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python-biopython  1.60
Public Member Functions | Public Attributes
test_Ace.AceTestTwo Class Reference

List of all members.

Public Member Functions

def setUp
def test_check_ACEParser
def test_check_record_parser

Public Attributes

 handle

Detailed Description

Test parsing example output from CAP3.

The sample input file seq.cap.ace was downloaded from:
http://genome.cs.mtu.edu/cap/data/seq.cap.ace

Definition at line 990 of file test_Ace.py.


Member Function Documentation

def test_Ace.AceTestTwo.setUp (   self)

Definition at line 996 of file test_Ace.py.

00996 
00997     def setUp(self):
00998         self.handle = open("Ace/seq.cap.ace")

Test to check that ACEParser can parse the whole file into one record.

Definition at line 999 of file test_Ace.py.

00999 
01000     def test_check_ACEParser(self):
01001         """Test to check that ACEParser can parse the whole file into one record."""
01002         record=Ace.read(self.handle)
01003         self.assertEqual(record.ncontigs, 1)
01004         self.assertEqual(record.nreads, 6)
01005         self.assertEqual(record.wa, None)
01006         self.assertEqual(len(record.contigs), 1)
01007 
01008         self.assertEqual(len(record.contigs[0].reads), 6)
01009         self.assertEqual(record.contigs[0].name, "Contig1")
01010         self.assertEqual(record.contigs[0].nbases, 1222)
01011         self.assertEqual(record.contigs[0].nreads, 6)
01012         self.assertEqual(record.contigs[0].nsegments, 0)
01013         self.assertEqual(record.contigs[0].uorc, "U")
01014         center = len(record.contigs[0].sequence)//2
01015         self.assertEqual(record.contigs[0].sequence[:10], "AGTTTTAGTT")
01016         self.assertEqual(record.contigs[0].sequence[center-5:center+5], "TGTGCGCGCA")
01017         self.assertEqual(record.contigs[0].sequence[-10:], "ATATCACATT")
01018         center = len(record.contigs[0].quality)//2
01019         self.assertEqual(record.contigs[0].quality[:10], [61, 66, 67, 70, 71, 73, 73, 77, 77, 87])
01020         self.assertEqual(record.contigs[0].quality[center-5:center+5], [97, 97, 97, 97, 97, 97, 97, 97, 97, 97])
01021         self.assertEqual(record.contigs[0].quality[-10:], [56, 51, 49, 41, 38, 39, 45, 44, 49, 46])
01022         self.assertEqual(len(record.contigs[0].af), 6)
01023         self.assertEqual(len(record.contigs[0].bs), 0)
01024         self.assertEqual(record.contigs[0].af[3].name, "R5")
01025         self.assertEqual(record.contigs[0].af[3].coru, "C")
01026         self.assertEqual(record.contigs[0].af[3].padded_start, 320)
01027         self.assertEqual(record.contigs[0].af[5].name, "R6")
01028         self.assertEqual(record.contigs[0].af[5].coru, "C")
01029         self.assertEqual(record.contigs[0].af[5].padded_start, 517)
01030         self.assertEqual(record.contigs[0].bs, [])
01031         self.assertEqual(record.contigs[0].ct, None)
01032         self.assertEqual(record.contigs[0].wa, None)
01033         self.assertEqual(len(record.contigs[0].reads), 6)
01034 
01035         self.assertEqual(record.contigs[0].reads[0].rd.name, "R3")
01036         self.assertEqual(record.contigs[0].reads[0].rd.padded_bases, 919)
01037         self.assertEqual(record.contigs[0].reads[0].rd.info_items, 0)
01038         self.assertEqual(record.contigs[0].reads[0].rd.read_tags, 0)
01039         center = len(record.contigs[0].reads[0].rd.sequence)//2
01040         self.assertEqual(record.contigs[0].reads[0].rd.sequence[:10], "NNNNNNNNNN")
01041         self.assertEqual(record.contigs[0].reads[0].rd.sequence[center-5:center+5], "ATGTGCGCTC")
01042         self.assertEqual(record.contigs[0].reads[0].rd.sequence[-10:], "CAGCTCACCA")
01043         self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_start, 55)
01044         self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_end, 916)
01045         self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_start, 55)
01046         self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_end, 916)
01047         self.assertEqual(record.contigs[0].reads[0].ds.chromat_file, "")
01048         self.assertEqual(record.contigs[0].reads[0].ds.phd_file, "")
01049         self.assertEqual(record.contigs[0].reads[0].ds.time, "")
01050         self.assertEqual(record.contigs[0].reads[0].ds.chem, "")
