a regular expression inquiry

Collapse
This topic is closed.
X
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • vito
    #1

    a regular expression inquiry




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

    gb:AF367205.1 DB_XREF=gi:1722 5988 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 reductoisomeras e precursor, mRNA, complete cds; nuclear gene for
    plastid product. PROD=1-deoxy-D-xylulose 5-phosphate
    reductoisomeras eprecursor 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 reductoisomeras eprecursor
    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


    Tags: None
    • Tim
      #2
      Re: a regular expression inquiry


      vito wrote:[color=blue]
      > for an array element $fields[$j] containing:
      >
      > gb:AF367205.1 DB_XREF=gi:1722 5988 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 reductoisomeras e precursor, mRNA, complete cds; nuclear gene for
      > plastid product. PROD=1-deoxy-D-xylulose 5-phosphate
      > reductoisomeras eprecursor 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 reductoisomeras eprecursor
      > 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.[/color]

      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

        Comment

        • Rik
          #3
          Re: a regular expression inquiry

          Tim wrote:[color=blue]
          > 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}[/color]


          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


            Comment

            • vito
              #4
              Re: a regular expression inquiry

              > Yeah thats it.[color=blue]
              >
              > (.+)\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
              >[/color]

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

              "/DEF=(.+)?\s{2}?/"


                Comment

                • vito
                  #5
                  Re: a regular expression inquiry

                  > Good explanation, totally correct, but nort the right regex:[color=blue]
                  > (.+)?\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.
                  >[/color]

                  you're correct! Thanks, it works.


                    Comment

                    Previous template Next
                    Working...