-Updated test cases

-Refactoring relative positions (#20 in progress)

Author: kwade4

poplars/sequence_locator.py

@@ -32,7 +32,7 @@ def __init__(self, region_name, ncoords=None, nt_seq=None, pcoords=None, aa_seq=
         self.nt_seq = nt_seq
         self.pcoords = pcoords
         self.aa_seq = aa_seq
-        self.cds, self.gstart, self.qstart, self.pstart = None, None, None, None
+        self.cds_offset, self.gstart, self.qstart, self.pstart = [], [], [], []
         self.codon_aln = ''
 
     def get_coords(self, base):
@@ -67,19 +67,30 @@ def set_seq_from_ref(self, sequence, base):
         else:
             self.aa_seq = sequence[self.pcoords[0] - 1: self.pcoords[1]]
 
-    def set_pos_from_cds(self, region_coords):
+    def set_pos_from_cds(self, ref_reg_name):
         """
-        Gives the position of a sequence relative to the start of the coding sequence
+        Gives the position of a the query sequence relative to the start of the coding sequence
         """
-        if self.ncoords is not None:
-            local_ncoords = self.global_to_local_index(self.get_coords('nucl'))
-            print('local ncoords {}'.format(local_ncoords))
 
-            if self.region_name != '5\'LTR':
-                len_region = region_coords[1] - region_coords[0]
-                cds_start = region_coords[0] - local_ncoords[0] + 1
-                cds_end = cds_start + len_region
-                self.cds = [cds_start, cds_end]
+        ref_region = GENOME_REGIONS[ref_reg_name]
+        if self.ncoords and ref_region.ncoords:
+
+            query_start = self.ncoords[0]
+            query_end = self.ncoords[1]
+            ref_start = ref_region.ncoords[0]
+            ref_end = ref_region.ncoords[1]
+
+            if query_start == ref_start:
+                start = 1
+            else:
+                start = query_start - ref_start
+
+            if query_end == ref_end:
+                end = query_end - query_start
+            else:
+                end = query_end - start
+
+            self.cds_offset = [start, end]
 
     def set_pos_from_gstart(self):
         self.gstart = self.ncoords
@@ -150,9 +161,9 @@ def set_pcoords_from_ncoords(self):
         """
         Sets protein coordinates relative to the protein start, given the nucleotide coordinates
         """
-        if self.cds is not None:
-            prot_start = self.cds[0] // 3 + 1
-            prot_end = self.cds['CDS'][1] // 3
+        if self.cds_offset is not None:
+            prot_start = self.cds_offset[0] // 3 + 1
+            prot_end = self.cds_offset[1] // 3
             self.pcoords = [prot_start, prot_end]
 
     def set_ncoords_from_pcoords(self):

poplars/tests/test_sequence_locator.py

@@ -1,5 +1,4 @@
 import unittest
-from io import StringIO
 from poplars.sequence_locator import *
 
 
@@ -20,15 +19,15 @@ def setUp(self):
                 open(self.hiv_ncoords_path) as hiv_ncoords, open(self.hiv_pcoords_path) as hiv_pcoords:
             self.hiv_nt_seq = convert_fasta(hiv_nt.read().split())[0][1]
             self.hiv_aa_seq = convert_fasta(hiv_aa.read().split())[0][1]
-            self.hiv_ncoords = hiv_ncoords.read()
-            self.hiv_pcoords = hiv_pcoords.read()
+            self.hiv_ncoords = hiv_ncoords
+            self.hiv_pcoords = hiv_pcoords
 
         with open(self.siv_nt_seq_path) as siv_nt, open(self.siv_aa_seq_path) as siv_aa, \
                 open(self.siv_ncoords_path) as siv_ncoords, open(self.siv_pcoords_path) as siv_pcoords:
             self.siv_nt_seq = convert_fasta(siv_nt.read().split())[0][1]
             self.siv_aa_seq = convert_fasta(siv_aa.read().split())[0][1]
-            self.siv_ncoords = siv_ncoords.read()
-            self.siv_pcoords = siv_pcoords.read()
+            self.siv_ncoords = siv_ncoords
+            self.siv_pcoords = siv_pcoords
 
