Sorry for not explaining things better...I have a hard time doing that sometimes. What I'm trying to do is take the target name (ex. 100000_at) and use that as the object to pattern match against. The target name is the only thing that the data sets have in common (I want all the 10000_at, 10001_at sets etc. together). By pattern matching, I hope to be able to print out the interegation positions (where the probe sequences are found in the genome) and sequences (actg's in repetition)for each probe that belongs to a single target. The way the file is arranged, it would seem like I could just use a counter and have it chop up the data for every such-and-such number of lines, but there are apparently a few targets with a varying number of probes. Since that is the case, I have to separate the probe sets based on their relevant target name. I can then import the output file into excel and have a spreadsheet of all the targets, with one row dedicated to the "probes" (stands of dna that are attached to a glass slide) that match that target.
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