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parsing confusion: for icarus gurus only

Tim Dudgeon dudgeon at britbio.co.uk
Fri Oct 3 10:24:34 EST 1997


Hi,

Could someone explain to me why this works

#!/bin/env icarus
$rules={

  entry:    ~ {$In:[file:text] $Out pre{$Skip:0}}
              ('>' {$Not} ln)* 
              '>' {$entryFip=$Fip $Wrt}
              ('>' {$Not} ln {$App})*
            ~
  ln:       ~ /[^\n]*\n/  ~
}
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/fasta/format/file']
  while:$JobHasInput:$job {
   $JobTokens:[$job name:entry print:1] 
    $JobNext:$job
  }
}

but this doesn't, because it only gets the first entry in the file

#!/bin/env icarus
$rules={
  data:     ~ {$In:[file:text] $Out pre{$Skip:0}}
              ln {$Wrt} (ln {$App})*
            ~

  entry:    ~ {$In:data $Out}
              ('>' {$Not} ln)* 
              '>' {$entryFip=$Fip $Wrt}
              ('>' {$Not} ln {$App})*
            ~
 
  ln:       ~ /[^\n]*\n/  ~
}
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/fasta/format/file']
  while:$JobHasInput:$job {
   $JobTokens:[$job name:entry print:1] 
    $JobNext:$job

  }
}


The example is a bit contrived, but I need to break up a file into bits
before parsing because the data for each entry is non-contiguous, and I
can't get it to work.

Many thanks for suggestions

Tim



-- 
Dr. Tim Dudgeon                           Phone: 01865 748747
British Biotech Pharmaceuticals Ltd.      FAX:   01865 717598
Watlington Road, Oxford, OX4 5LY, UK      email: dudgeon at britbio.co.uk




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