Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/raw-rev/6b32ed63555a Дата изменения: Unknown Дата индексирования: Tue Oct 2 07:49:55 2012 Кодировка: Поисковые слова: ccd

# HG changeset patch
# User Daniil Alexeyevsky
# Date 1338652326 -14400
# Node ID 6b32ed63555ab8980cf12ea3e8dfcbe22da84c15
# Parent afed1fd8920c152e352c47060d59d5cf24cf579b
Renamed test_fastq -> test_io_fastq for uniformity

diff -r afed1fd8920c -r 6b32ed63555a test/test_fastq.py
--- a/test/test_fastq.py Sat Jun 02 19:33:42 2012 +0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-from StringIO import StringIO
-from allpy import dna
-
-example = """
-@HWI-ST992:108:D06T0ACXX:6:1107:13562:94150 1:N:0:
-TCAATGGTGCTGTATAAAACACGTAGAATTACTATTATGGATTATATTCGTCTTCATTTGTTAAAATCAGTGGCTTAACTGGCTAAATTTTGTGGACTATA
-+
-#8::4AD,A+CEDEIEDFIE:FF;(>AAAA>
-@HWI-ST992:108:D06T0ACXX:6:1107:13630:94150 1:N:0:
-GGTGAAGCGCTTTGAGTCCCTCTCCAGCCAGCGCTTCCTGCAGGGCGTGATCGTGGCGCTCATCACGGGCATGTTCTGGTGGCAGCGCGGCCGCGGCGGCT
-+
-<@@DDFDBHHGFHIAHHIIIIIIIIIGHGIGAGHIHIIIIHIIII?G@BHHHHABDDDDDDDDDDDD?B@BCD@C@CDDACDDDDDDDDDBDBDBDD@B<>
-""".strip()
-
-def test_fastq_io():
- file = StringIO(example)
- aln = dna.Alignment().append_file(file, format="fastq")
- assert len(aln.sequences) == 2
- a, b = aln.sequences
- assert str(a)[:10] == "TCAATGGTGC"
- assert str(b)[:10] == "GGTGAAGCGC"
- qa = list(a.markups['quality'].sorted_values())
- assert qa[:10] == [2, 23, 25, 25, 19, 32, 35, 11, 32, 10]
- qb = list(b.markups['quality'].sorted_values())
- assert qb[:10] == [27, 31, 31, 35, 35, 37, 35, 33, 39, 39]
-
-# vim: set et ts=4 sts=4 sw=4:
diff -r afed1fd8920c -r 6b32ed63555a test/test_io_fastq.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test/test_io_fastq.py Sat Jun 02 19:52:06 2012 +0400
@@ -0,0 +1,27 @@
+from StringIO import StringIO
+from allpy import dna
+
+example = """
+@HWI-ST992:108:D06T0ACXX:6:1107:13562:94150 1:N:0:
+TCAATGGTGCTGTATAAAACACGTAGAATTACTATTATGGATTATATTCGTCTTCATTTGTTAAAATCAGTGGCTTAACTGGCTAAATTTTGTGGACTATA
++
+#8::4AD,A+CEDEIEDFIE:FF;(>AAAA>
+@HWI-ST992:108:D06T0ACXX:6:1107:13630:94150 1:N:0:
+GGTGAAGCGCTTTGAGTCCCTCTCCAGCCAGCGCTTCCTGCAGGGCGTGATCGTGGCGCTCATCACGGGCATGTTCTGGTGGCAGCGCGGCCGCGGCGGCT
++
+<@@DDFDBHHGFHIAHHIIIIIIIIIGHGIGAGHIHIIIIHIIII?G@BHHHHABDDDDDDDDDDDD?B@BCD@C@CDDACDDDDDDDDDBDBDBDD@B<>
+""".strip()
+
+def test_fastq_io():
+ file = StringIO(example)
+ aln = dna.Alignment().append_file(file, format="fastq")
+ assert len(aln.sequences) == 2
+ a, b = aln.sequences
+ assert str(a)[:10] == "TCAATGGTGC"
+ assert str(b)[:10] == "GGTGAAGCGC"
+ qa = list(a.markups['quality'].sorted_values())
+ assert qa[:10] == [2, 23, 25, 25, 19, 32, 35, 11, 32, 10]
+ qb = list(b.markups['quality'].sorted_values())
+ assert qb[:10] == [27, 31, 31, 35, 35, 37, 35, 33, 39, 39]
+
+# vim: set et ts=4 sts=4 sw=4: