hi Cee -

  hmm, i'm getting a bit confused as to what exactly you're trying to do 
- but if you want to load all this stuff into a buffer without the 
newlines, and regardless of how many newlines you have between each 
entry (assuming that an "entry" is something that starts with ">") - i 
don't see why this wouldn't work:

f = "0text.txt"
file  = File.open(f)
buffer = []
bufferindex = 0

file.each(sep = ">"){|line|
  buffer[bufferindex] = line
  bufferindex += 1
}

## here you would do something more interesting
buffer.collect{|line|
  line = line.delete("\n")
  p ">#{line}"
}


  which will return...
">>"
">gi|329295464|ref|NM_2005745.3Acc1| Def1 zgc:65895 (zgc:65895), 
mRNAAGCTCGGGGGCTCTAGCGATTTAAGGAGCGATGCGATCGAGCTGACCGTCGCG>"
">gi|456299107|ref|NM_2342343.3Acc2| Def2 zgc:65895 (zgc:65895), 
mRNAGTCGCTGGGTCGAAAAGTGGTGCTATATCGCGGCTCGCGTCGATGTCGCGATGCGTGCGCGCGAGAGCGCGCTATGATGAAAGGATGAGAGAG>"
">gi|3542945647|ref|NM_7453343.5Acc3| Def3 zgc:65895 (zgc:65895), 
mRNACGTGCGGGGABCCGTACGTGCCGTGGGGGTTTAATAGCGCGCCATCTGAGCAGTTAGTCGCTGACGCATGCACG"

  ...whether you have 0 or 100,000 newlines between each entry.  is this 
not what you're looking for?

 -j

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