 
 class TestGetCoords(InputTestCase):
@@ -136,42 +135,44 @@ def testHIVLTR5Start(self):
         region.set_coords([1, 634], 'nucl')
         region.set_pos_from_cds([1, 634])
         expected = []
-        result = region.rel_pos['CDS']
+        result = region.cds_offset
         self.assertEqual(expected, result)
 
     def testFromSIVLTR5Start(self):
         region = GenomeRegion('5\'LTR')
         region.set_pos_from_cds([1, 1110])
         expected = []
-        result = region.rel_pos['CDS']
+        result = region.cds_offset
         self.assertEqual(expected, result)
 
     def testFromHIVStart(self):
-        region = GenomeRegion('Gag', [790, 2292])
-        region.set_pos_from_cds([790, 2292])
+        ref_region = GenomeRegion('Gag', [790, 2292])
+        query_region = GenomeRegion('Gag', [790, 2292])
+        query_region.set_pos_from_cds(ref_region)
         expected = [1, 1503]
-        result = region.rel_pos['CDS']
+        result = query_region.cds_offset
         self.assertEqual(expected, result)
 
     def testFromSIVStart(self):
-        region = GenomeRegion('Integrase', [4785, 5666])
-        region.set_pos_from_cds([4785, 5666])
+        ref_region = GenomeRegion('Integrase', [4785, 5666])
+        query_region = GenomeRegion('Integrase', [4785, 5666])
+        query_region.set_pos_from_cds(ref_region)
         expected = [1, 882]
-        result = region.rel_pos['CDS']
+        result = query_region.cds_offset
         self.assertEqual(expected, result)
 
     def testGagfromP1Start(self):
         region = GenomeRegion('Gag', [2086, 2133])
         region.set_pos_from_cds([2086, 2133])
         expected = [1297, 1344]
-        result = region.rel_pos['CDS']
+        result = region.cds_offset
         self.assertEqual(expected, result)
 
     def testPolFromP1Start(self):
         region = GenomeRegion('Pol', [2086, 2133])
         region.set_pos_from_cds([2086, 2133])
         expected = [2, 49]
-        result = region.rel_pos['CDS']
+        result = region.cds_offset
         self.assertEqual(expected, result)
 
 
@@ -194,14 +195,14 @@ def testCapsidFromAAStart(self):
                                         'PKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL')
         region.set_pos_from_pstart()
         expected = [1, 231]
-        result = region.rel_pos['pstart']
+        result = region.pstart
         self.assertEqual(expected, result)
 
     def testLTR5FromAAStart(self):
         region = GenomeRegion('5\'LTR')
         region.set_pos_from_pstart()
         expected = []
-        result = region.rel_pos['pstart']
+        result = region.pstart
         self.assertEqual(expected, result)
 
     def testGagFromAAStart(self):
@@ -212,7 +213,7 @@ def testGagFromAAStart(self):
                               [450, 500],   'QSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ')
         region.set_pos_from_pstart()
         expected = [450, 500]
-        result = region.rel_pos['pstart']
+        result = region.pstart
         self.assertEqual(expected, result)
 
 
@@ -278,7 +279,6 @@ class TestProtCoordsFromNuclCoords(unittest.TestCase):
     def testSimpleUse(self):
         region = GenomeRegion('Gag', [2086, 2133], 'TTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTT', None, None)
         region.set_pos_from_cds([2086, 2133])
-        print(region.rel_pos['CDS'])
         region.set_pcoords_from_ncoords()
         expected = [433, 448]
         self.assertEqual(expected, region.pcoords)
@@ -349,7 +349,7 @@ def testSIVInputCoords(self):
         aa_coords = configs[3]
 
         with open(nt_coords) as ncoords, open(aa_coords) as pcoords:
-            result = set_regions('nucl', ncoords, ref_nt_seq, pcoords, ref_aa_seq)
+            result = make_regions(ncoords, ref_nt_seq, pcoords, ref_aa_seq)
 
             for i, reg in enumerate(result):
                 self.assertEqual(list(region_names.keys())[i], reg.region_name)
@@ -430,7 +430,7 @@ def testHIVInputCoords(self):
         aa_coords = configs[3]
 
         with open(nt_coords) as ncoords, open(aa_coords) as pcoords:
-            result = set_regions('prot', ncoords, ref_nt_seq, pcoords, ref_aa_seq)
+            result = make_regions(ncoords, ref_nt_seq, pcoords, ref_aa_seq)
 
