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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.parse.foldalign import find_struct
from cogent.parse.pfold import tree_struct_sep
from cogent.parse.column import column_parser
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class ColumnParserTest(TestCase):
"""Provides tests for Column format RNA secondary structure parsers"""
def setUp(self):
"""Setup function"""
#output
self.pfold_out = PFOLD
self.foldalign_out = FOLDALIGN
#expected
self.pfold_exp = [['GCAGAUUUAGAUGC',[(0,13),(1,12),(2,11),(6,10)]]]
self.foldalign_exp = [['GCAGAUUUAGAUGC',[(0,13),(1,12),(2,11),(6,10)]]]
self.find_struct_exp = [[[(0,13),(1,12),(2,11),(6,10)],'GCCACGUAGCUCAG',
'GCCGUAUGUUUCAG']]
def test_pfold_output(self):
"""Test for column_parser for pfold format"""
tree,lines = tree_struct_sep(self.pfold_out)
self.assertEqual(tree,PFOLD_tree)
obs = column_parser(lines)
self.assertEqual(obs,self.pfold_exp)
def test_foldalign_output(self):
"""Test for column_parser for foldalign format"""
obs = column_parser(self.foldalign_out)
self.assertEqual(obs,self.foldalign_exp)
def test_foldalign_find_struct(self):
""" Test for foldalign parser find struct function"""
obs = find_struct(self.foldalign_out)
self.assertEqual(obs,self.find_struct_exp)
FOLDALIGN = ['; FOLDALIGN 2.0.3\n',
'; REFERENCE J.H. Havgaard, R.B. Lyngs\xf8, G.D. Stormo, J. Gorodkin\n',
'; REFERENCE Pairwise local structural alignment of RNA sequences\n',
'; REFERENCE with sequence similarity less than 40%\n',
'; REFERENCE Bioinformatics 21(9), 1815-1824, 2005\n',
'; ALIGNMENT_ID n.a.\n', '; ALIGNING seq1 against seq2\n',
'; ALIGN seq1 \n',
'; ALIGN seq2 \n',
'; ALIGN Score: 929\n',
'; ALIGN Identity: 69 % ( 48 / 70 )\n',
'; ALIGN Begin\n', '; ALIGN\n',
'; ALIGN seq1 GCCACGUAGC UCAG\n',
'; ALIGN Structure (((...(... ))))\n',
'; ALIGN seq2 GCCGUAUGUU UCAG\n',
'; ALIGN \n', '; ALIGN End\n',
'; ==============================================================================\n',
'; TYPE RNA\n', '; COL 1 label\n',
'; COL 2 residue\n', '; COL 3 seqpos\n',
'; COL 4 alignpos\n', '; COL 5 align_bp\n',
'; COL 6 seqpos_bp\n', '; ENTRY seq1\n',
'; ALIGNMENT_ID n.a.\n', '; ALIGNMENT_LIST seq1 seq2\n',
'; FOLDALIGN_SCORE 929\n', '; GROUP 1\n',
'; FILENAME seq1.fasta\n', '; START_POSITION 2\n',
'; END_POSITION 71\n', '; ALIGNMENT_SIZE 2\n',
'; ALIGNMENT_LENGTH 70\n', '; SEQUENCE_LENGTH 76\n',
'; PARAMETER max_length=76\n',
'; PARAMETER max_diff=76\n',
'; PARAMETER min_loop=3\n',
'; PARAMETER score_matrix=<default>\n',
'; PARAMETER nobranching=<false>\n',
'; PARAMETER global=<false>\n',
'; ----------\n',
'N G 1 1 14 0.90\n',
'N C 2 2 13 0.79\n',
'N A 3 3 12 0.87\n',
'N G 4 4 . 0.60\n',
'N A 5 5 . 0.34\n',
'N U 6 6 . 0.34\n',
'N U 7 7 11 0.98\n',
'N U 8 8 . 0.34\n',
'N A 9 9 . 0.56\n',
'N G 10 10 . 0.67\n',
'N A 11 11 7 0.78\n',
'N U 12 12 3 0.87\n',
'N G 13 13 2 0.87\n',
'N C 14 14 1 0.90\n',
'; **********\n']
PFOLD = ['; generated by fasta2col\n',
'; ============================================================\n',
'; TYPE TREE\n', '; COL 1 label\n',
'; COL 2 number\n', '; COL 3 name\n',
'; COL 4 uplen\n', '; COL 5 child\n',
'; COL 6 brother\n', '; ENTRY tree\n',
'; root 1\n', '; ----------\n',
' N 1 seq1 0.001000 . .\n',
'; **********\n', '; TYPE RNA\n', '; COL 1 label\n',
'; COL 2 residue\n', '; COL 3 seqpos\n',
'; COL 4 alignpos\n', '; COL 5 align_bp\n',
'; COL 6 certainty\n', '; ENTRY seq1\n',
'; ----------\n',
'N G 1 1 14 0.90\n',
'N C 2 2 13 0.79\n',
'N A 3 3 12 0.87\n',
'N G 4 4 . 0.60\n',
'N A 5 5 . 0.34\n',
'N U 6 6 . 0.34\n',
'N U 7 7 11 0.98\n',
'N U 8 8 . 0.34\n',
'N A 9 9 . 0.56\n',
'N G 10 10 . 0.67\n',
'N A 11 11 7 0.78\n',
'N U 12 12 3 0.87\n',
'N G 13 13 2 0.87\n',
'N C 14 14 1 0.90\n',
'; **********\n']
PFOLD_tree = ['; generated by fasta2col\n',
'; ============================================================\n',
'; TYPE TREE\n', '; COL 1 label\n',
'; COL 2 number\n', '; COL 3 name\n',
'; COL 4 uplen\n', '; COL 5 child\n',
'; COL 6 brother\n', '; ENTRY tree\n',
'; root 1\n', '; ----------\n',
' N 1 seq1 0.001000 . .\n', '; **********\n']
if __name__ == '__main__':
main()
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