01051         self.assertEqual(record.contigs[0].reads[0].ds.dye, "")
01052         self.assertEqual(record.contigs[0].reads[0].ds.template, "")
01053         self.assertEqual(record.contigs[0].reads[0].ds.direction, "")
01054         self.assertEqual(record.contigs[0].reads[0].rt, None)
01055         self.assertEqual(record.contigs[0].reads[0].wr, None)
01056 
01057         self.assertEqual(record.contigs[0].reads[1].rd.name, "R1")
01058         self.assertEqual(record.contigs[0].reads[1].rd.padded_bases, 864)
01059         self.assertEqual(record.contigs[0].reads[1].rd.info_items, 0)
01060         self.assertEqual(record.contigs[0].reads[1].rd.read_tags, 0)
01061         center = len(record.contigs[0].reads[1].rd.sequence)//2
01062         self.assertEqual(record.contigs[0].reads[1].rd.sequence[:10], "AGCCGGTACC")
01063         self.assertEqual(record.contigs[0].reads[1].rd.sequence[center-5:center+5], "GGGATGGCAC")
01064         self.assertEqual(record.contigs[0].reads[1].rd.sequence[-10:], "GGGCTGGGAG")
01065         self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_start, 12)
01066         self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_end, 863)
01067         self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_start, 12)
01068         self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_end, 863)
01069         self.assertEqual(record.contigs[0].reads[1].ds.chromat_file, "")
01070         self.assertEqual(record.contigs[0].reads[1].ds.phd_file, "")
01071         self.assertEqual(record.contigs[0].reads[1].ds.time, "")
01072         self.assertEqual(record.contigs[0].reads[1].ds.chem, "")
01073         self.assertEqual(record.contigs[0].reads[1].ds.dye, "")
01074         self.assertEqual(record.contigs[0].reads[1].ds.template, "")
01075         self.assertEqual(record.contigs[0].reads[1].ds.direction, "")
01076         self.assertEqual(record.contigs[0].reads[1].rt, None)
01077         self.assertEqual(record.contigs[0].reads[1].wr, None)
01078 
01079         self.assertEqual(record.contigs[0].reads[2].rd.name, "R2")
01080         self.assertEqual(record.contigs[0].reads[2].rd.padded_bases, 1026)
01081         self.assertEqual(record.contigs[0].reads[2].rd.info_items, 0)
01082         self.assertEqual(record.contigs[0].reads[2].rd.read_tags, 0)
01083         center = len(record.contigs[0].reads[2].rd.sequence)//2
01084         self.assertEqual(record.contigs[0].reads[2].rd.sequence[:10], "NNNNNNNNNN")
01085         self.assertEqual(record.contigs[0].reads[2].rd.sequence[center-5:center+5], "GGATGCCTGG")
01086         self.assertEqual(record.contigs[0].reads[2].rd.sequence[-10:], "GGTTGAGGCC")
01087         self.assertEqual(record.contigs[0].reads[2].qa.qual_clipping_start, 55)
01088         self.assertEqual(record.contigs[0].reads[2].qa.qual_clipping_end, 1000)
01089         self.assertEqual(record.contigs[0].reads[2].qa.align_clipping_start, 55)
01090         self.assertEqual(record.contigs[0].reads[2].qa.align_clipping_end, 1000)
01091         self.assertEqual(record.contigs[0].reads[2].ds.chromat_file, "")
01092         self.assertEqual(record.contigs[0].reads[2].ds.phd_file, "")
01093         self.assertEqual(record.contigs[0].reads[2].ds.time, "")
01094         self.assertEqual(record.contigs[0].reads[2].ds.chem, "")
01095         self.assertEqual(record.contigs[0].reads[2].ds.dye, "")
01096         self.assertEqual(record.contigs[0].reads[2].ds.template, "")
01097         self.assertEqual(record.contigs[0].reads[2].ds.direction, "")
01098         self.assertEqual(record.contigs[0].reads[2].rt, None)
01099         self.assertEqual(record.contigs[0].reads[2].wr, None)
01100 
01101         self.assertEqual(record.contigs[0].reads[3].rd.name, "R5")
01102         self.assertEqual(record.contigs[0].reads[3].rd.padded_bases, 925)
01103         self.assertEqual(record.contigs[0].reads[3].rd.info_items, 0)
01104         self.assertEqual(record.contigs[0].reads[3].rd.read_tags, 0)
01105         center = len(record.contigs[0].reads[3].rd.sequence)//2
01106         self.assertEqual(record.contigs[0].reads[3].rd.sequence[:10], "NNNNNNNNNN")
01107         self.assertEqual(record.contigs[0].reads[3].rd.sequence[center-5:center+5], "CCTCCCTACA")
01108         self.assertEqual(record.contigs[0].reads[3].rd.sequence[-10:], "GCCCCCGGNN")
