=Os.1005.1 CNT=36 FEA=FLmRNA
TIER=FL+Stack STK=9 UG=Os.1005 DEF=Oryza sativa 1-deoxy-D-xylulose
5-phosphate reductoisomerase precursor, mRNA, complete cds; nuclear gene for
plastid product. PROD=1-deoxy-D-xylulose 5-phosphate
reductoisomeraseprecursor FL=gb:AK059692.1 gb:AK099702.1 gb:AF367205.1
REP_ORG=O. sativa

i try to extract useful content by:

if (preg_match("/PROD=(.+)\s{2}/", $fields[$j], $match ) )
$fields[$j] = $match[1];
else if (preg_match("/UG_TITLE=(.+)\s{2}/", $fields[$j], $match ) )
$fields[$j] = $match[1];
else if (preg_match("/DEF=(.+)\s{2}/", $fields[$j], $match ) )
$fields[$j] = $match[1];
i have confirmed it is 2 spaces (i.e. not tab, linefeed, new line). i just
don't know why sometimes it gives me:

PROD=1-deoxy-D-xylulose 5-phosphate reductoisomeraseprecursor
FL=gb:AK059692.1 gb:AK099702.1 gb:AF367205.1

or more (i.e. run-on matching). i don't know if it deals anything with
matching as much as possible.


Yeah thats it.

(.+)\s{2}

Is a greedy match, it will match to the last two spaces it finds and
not the first.
Adding a ? after the brackets make it a non greedy match.

(.+)?\s{2}

Tim

Jun 9 '06 #2
Rik
Tim wrote:
Yeah thats it.

(.+)\s{2}

Is a greedy match, it will match to the last two spaces it finds and
not the first.
Adding a ? after the brackets make it a non greedy match.

(.+)?\s{2}

Good explanation, totally correct, but nort the right regex:
(.+)?\s{2}
means:
(A random character 1 or mor times) zero or once.

explanation was good, regex should be:

(.+?)\s{2}

As I've learned, correct me if I'm wrong, the ? to make a selector
non-greedy should be directly after the selector itself AFAIK.

Grtz,
--
Rik Wasmus
Jun 10 '06 #3
> Yeah thats it.

(.+)\s{2}

Is a greedy match, it will match to the last two spaces it finds and
not the first.
Adding a ? after the brackets make it a non greedy match.

(.+)?\s{2}

Tim


thanks but it seems it doesn't work. adding one more ? at the end also
helps nothing. :(

"/DEF=(.+)?\s{2}?/"
Jun 10 '06 #4
> Good explanation, totally correct, but nort the right regex:
(.+)?\s{2}
means:
(A random character 1 or mor times) zero or once.

explanation was good, regex should be:

(.+?)\s{2}

As I've learned, correct me if I'm wrong, the ? to make a selector
non-greedy should be directly after the selector itself AFAIK.


you're correct! Thanks, it works.
Jun 10 '06 #5

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