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Adding 454 and Solexa derived PHD files from the Consed author David …

…Gordon (see also Bug 2865)
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commit a5207620367b63d85378fdcee8127c7909399697 1 parent 28f8383
@peterjc peterjc authored
Showing with 150 additions and 1 deletion.
  1. +48 −0 Tests/Phd/phd_454
  2. +99 −0 Tests/Phd/phd_solexa
  3. +3 −1 Tests/test_SeqIO.py
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48 Tests/Phd/phd_454
@@ -0,0 +1,48 @@
+BEGIN_SEQUENCE EBE03TV04IHLTF.77-243 1
+
+BEGIN_COMMENT
+
+CHROMAT_FILE: sff:reads.sff:EBE03TV04IHLTF
+QUALITY_LEVELS: 99
+TIME: Thu Jul 27 12:33:48 2000
+TRACE_ARRAY_MIN_INDEX: 0
+TRACE_ARRAY_MAX_INDEX: 4723
+CHEM: 454
+
+END_COMMENT
+
+BEGIN_DNA
+g 37 91
+g 37 110
+g 37 129
+g 37 148
+a 37 167
+t 37 186
+g 37 205
+a 37 224
+a 37 243
+a 37 262
+g 37 281
+g 37 300
+g 37 319
+a 26 4385
+t 26 4404
+c 26 4423
+t 30 4442
+c 33 4461
+g 33 4480
+g 33 4499
+t 33 4518
+g 33 4537
+g 36 4556
+t 36 4575
+a 33 4594
+g 33 4613
+g 33 4632
+t 36 4651
+g 26 4670
+a 22 4689
+END_DNA
+
+END_SEQUENCE
+
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99 Tests/Phd/phd_solexa
@@ -0,0 +1,99 @@
+# solexa file ../solexa_dir/solexa_reads.fastq (beginning)
+
+BEGIN_SEQUENCE HWI-EAS94_4_1_1_537_446 1
+BEGIN_COMMENT
+TIME: Wed Dec 24 11:21:50 2008
+CHEM: solexa
+END_COMMENT
+BEGIN_DNA
+g 30
+c 30
+c 30
+a 30
+a 30
+t 30
+c 30
+a 30
+g 30
+g 30
+t 30
+t 30
+t 30
+c 30
+t 30
+c 30
+t 30
+g 30
+c 30
+a 30
+a 28
+g 23
+c 30
+c 30
+c 30
+c 30
+t 30
+t 30
+t 28
+a 22
+g 8
+c 22
+a 7
+g 15
+c 15
+t 15
+g 10
+a 10
+g 11
+c 15
+END_DNA
+END_SEQUENCE
+
+BEGIN_SEQUENCE HWI-EAS94_4_1_1_602_99 1
+BEGIN_COMMENT
+TIME: Wed Dec 24 11:21:50 2008
+CHEM: solexa
+END_COMMENT
+BEGIN_DNA
+g 30
+c 30
+c 30
+a 30
+t 30
+g 30
+g 30
+c 30
+a 30
+c 30
+a 30
+t 30
+a 30
+t 30
+a 30
+t 30
+g 30
+a 30
+a 30
+g 30
+g 30
+t 30
+c 30
+a 30
+g 30
+a 30
+g 16
+g 30
+a 28
+c 22
+a 22
+a 22
+c 14
+t 15
+t 15
+g 5
+c 10
+t 15
+g 10
+t 5
+END_DNA
+END_SEQUENCE
View
4 Tests/test_SeqIO.py
@@ -142,7 +142,9 @@
#Following PHD (PHRAP) sequencing files are also used in test_Phd.py
("phd", False, 'Phd/phd1', 3),
("phd", False, 'Phd/phd2', 1),
-#Following ACE assembly files are also used in test_Phd.py
+ ("phd", False, 'Phd/phd_solexa', 2),
+ ("phd", False, 'Phd/phd_454', 1),
+#Following ACE assembly files are also used in test_Ace.py
("ace", False, 'Ace/contig1.ace', 2),
("ace", False, 'Ace/consed_sample.ace', 1),
("ace", False, 'Ace/seq.cap.ace', 1),
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