diff options
| -rw-r--r-- | pepseq/__init__.py | 4 | ||||
| -rw-r--r-- | pepseq/amino_acid.py | 23 | ||||
| -rw-r--r-- | pepseq/fragment.py | 6 | ||||
| -rw-r--r-- | pepseq/peptide.py | 6 | ||||
| -rw-r--r-- | pepseq/test_fragment.py | 14 | ||||
| -rw-r--r-- | pepseq/test_peptide.py | 11 |
6 files changed, 24 insertions, 40 deletions
diff --git a/pepseq/__init__.py b/pepseq/__init__.py index b6d92ae..67db17e 100644 --- a/pepseq/__init__.py +++ b/pepseq/__init__.py @@ -3,7 +3,5 @@ __version__ = '0.0.0' from amino_acid import * -from peptide import * -from fragment import * -__all__ = ['amino_acid', 'peptide', 'fragment'] +__all__ = ['amino_acid'] diff --git a/pepseq/amino_acid.py b/pepseq/amino_acid.py index b0badb6..429c089 100644 --- a/pepseq/amino_acid.py +++ b/pepseq/amino_acid.py @@ -36,3 +36,26 @@ class AminoAcid(object): def __str__(self): return "%s (%s, %s) MW: %.2f" % ( self.name, self.triple, self.letter, self.weight) + +if __name__ == '__main__': + + import itertools + + fragment = ( + ((AminoAcid('a'), AminoAcid('t'), AminoAcid('k'))), + ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))), + ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))), + ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))), + ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))), + ) + + sequences = list(itertools.product(*fragment)) + for sequence in sequences: + weight = 0 + string = "" + for amino_acid in sequence: + weight += amino_acid.weight + string += ('%s' % (amino_acid.letter)) + if amino_acid is not sequence[-1]: + string += ',' + print "%d: %s" % (weight, string) diff --git a/pepseq/fragment.py b/pepseq/fragment.py deleted file mode 100644 index 02e676b..0000000 --- a/pepseq/fragment.py +++ /dev/null @@ -1,6 +0,0 @@ -# -*- coding: utf-8 -*- - - -class Fragment(object): - """ A sequence of peptides. """ - pass diff --git a/pepseq/peptide.py b/pepseq/peptide.py deleted file mode 100644 index 4bde63d..0000000 --- a/pepseq/peptide.py +++ /dev/null @@ -1,6 +0,0 @@ -# -*- coding: utf-8 -*- - - -class Peptide(object): - """ Peptides are short polymers of amino acids linked by peptide bonds. """ - pass diff --git a/pepseq/test_fragment.py b/pepseq/test_fragment.py deleted file mode 100644 index 4a857a2..0000000 --- a/pepseq/test_fragment.py +++ /dev/null @@ -1,14 +0,0 @@ -# -*- coding: utf-8 -*- - -import unittest - - -class FragmentTestCase(unittest.TestCase): - pass - -def suite(): - suite = unittest.TestLoader().loadTestsFromTestCase(FragmentTestCase) - return suite - -if __name__ == '__main__': - unittest.TextTestRunner().run(suite()) diff --git a/pepseq/test_peptide.py b/pepseq/test_peptide.py deleted file mode 100644 index 9a87b57..0000000 --- a/pepseq/test_peptide.py +++ /dev/null @@ -1,11 +0,0 @@ -# -*- coding: utf-8 -*- - -import unittest - - -class PeptideTestCase(unittest.TestCase): - pass - -if __name__ == '__main__': - suite = unittest.TestLoader().loadTestsFromTestCase(PeptideTestCase) - unittest.TextTestRunner(verbosity=2).run(suite) |