01109         self.assertEqual(record.contigs[0].reads[3].qa.qual_clipping_start, 293)
01110         self.assertEqual(record.contigs[0].reads[3].qa.qual_clipping_end, 874)
01111         self.assertEqual(record.contigs[0].reads[3].qa.align_clipping_start, 293)
01112         self.assertEqual(record.contigs[0].reads[3].qa.align_clipping_end, 874)
01113         self.assertEqual(record.contigs[0].reads[3].ds.chromat_file, "")
01114         self.assertEqual(record.contigs[0].reads[3].ds.phd_file, "")
01115         self.assertEqual(record.contigs[0].reads[3].ds.time, "")
01116         self.assertEqual(record.contigs[0].reads[3].ds.chem, "")
01117         self.assertEqual(record.contigs[0].reads[3].ds.dye, "")
01118         self.assertEqual(record.contigs[0].reads[3].ds.template, "")
01119         self.assertEqual(record.contigs[0].reads[3].ds.direction, "")
01120         self.assertEqual(record.contigs[0].reads[3].rt, None)
01121         self.assertEqual(record.contigs[0].reads[3].wr, None)
01122 
01123         self.assertEqual(record.contigs[0].reads[4].rd.name, "R4")
01124         self.assertEqual(record.contigs[0].reads[4].rd.padded_bases, 816)
01125         self.assertEqual(record.contigs[0].reads[4].rd.info_items, 0)
01126         self.assertEqual(record.contigs[0].reads[4].rd.read_tags, 0)
01127         center = len(record.contigs[0].reads[4].rd.sequence)//2
01128         self.assertEqual(record.contigs[0].reads[4].rd.sequence[:10], "CACTCAGCTC")
01129         self.assertEqual(record.contigs[0].reads[4].rd.sequence[center-5:center+5], "TCCAAAGGGT")
01130         self.assertEqual(record.contigs[0].reads[4].rd.sequence[-10:], "AGCTGAATCG")
01131         self.assertEqual(record.contigs[0].reads[4].qa.qual_clipping_start, 1)
01132         self.assertEqual(record.contigs[0].reads[4].qa.qual_clipping_end, 799)
01133         self.assertEqual(record.contigs[0].reads[4].qa.align_clipping_start, 1)
01134         self.assertEqual(record.contigs[0].reads[4].qa.align_clipping_end, 799)
01135         self.assertEqual(record.contigs[0].reads[4].ds.chromat_file, "")
01136         self.assertEqual(record.contigs[0].reads[4].ds.phd_file, "")
01137         self.assertEqual(record.contigs[0].reads[4].ds.time, "")
01138         self.assertEqual(record.contigs[0].reads[4].ds.chem, "")
01139         self.assertEqual(record.contigs[0].reads[4].ds.dye, "")
01140         self.assertEqual(record.contigs[0].reads[4].ds.template, "")
01141         self.assertEqual(record.contigs[0].reads[4].ds.direction, "")
01142         self.assertEqual(record.contigs[0].reads[4].rt, None)
01143         self.assertEqual(record.contigs[0].reads[4].wr, None)
01144 
01145         self.assertEqual(record.contigs[0].reads[5].rd.name, "R6")
01146         self.assertEqual(record.contigs[0].reads[5].rd.padded_bases, 857)
01147         self.assertEqual(record.contigs[0].reads[5].rd.info_items, 0)
01148         self.assertEqual(record.contigs[0].reads[5].rd.read_tags, 0)
01149         center = len(record.contigs[0].reads[5].rd.sequence)//2
01150         self.assertEqual(record.contigs[0].reads[5].rd.sequence[:10], "CCGGCAGTGA")
01151         self.assertEqual(record.contigs[0].reads[5].rd.sequence[center-5:center+5], "AAAAAAAACC")
01152         self.assertEqual(record.contigs[0].reads[5].rd.sequence[-10:], "NNNNNNNNNN")
01153         self.assertEqual(record.contigs[0].reads[5].qa.qual_clipping_start, 24)
01154         self.assertEqual(record.contigs[0].reads[5].qa.qual_clipping_end, 706)
01155         self.assertEqual(record.contigs[0].reads[5].qa.align_clipping_start, 24)
01156         self.assertEqual(record.contigs[0].reads[5].qa.align_clipping_end, 706)
01157         self.assertEqual(record.contigs[0].reads[5].ds.chromat_file, "")
01158         self.assertEqual(record.contigs[0].reads[5].ds.phd_file, "")
01159         self.assertEqual(record.contigs[0].reads[5].ds.time, "")
01160         self.assertEqual(record.contigs[0].reads[5].ds.chem, "")
01161         self.assertEqual(record.contigs[0].reads[5].ds.dye, "")
01162         self.assertEqual(record.contigs[0].reads[5].ds.template, "")
01163         self.assertEqual(record.contigs[0].reads[5].ds.direction, "")
01164         self.assertEqual(record.contigs[0].reads[5].rt, None)
01165         self.assertEqual(record.contigs[0].reads[5].wr, None)
    
