frozenleaves/biopython
1
0
Fork 0
mirror of https://github.com/biopython/biopython.git synced 2025-10-20 13:43:47 +08:00
Code Issues Packages Projects Releases Wiki Activity

str

Browse Source
This commit is contained in:
Michiel de Hoon
2020-11-27 23:09:42 +09:00
committed by Peter Cock
parent 4dd0e70a5b
commit 50d0c7d33f
1 changed files with 13 additions and 13 deletions
Download Patch File Download Diff File Expand all files Collapse all files

26
Tests/test_Phd.py
View File

@ -116,10 +116,10 @@ class PhdTestOne(unittest.TestCase):
self.assertEqual(record.sites[-3], ("g", "11", "10840")) self.assertEqual(record.sites[-3], ("g", "11", "10840"))
self.assertEqual(record.sites[-2], ("t", "11", "10855")) self.assertEqual(record.sites[-2], ("t", "11", "10855"))
self.assertEqual(record.sites[-1], ("g", "11", "10864")) self.assertEqual(record.sites[-1], ("g", "11", "10864"))
self.assertEqual(str(record.seq)[:10], "ctccgtcgga") self.assertEqual(record.seq[:10], "ctccgtcgga")
self.assertEqual(str(record.seq)[-10:], "ccaaagcgtg") self.assertEqual(record.seq[-10:], "ccaaagcgtg")
self.assertEqual(str(record.seq_trimmed)[:10], "cgtcggaaca") self.assertEqual(record.seq_trimmed[:10], "cgtcggaaca")
self.assertEqual(str(record.seq_trimmed)[-10:], "tatttcggag") self.assertEqual(record.seq_trimmed[-10:], "tatttcggag")
# Record 2 # Record 2
record = next(records) record = next(records)
center = len(record.sites) // 2 center = len(record.sites) // 2
@ -168,10 +168,10 @@ class PhdTestOne(unittest.TestCase):
self.assertEqual(record.sites[-3], ("a", "8", "10574")) self.assertEqual(record.sites[-3], ("a", "8", "10574"))
self.assertEqual(record.sites[-2], ("a", "7", "10584")) self.assertEqual(record.sites[-2], ("a", "7", "10584"))
self.assertEqual(record.sites[-1], ("g", "7", "10599")) self.assertEqual(record.sites[-1], ("g", "7", "10599"))
self.assertEqual(str(record.seq)[:10], "cgggatccca") self.assertEqual(record.seq[:10], "cgggatccca")
self.assertEqual(str(record.seq)[-10:], "cccagccaag") self.assertEqual(record.seq[-10:], "cccagccaag")
self.assertEqual(str(record.seq_trimmed)[:10], "cctgatccga") self.assertEqual(record.seq_trimmed[:10], "cctgatccga")
self.assertEqual(str(record.seq_trimmed)[-10:], "ggggccgcca") self.assertEqual(record.seq_trimmed[-10:], "ggggccgcca")
# Record 3 # Record 3
record = next(records) record = next(records)
center = len(record.sites) // 2 center = len(record.sites) // 2
@ -220,8 +220,8 @@ class PhdTestOne(unittest.TestCase):
self.assertEqual(record.sites[-3], ("t", "8", "9495")) self.assertEqual(record.sites[-3], ("t", "8", "9495"))
self.assertEqual(record.sites[-2], ("t", "3", "9504")) self.assertEqual(record.sites[-2], ("t", "3", "9504"))
self.assertEqual(record.sites[-1], ("n", "0", "9511")) self.assertEqual(record.sites[-1], ("n", "0", "9511"))
self.assertEqual(str(record.seq)[:10], "acataaatca") self.assertEqual(record.seq[:10], "acataaatca")
self.assertEqual(str(record.seq)[-10:], "atctgctttn") self.assertEqual(record.seq[-10:], "atctgctttn")
# Make sure that no further records are found # Make sure that no further records are found
self.assertRaises(StopIteration, next, records) self.assertRaises(StopIteration, next, records)
@ -277,7 +277,7 @@ class PhdTest454(unittest.TestCase):
self.assertEqual(record.id, "EBE03TV04IHLTF.77-243") self.assertEqual(record.id, "EBE03TV04IHLTF.77-243")
self.assertEqual(record.name, "EBE03TV04IHLTF.77-243") self.assertEqual(record.name, "EBE03TV04IHLTF.77-243")
self.assertEqual(record.description, "EBE03TV04IHLTF.77-243 1") self.assertEqual(record.description, "EBE03TV04IHLTF.77-243 1")
self.assertEqual(str(record.seq), "ggggatgaaagggatctcggtggtaggtga") self.assertEqual(record.seq, "ggggatgaaagggatctcggtggtaggtga")
self.assertEqual( self.assertEqual(
record.letter_annotations["phred_quality"][:10], record.letter_annotations["phred_quality"][:10],
[37, 37, 37, 37, 37, 37, 37, 37, 37, 37], [37, 37, 37, 37, 37, 37, 37, 37, 37, 37],
@ -323,7 +323,7 @@ class PhdTestSolexa(unittest.TestCase):
self.assertEqual(record.id, "HWI-EAS94_4_1_1_537_446") self.assertEqual(record.id, "HWI-EAS94_4_1_1_537_446")
self.assertEqual(record.name, "HWI-EAS94_4_1_1_537_446") self.assertEqual(record.name, "HWI-EAS94_4_1_1_537_446")
self.assertEqual(record.description, "HWI-EAS94_4_1_1_537_446 1") self.assertEqual(record.description, "HWI-EAS94_4_1_1_537_446 1")
self.assertEqual(str(record.seq), "gccaatcaggtttctctgcaagcccctttagcagctgagc") self.assertEqual(record.seq, "gccaatcaggtttctctgcaagcccctttagcagctgagc")
self.assertEqual( self.assertEqual(
record.letter_annotations["phred_quality"], record.letter_annotations["phred_quality"],
[ [
@ -400,7 +400,7 @@ class PhdTestSolexa(unittest.TestCase):
self.assertEqual(record.id, "HWI-EAS94_4_1_1_602_99") self.assertEqual(record.id, "HWI-EAS94_4_1_1_602_99")
self.assertEqual(record.name, "HWI-EAS94_4_1_1_602_99") self.assertEqual(record.name, "HWI-EAS94_4_1_1_602_99")
self.assertEqual(record.description, "HWI-EAS94_4_1_1_602_99 1") self.assertEqual(record.description, "HWI-EAS94_4_1_1_602_99 1")
self.assertEqual(str(record.seq), "gccatggcacatatatgaaggtcagaggacaacttgctgt") self.assertEqual(record.seq, "gccatggcacatatatgaaggtcagaggacaacttgctgt")
self.assertEqual( self.assertEqual(
record.letter_annotations["phred_quality"], record.letter_annotations["phred_quality"],
[ [