Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

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

…Gordon (see also Bug 2865)
  • Loading branch information...
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
View
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
+
View
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),
Please sign in to comment.
Something went wrong with that request. Please try again.