Test to check that record parser parses each contig into a record.

Definition at line 1166 of file test_Ace.py.

01166 
01167     def test_check_record_parser(self):
01168         """Test to check that record parser parses each contig into a record."""
01169         contigs=Ace.parse(self.handle)
01170 
01171         # First (and only) contig
01172         contig = contigs.next()
01173 
01174         self.assertEqual(len(contig.reads), 6)
01175         self.assertEqual(contig.name, "Contig1")
01176         self.assertEqual(contig.nbases, 1222)
01177         self.assertEqual(contig.nreads, 6)
01178         self.assertEqual(contig.nsegments, 0)
01179         self.assertEqual(contig.uorc, "U")
01180         center = len(contig.sequence)//2
01181         self.assertEqual(contig.sequence[:10], "AGTTTTAGTT")
01182         self.assertEqual(contig.sequence[center-5:center+5], "TGTGCGCGCA")
01183         self.assertEqual(contig.sequence[-10:], "ATATCACATT")
01184         center = len(contig.quality)//2
01185         self.assertEqual(contig.quality[:10], [61, 66, 67, 70, 71, 73, 73, 77, 77, 87])
01186         self.assertEqual(contig.quality[center-5:center+5], [97, 97, 97, 97, 97, 97, 97, 97, 97, 97])
01187         self.assertEqual(contig.quality[-10:], [56, 51, 49, 41, 38, 39, 45, 44, 49, 46])
01188         self.assertEqual(len(contig.af), 6)
01189         self.assertEqual(len(contig.bs), 0)
01190         self.assertEqual(contig.af[3].name, "R5")
01191         self.assertEqual(contig.af[3].coru, "C")
01192         self.assertEqual(contig.af[3].padded_start, 320)
01193         self.assertEqual(contig.af[5].name, "R6")
01194         self.assertEqual(contig.af[5].coru, "C")
01195         self.assertEqual(contig.af[5].padded_start, 517)
01196         self.assertEqual(contig.bs, [])
01197         self.assertEqual(contig.ct, None)
01198         self.assertEqual(contig.wa, None)
01199         self.assertEqual(len(contig.reads), 6)
01200 
01201         self.assertEqual(contig.reads[0].rd.name, "R3")
01202         self.assertEqual(contig.reads[0].rd.padded_bases, 919)
01203         self.assertEqual(contig.reads[0].rd.info_items, 0)
01204         self.assertEqual(contig.reads[0].rd.read_tags, 0)
01205         center = len(contig.reads[0].rd.sequence)//2
01206         self.assertEqual(contig.reads[0].rd.sequence[:10], "NNNNNNNNNN")
01207         self.assertEqual(contig.reads[0].rd.sequence[center-5:center+5], "ATGTGCGCTC")
01208         self.assertEqual(contig.reads[0].rd.sequence[-10:], "CAGCTCACCA")
01209         self.assertEqual(contig.reads[0].qa.qual_clipping_start, 55)
01210         self.assertEqual(contig.reads[0].qa.qual_clipping_end, 916)
01211         self.assertEqual(contig.reads[0].qa.align_clipping_start, 55)
01212         self.assertEqual(contig.reads[0].qa.align_clipping_end, 916)
01213         self.assertEqual(contig.reads[0].ds.chromat_file, "")
01214         self.assertEqual(contig.reads[0].ds.phd_file, "")
01215         self.assertEqual(contig.reads[0].ds.time, "")
01216         self.assertEqual(contig.reads[0].ds.chem, "")
01217         self.assertEqual(contig.reads[0].ds.dye, "")
01218         self.assertEqual(contig.reads[0].ds.template, "")
01219         self.assertEqual(contig.reads[0].ds.direction, "")
01220         self.assertEqual(contig.reads[0].rt, None)
01221         self.assertEqual(contig.reads[0].wr, None)
01222 
01223         self.assertEqual(contig.reads[1].rd.name, "R1")
01224         self.assertEqual(contig.reads[1].rd.padded_bases, 864)
01225         self.assertEqual(contig.reads[1].rd.info_items, 0)
