<?xml version="1.0"?>
<!DOCTYPE gs540_hw [ 
  <!ELEMENT gs540_hw (results, results, results, analysis, program)>
  <!ELEMENT result ANY>
  <!ELEMENT results ANY>
  <!ELEMENT program (comments, file+)>
  <!ELEMENT comments ANY>
  <!ELEMENT file ANY>
  <!ELEMENT analysis ANY>
  <!ATTLIST file name CDATA #REQUIRED>
  <!ATTLIST gs540_hw assignment CDATA #REQUIRED>
  <!ATTLIST gs540_hw name CDATA #REQUIRED>
  <!ATTLIST gs540_hw email CDATA #REQUIRED>
  <!ATTLIST results type (part1|part2|part3) #REQUIRED>
  <!ATTLIST results file CDATA #IMPLIED>
  <!ATTLIST result type (first_line|edge_weights|edge_histogram|score|beginning_vertex|ending_vertex|path) #REQUIRED>
  <!ATTLIST result file CDATA #IMPLIED>
]>
<gs540_hw assignment='2' name='Alan Rubin' email='afrubin@u.washington.edu'>
  <results type='part1' file='../data/sample_graph.txt'>
    <result type='edge_weights'>
      A=-1, B=5, C=-2, D=4, E=-3, F=2, G=-3, H=-5, I=4, J=-3, K=1, L=-3
    </result>
    <result type='edge_histogram'>
      A=1, B=1, C=1, D=1, E=1, F=1, G=1, H=1, I=1, J=1, K=1, L=1
    </result>
    <result type='score'>
      8
    </result>
    <result type='beginning_vertex'>
       vi 
    </result>
    <result type='ending_vertex'>
       ii 
    </result>
    <result type='path'>
      ID
    </result>
  </results>

  <results type='part2' file='../data/sample_graph_constrained.txt'>
    <result type='edge_weights'>
      A=-1, B=5, C=-2, D=4, E=-3, F=2, G=-3, H=-5, I=4, J=-3, K=1, L=-3
    </result>
    <result type='edge_histogram'>
      A=1, B=1, C=1, D=1, E=1, F=1, G=1, H=1, I=1, J=1, K=1, L=1
    </result>
    <result type='score'>
      4
    </result>
    <result type='beginning_vertex'>
       vii 
    </result>
    <result type='ending_vertex'>
       i 
    </result>
    <result type='path'>
      LIDA
    </result>
  </results>

  <results type='part3' file='../results/Pyrococcus_furiousus.graph.txt'>
    <result type='first_line' file='Pyrococcus_furiousus.fasta'>
      >gi|18976372|ref|NC_003413.1| Pyrococcus furiosus DSM 3638, complete genome
    </result>
    <result type='edge_weights'>
      A=-1.49,T=-1.49,G=0.74,C=0.74
    </result>
    <result type='edge_histogram'>
      A=565156, C=388629, T=565106, G=389365
    </result>
    <result type='score'>
       50.22
    </result>
    <result type='beginning_vertex'>
      9569
    </result>
    <result type='ending_vertex'>
      9890
    </result>
    <result type='path'>
    GGCGGCGGGCTAGGCCGGGGGGTTCGGCGTCCCCTGTAACCGGAAACCGCCGATATGCCG
    GGGCCGAAGCCCGGGGGGCGGTTCCCAAAGCCGCTCCCAGAAGCCGAGGTCGAACGATGA
    GTCCTCGTCCCGCGGGGTGCCCGGTGGGGGAGGCACGGCTGAAGGGCCGTGCTAACCCCC
    TTTGGGCCCCGAACCCCGCAAGGCCCGGAAGGGAGCAGCGGTAGGGGCCACGGAGCACGC
    TCGCGGGGGTGCGGGGATGAGATAGGCCTCGGTGGATGGGAGCGGTGGAGGGTTCCCACC
    CTCGGGCGTGCCCGCCGCCGC
    </result>
  </results>
  <analysis>
    This sequence corresponds to the structural RNA gene PF_s001.  
  </analysis>
  <program>
     <comments> 
       Run the two bash files, the first for part 1, the second for part2. 
       They call the python scripts, which write results to standard out.
     </comments>
     <file name='hw2_part1.bash'>
<![CDATA[
        python hello_world_part1.py 
]]>
     </file>
     <file name='hello_world_part1.py'>
<![CDATA[
        """
  This script writes 'hello world' to the standard out
        """
        if __name__ == '__main__':
     print "hello world"
]]>
      </file>

     <file name='hw2_part2.bash'>
<![CDATA[
       python hello_world.py 
]]>
     </file>
     <file name='hello_world_part2.py'>
<![CDATA[
        """
  This script writes 'hello world' to the standard out
        """
        if __name__ == '__main__':
     print "hello world"
]]>
      </file>

  </program>
</gs540_hw>

