text: user3209: I was looking for a simple way to do a glocal alignment.
  The case I have is I have a small sequence which should be find in a bigger one, thus typically a glocal alignment.
  Also I can not Install anything on the target machine (Python 3.6 with Biopython is already installed), all I can do is pip install.
  My question is : are there any glocal alignment implementation out there ?
  I was unable to found one and I don't feel proficient enough with Python yet to implement it myself.
  
  user11905: As suggested in the comments, the built-in BioPython pairwise aligner should work for this. You can find a short sequence match in a longer sequence using a global alignment with the right score parameters (query_end_... = 0). The other scoring parameters are values that I've found to be good for aligning similar sequences.
  Example code:
  from Bio import Align
  
  aligner = Align.PairwiseAligner()
  aligner = Align.PairwiseAligner()
  aligner.match_score = 5
  aligner.mismatch_score = -9
  aligner.mode = 'global'
  aligner.target_internal_open_gap_score = -12
  aligner.target_internal_extend_gap_score = -3
  aligner.target_end_open_gap_score = -12
  aligner.target_end_extend_gap_score = -3
  aligner.query_internal_open_gap_score = -12
  aligner.query_internal_extend_gap_score = -3
  
  # Set the query_end penalties to zero to effectively implement a 'glocal' alignment as described in the question
  # These are the default values, so you could skip the next two lines, 
  #    but this is relevant to the question, so I'm including them in the example.
  aligner.query_end_open_gap_score = 0
  aligner.query_end_extend_gap_score = 0
      
  alignments = aligner.align("GAACTCGCATCGATGATCCGTGCGCTGAGATCCGCTGACATGATC", "GATCCG")
  
  for a in alignments:
      print(a)
  print()
  print()
  
  alignments = aligner.align("GAACTCGCATCGATGATCCGTGCGCTGAGATCCGCTGACATGATC", "GATACG")
  
  for a in alignments:
      print(a)
  print()
  print()
  
  alignments = aligner.align("GAACTCGCATCGATGATCCGTGCGCTGAGATCCGCTGACATGATC", "GATACCG")
  
  for a in alignments:
      print(a)
  
  
original_text: 3209: <p>I was looking for a simple way to do a <a href="https://en.wikipedia.org/wiki/Sequence_alignment#Global_and_local_alignments" rel="nofollow noreferrer">glocal alignment</a>.
  The case I have is I have a small sequence which should be find in a bigger one, thus typically a glocal alignment.
  Also I can not Install anything on the target machine (Python 3.6 with Biopython is already installed), all I can do is pip install.</p>
  
  <p>My question is : are there any glocal alignment implementation out there ?</p>
  
  <p>I was unable to found one and I don't feel proficient enough with Python yet to implement it myself.</p>
   11905: <p>As suggested in the comments, the built-in BioPython pairwise aligner should work for this. You can find a short sequence match in a longer sequence using a global alignment with the right score parameters (<code>query_end_... = 0</code>). The other scoring parameters are values that I've found to be good for aligning similar sequences.</p>
  <p>Example code:</p>
  <pre><code>from Bio import Align
  
  aligner = Align.PairwiseAligner()
  aligner = Align.PairwiseAligner()
  aligner.match_score = 5
  aligner.mismatch_score = -9
  aligner.mode = 'global'
  aligner.target_internal_open_gap_score = -12
  aligner.target_internal_extend_gap_score = -3
  aligner.target_end_open_gap_score = -12
  aligner.target_end_extend_gap_score = -3
  aligner.query_internal_open_gap_score = -12
  aligner.query_internal_extend_gap_score = -3
  
  # Set the query_end penalties to zero to effectively implement a 'glocal' alignment as described in the question
  # These are the default values, so you could skip the next two lines, 
  #    but this is relevant to the question, so I'm including them in the example.
  aligner.query_end_open_gap_score = 0
  aligner.query_end_extend_gap_score = 0
      
  alignments = aligner.align(&quot;GAACTCGCATCGATGATCCGTGCGCTGAGATCCGCTGACATGATC&quot;, &quot;GATCCG&quot;)
  
  for a in alignments:
      print(a)
  print()
  print()
  
  alignments = aligner.align(&quot;GAACTCGCATCGATGATCCGTGCGCTGAGATCCGCTGACATGATC&quot;, &quot;GATACG&quot;)
  
  for a in alignments:
      print(a)
  print()
  print()
  
  alignments = aligner.align(&quot;GAACTCGCATCGATGATCCGTGCGCTGAGATCCGCTGACATGATC&quot;, &quot;GATACCG&quot;)
  
  for a in alignments:
      print(a)
  </code></pre>
  