01226         self.assertEqual(contig.reads[1].rd.read_tags, 0)
01227         center = len(contig.reads[1].rd.sequence)//2
01228         self.assertEqual(contig.reads[1].rd.sequence[:10], "AGCCGGTACC")
01229         self.assertEqual(contig.reads[1].rd.sequence[center-5:center+5], "GGGATGGCAC")
01230         self.assertEqual(contig.reads[1].rd.sequence[-10:], "GGGCTGGGAG")
01231         self.assertEqual(contig.reads[1].qa.qual_clipping_start, 12)
01232         self.assertEqual(contig.reads[1].qa.qual_clipping_end, 863)
01233         self.assertEqual(contig.reads[1].qa.align_clipping_start, 12)
01234         self.assertEqual(contig.reads[1].qa.align_clipping_end, 863)
01235         self.assertEqual(contig.reads[1].ds.chromat_file, "")
01236         self.assertEqual(contig.reads[1].ds.phd_file, "")
01237         self.assertEqual(contig.reads[1].ds.time, "")
01238         self.assertEqual(contig.reads[1].ds.chem, "")
01239         self.assertEqual(contig.reads[1].ds.dye, "")
01240         self.assertEqual(contig.reads[1].ds.template, "")
01241         self.assertEqual(contig.reads[1].ds.direction, "")
01242         self.assertEqual(contig.reads[1].rt, None)
01243         self.assertEqual(contig.reads[1].wr, None)
01244 
01245         self.assertEqual(contig.reads[2].rd.name, "R2")
01246         self.assertEqual(contig.reads[2].rd.padded_bases, 1026)
01247         self.assertEqual(contig.reads[2].rd.info_items, 0)
01248         self.assertEqual(contig.reads[2].rd.read_tags, 0)
01249         center = len(contig.reads[2].rd.sequence)//2
01250         self.assertEqual(contig.reads[2].rd.sequence[:10], "NNNNNNNNNN")
01251         self.assertEqual(contig.reads[2].rd.sequence[center-5:center+5], "GGATGCCTGG")
01252         self.assertEqual(contig.reads[2].rd.sequence[-10:], "GGTTGAGGCC")
01253         self.assertEqual(contig.reads[2].qa.qual_clipping_start, 55)
01254         self.assertEqual(contig.reads[2].qa.qual_clipping_end, 1000)
01255         self.assertEqual(contig.reads[2].qa.align_clipping_start, 55)
01256         self.assertEqual(contig.reads[2].qa.align_clipping_end, 1000)
01257         self.assertEqual(contig.reads[2].ds.chromat_file, "")
01258         self.assertEqual(contig.reads[2].ds.phd_file, "")
01259         self.assertEqual(contig.reads[2].ds.time, "")
01260         self.assertEqual(contig.reads[2].ds.chem, "")
01261         self.assertEqual(contig.reads[2].ds.dye, "")
01262         self.assertEqual(contig.reads[2].ds.template, "")
01263         self.assertEqual(contig.reads[2].ds.direction, "")
01264         self.assertEqual(contig.reads[2].rt, None)
01265         self.assertEqual(contig.reads[2].wr, None)
01266 
01267         self.assertEqual(contig.reads[3].rd.name, "R5")
01268         self.assertEqual(contig.reads[3].rd.padded_bases, 925)
01269         self.assertEqual(contig.reads[3].rd.info_items, 0)
01270         self.assertEqual(contig.reads[3].rd.read_tags, 0)
01271         center = len(contig.reads[3].rd.sequence)//2
01272         self.assertEqual(contig.reads[3].rd.sequence[:10], "NNNNNNNNNN")
01273         self.assertEqual(contig.reads[3].rd.sequence[center-5:center+5], "CCTCCCTACA")
01274         self.assertEqual(contig.reads[3].rd.sequence[-10:], "GCCCCCGGNN")
01275         self.assertEqual(contig.reads[3].qa.qual_clipping_start, 293)
01276         self.assertEqual(contig.reads[3].qa.qual_clipping_end, 874)
01277         self.assertEqual(contig.reads[3].qa.align_clipping_start, 293)
01278         self.assertEqual(contig.reads[3].qa.align_clipping_end, 874)
01279         self.assertEqual(contig.reads[3].ds.chromat_file, "")
