old_contents: #!/usr/bin/env python
  
  #script to tease apart maker gff into EVM input
  
  import sys
  
  tr = 'transcript_alignments.gff3'
  pr = 'protein_alignments.gff3'
  gr = 'gene_predictions.gff3'
  
  with open(tr, 'w') as trout:
      with open(pr, 'w') as prout:
          with open(gr, 'w') as grout:
              with open(sys.argv[1], 'rU') as input:
                  for line in input:
                      if line.startswith('#'):
                          continue
                      cols = line.split('\t')
                      if 'maker' in cols[1]:
                          if not 'trnascan' in cols[8]:
                              grout.write(line)
                      elif 'protein2genome' in cols[1]:
                          if 'match_part' in cols[2]:
                              line = line.replace('match_part', 'nucleotide_to_protein_match')
                              prout.write(line)
                      elif 'est2genome' in cols[1]:
                          if 'match_part' in cols[2]:
                              line = line.replace('match_part', 'EST_match')
                              trout.write(line)
                      elif 'cdna2genome' in cols[1]:
                          if 'match_part' in cols[2]:
                              line = line.replace('match_part', 'EST_match')
                              trout.write(line)
new_contents: #!/usr/bin/env python
  
  #script to tease apart maker gff into EVM input
  
  import sys
  
  tr = 'transcript_alignments.gff3'
  pr = 'protein_alignments.gff3'
  gr = 'gene_predictions.gff3'
  
  with open(tr, 'w') as trout:
      with open(pr, 'w') as prout:
          with open(gr, 'w') as grout:
              with open(sys.argv[1], 'rU') as input:
                  for line in input:
                      if line.startswith('#'):
                          continue
                      if 'ID=trnascan' in line:
                          continue
                      cols = line.split('\t')
                      if 'maker' in cols[1]:
                          grout.write(line)
                      elif 'protein2genome' in cols[1]:
                          if 'match_part' in cols[2]:
                              line = line.replace('match_part', 'nucleotide_to_protein_match')
                              prout.write(line)
                      elif 'est2genome' in cols[1]:
                          if 'match_part' in cols[2]:
                              line = line.replace('match_part', 'EST_match')
                              trout.write(line)
                      elif 'cdna2genome' in cols[1]:
                          if 'match_part' in cols[2]:
                              line = line.replace('match_part', 'EST_match')
                              trout.write(line)
subject: update to maker parsing