             for i, reg in enumerate(result):
                 self.assertEqual(list(region_names.keys())[i], reg.region_name)
@@ -713,7 +713,7 @@ def testNuclAlignment(self):
                'CCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCT'
                'TTGGCAACGACCCCTCGTCACAATAA']
         expected = [(2133, 2292)]
-        result = get_region_coordinates(aln)
+        result = query_region_coordinates(aln)
         self.assertEqual(expected, result)
 
     def testProtAlignment(self):
@@ -724,7 +724,7 @@ def testProtAlignment(self):
                '-------------------------------------------------------------------------------------------------------'
                '----------------------------------------------------------------------------------------']
         expected = [(0, 132)]
-        result = get_region_coordinates(aln)
+        result = query_region_coordinates(aln)
         self.assertEqual(expected, result)
 
 
@@ -854,7 +854,7 @@ def testDefaultInput(self):
         aa_coords = configs[3]
 
         with open(nt_coords) as ncoords, open(aa_coords) as pcoords:
-            ref_regions = set_regions('nucl', ncoords, ref_nt_seq, pcoords, ref_aa_seq)
+            ref_regions = make_regions(ncoords, ref_nt_seq, pcoords, ref_aa_seq)
 
         result = retrieve('hiv', 'nucl', ref_regions, 'p2')
         query_region = result[0]
@@ -898,9 +898,9 @@ def testSIVInput(self):
         aa_coords = configs[3]
 
         with open(nt_coords) as ncoords, open(aa_coords) as pcoords:
-            ref_regions = set_regions('nucl', ncoords, ref_nt_seq, pcoords, ref_aa_seq)
+            ref_regions = make_regions(ncoords, ref_nt_seq, pcoords, ref_aa_seq)
 
-        result = retrieve('nucl', ref_regions, 'Nef', 20, 80)
+        result = retrieve('nucl', 'Nef', 20, 80)
         result_region = result[0]
         expected_region = 'Nef'
         expected_seq = 'TGAGGCGGTCCAGGCCGTCTGGAGATCTGCGACAGAGACTCTTGCGGGCGCGTGGGGAGAC'
@@ -1078,15 +1078,15 @@ def testSimpleNuclEquiv(self):
         aa_coords = configs[3]
 
         with open(nt_coords) as ncoords, open(aa_coords) as pcoords:
-            ref_regions = set_regions('prot', ncoords, ref_nt_seq, pcoords, ref_aa_seq)
+            ref_regions = make_regions(ncoords, ref_nt_seq, pcoords, ref_aa_seq)
         for region in ref_regions:
             region.make_codon_aln()
 
         query_region = GenomeRegion('Gag', [2133, 2292], 'GCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATG',
                                     [364, 377], 'AEAMSQVTNSATIM')
 
         expected = 'GCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATG'
-        result = set_nucleotide_equivalents(query_region, ref_regions)
+        result = set_nucleotide_equivalents(query_region)
         self.assertEqual(expected, result)
 
     def testWithGaps(self):
@@ -1095,7 +1095,7 @@ def testWithGaps(self):
             region.make_codon_aln()
         q_region = GenomeRegion('test1', [12, 27],  'TTAAACCCGGGTTTA', [1, 5], 'LNPGL')
         expected = 'TTAAACCCGGGTTTA'
-        result = set_nucleotide_equivalents(q_region, ref_regions)
+        result = set_nucleotide_equivalents(q_region)
         self.assertEqual(expected, result)
 
 
@@ -1111,15 +1111,15 @@ def testHIV(self):
         aa_coords = configs[3]
 
         with open(nt_coords) as ncoords, open(aa_coords) as pcoords:
-            ref_regions = set_regions('nucl', ncoords, ref_nt_seq, pcoords, ref_aa_seq)
+            ref_regions = make_regions(ncoords, ref_nt_seq, pcoords, ref_aa_seq)
 
         for reg in ref_regions:
             reg.make_codon_aln()
 
         query_region = GenomeRegion('Gag', [2133, 2292], 'GCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATG',
                                     [364, 377], 'AEAMSQVTNSATIM')
         expected = 'AEAMSQVTNSATIM'
-        result = set_protein_equivalents(query_region, ref_regions)
+        result = set_protein_equivalents(query_region)
         self.assertEqual(expected, result)