01280         self.assertEqual(contig.reads[3].ds.phd_file, "")
01281         self.assertEqual(contig.reads[3].ds.time, "")
01282         self.assertEqual(contig.reads[3].ds.chem, "")
01283         self.assertEqual(contig.reads[3].ds.dye, "")
01284         self.assertEqual(contig.reads[3].ds.template, "")
01285         self.assertEqual(contig.reads[3].ds.direction, "")
01286         self.assertEqual(contig.reads[3].rt, None)
01287         self.assertEqual(contig.reads[3].wr, None)
01288 
01289         self.assertEqual(contig.reads[4].rd.name, "R4")
01290         self.assertEqual(contig.reads[4].rd.padded_bases, 816)
01291         self.assertEqual(contig.reads[4].rd.info_items, 0)
01292         self.assertEqual(contig.reads[4].rd.read_tags, 0)
01293         center = len(contig.reads[4].rd.sequence)//2
01294         self.assertEqual(contig.reads[4].rd.sequence[:10], "CACTCAGCTC")
01295         self.assertEqual(contig.reads[4].rd.sequence[center-5:center+5], "TCCAAAGGGT")
01296         self.assertEqual(contig.reads[4].rd.sequence[-10:], "AGCTGAATCG")
01297         self.assertEqual(contig.reads[4].qa.qual_clipping_start, 1)
01298         self.assertEqual(contig.reads[4].qa.qual_clipping_end, 799)
01299         self.assertEqual(contig.reads[4].qa.align_clipping_start, 1)
01300         self.assertEqual(contig.reads[4].qa.align_clipping_end, 799)
01301         self.assertEqual(contig.reads[4].ds.chromat_file, "")
01302         self.assertEqual(contig.reads[4].ds.phd_file, "")
01303         self.assertEqual(contig.reads[4].ds.time, "")
01304         self.assertEqual(contig.reads[4].ds.chem, "")
01305         self.assertEqual(contig.reads[4].ds.dye, "")
01306         self.assertEqual(contig.reads[4].ds.template, "")
01307         self.assertEqual(contig.reads[4].ds.direction, "")
01308         self.assertEqual(contig.reads[4].rt, None)
01309         self.assertEqual(contig.reads[4].wr, None)
01310 
01311         self.assertEqual(contig.reads[5].rd.name, "R6")
01312         self.assertEqual(contig.reads[5].rd.padded_bases, 857)
01313         self.assertEqual(contig.reads[5].rd.info_items, 0)
01314         self.assertEqual(contig.reads[5].rd.read_tags, 0)
01315         center = len(contig.reads[5].rd.sequence)//2
01316         self.assertEqual(contig.reads[5].rd.sequence[:10], "CCGGCAGTGA")
01317         self.assertEqual(contig.reads[5].rd.sequence[center-5:center+5], "AAAAAAAACC")
01318         self.assertEqual(contig.reads[5].rd.sequence[-10:], "NNNNNNNNNN")
01319         self.assertEqual(contig.reads[5].qa.qual_clipping_start, 24)
01320         self.assertEqual(contig.reads[5].qa.qual_clipping_end, 706)
01321         self.assertEqual(contig.reads[5].qa.align_clipping_start, 24)
01322         self.assertEqual(contig.reads[5].qa.align_clipping_end, 706)
01323         self.assertEqual(contig.reads[5].ds.chromat_file, "")
01324         self.assertEqual(contig.reads[5].ds.phd_file, "")
01325         self.assertEqual(contig.reads[5].ds.time, "")
01326         self.assertEqual(contig.reads[5].ds.chem, "")
01327         self.assertEqual(contig.reads[5].ds.dye, "")
01328         self.assertEqual(contig.reads[5].ds.template, "")
01329         self.assertEqual(contig.reads[5].ds.direction, "")
01330         self.assertEqual(contig.reads[5].rt, None)
01331         self.assertEqual(contig.reads[5].wr, None)
01332     
01333         # Make sure there are no more contigs
01334         self.assertRaises(StopIteration, contigs.next)
01335 


Member Data Documentation

Definition at line 997 of file test_Ace.py.


The documentation for this class was generated from the following file: