[Bioperl-l] tarball
Jonathan Epstein
Jonathan_Epstein@nih.gov
Wed, 28 Feb 2001 13:26:33 -0500
Thanks for putting up the archive, Jason.
This is probably just a subtle parsing error... I can take a shot at it
if you like.
I am using ActivePerl 5.60 (sorry, I thought that I was using 5.004 until I
just checked) on Windows 2000. This is the output for Blast.t... test
numbered 4 and 29 fail.
- Jonathan
1..29
ok 1
QUERY NAME : gi|1401126
QUERY DESC : UNKNOWN
LENGTH : 504
FILE : t\blast.report
DATE : Thu, 16 Apr 1998 18:56:18 -0400
PROGRAM : TBLASTN
VERSION : 2.0.4 [Feb-24-1998]</b>
DB-NAME : Non-redundant GenBank+EMBL+DDBJ+PDB sequences
DB-RELEASE : Apr 16, 1998 9:38 AM
DB-LETTERS : 677679054
DB-SEQUENCES : 336723
GAPPED : YES
TOTAL HITS : 100
CHECKED ALL : YES
FILT FUNC : NO
SIGNIF HITS : 4
SIGNIF CUTOFF : 1.0e-005 (EXPECT-VALUE)
LOWEST EXPECT : 0.0
HIGHEST EXPECT : 1e-05
HIGHEST EXPECT : 7.6 (OVERALL)
MATRIX : BLOSUM62
FILTER : NONE
EXPECT : 10
LAMBDA, K, H : 0.270, 0.0470, 0.230 (SHARED STATS)
WORD SIZE : 13
S : 42, 74 (SHARED STATS)
GAP CREATION : 11
GAP EXTENSION : 1
ok 2
ok 3
not ok 4
# Test 4 got: '1.0e-005' (t/Blast.t at line 38)
# Expected: '1.0e-05' (Signif: 1.0e-005)
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
checking expected output...
3,6c3,6
<
gi|1401126 504 gb|U49928|HSU49928 3096 0.0e+000 2580
1009 1 1.00 1.00 504 504 0 0 1
04 21 1532 1 Homo sapiens TAK1 binding
protein (TAB1) mRNA, complete cds
<
gi|1401126 504 emb|Z36985|PTPP2CMR 969 4.0e-007 137
57 1 0.25 0.43 261 221 2 42 64
24 182 844 1 P.tetraurelia mRNA for
protein phosphatase type 2C
<
gi|1401126 504 emb|X77116|ATMRABI1 1981 1.0e-005 124
52 1 0.24 0.43 242 191 6 57 55
96 918 1490 1 A.thaliana mRNA for ABI1 protein
<
gi|1401126 504 gb|U12856|ATU12856 2000 1.0e-005 124
52 1 0.24 0.43 242 191 6 57 55
96 918 1490 1 Arabidopsis thaliana Col-0
abscisic acid insensitive protein (ABI1) mRNA, complete cds
---
> gi|1401126 504 gb|U49928|HSU49928 3096 0.0e+00
2580 1009 1 1.00 1.00 504 504 0 0 1
504 21 1532 1 Homo sapiens TAK1
inding protein (TAB1) mRNA, complete cds
> gi|1401126 504 emb|Z36985|PTPP2CMR 969 4.0e-07
137 57 1 0.25 0.43 261 221 2 42 64
324 182 844 1 P.tetraurelia mRNA for
rotein phosphatase type 2C
> gi|1401126 504 emb|X77116|ATMRABI1 1981 1.0e-05
124 52 1 0.24 0.43 242 191 6 57 55
296 918 1490 1 A.thaliana mRNA for
BI1 protein
> gi|1401126 504 gb|U12856|ATU12856 2000 1.0e-05
124 52 1 0.24 0.43 242 191 6 57 55
296 918 1490 1 Arabidopsis thaliana
ol-0 abscisic acid insensitive protein (ABI1) mRNA, complete cds
11,14c11,14
<
gi|1401126 504 gb|U49928|HSU49928 3096 0.0e+000 2580
1009 1 1.00 1.00 1.00 0.49 504 504 0
1 504 21 1532 - Homo sapiens TAK1 binding
rotein (TAB1) mRNA, complete cds
<
gi|1401126 504 emb|Z36985|PTPP2CMR 969 4.0e-007 137
57 1 0.25 0.43 0.52 0.68 261 221 2
2 64 324 182 844 - P.tetraurelia mRNA for
protein phosphatase type 2C
<
gi|1401126 504 emb|X77116|ATMRABI1 1981 1.0e-005 124
52 1 0.24 0.43 0.48 0.29 242 191 6
7 55 296 918 1490 - A.thaliana mRNA for ABI1 protein
<
gi|1401126 504 gb|U12856|ATU12856 2000 1.0e-005 124
52 1 0.24 0.43 0.48 0.29 242 191 6
7 55 296 918 1490 - Arabidopsis thaliana Col-0
abscisic acid insensitive protein (ABI1) mRNA, complete cds
---
> gi|1401126 504 gb|U49928|HSU49928 3096 0.0e+00
2580 1009 1 1.00 1.00 1.00 0.49 504 504 0
0 1 504 21 1532 - Homo sapiens TAK1
inding protein (TAB1) mRNA, complete cds
> gi|1401126 504 emb|Z36985|PTPP2CMR 969 4.0e-07
137 57 1 0.25 0.43 0.52 0.68 261 221 2
42 64 324 182 844 - P.tetraurelia mRNA for
rotein phosphatase type 2C
> gi|1401126 504 emb|X77116|ATMRABI1 1981 1.0e-05
124 52 1 0.24 0.43 0.48 0.29 242 191 6
57 55 296 918 1490 - A.thaliana mRNA for
BI1 protein
> gi|1401126 504 gb|U12856|ATU12856 2000 1.0e-05
124 52 1 0.24 0.43 0.48 0.29 242 191 6
57 55 296 918 1490 - Arabidopsis thaliana
ol-0 abscisic acid insensitive protein (ABI1) mRNA, complete cds
not ok 29
# Test 29 got: '256' (t/Blast.t at line 75)
# Expected: '0' (diff blast.t.out t\expected.blast.out)
At 12:17 PM 2/28/2001 , Jason Stajich wrote:
>Tarball of 'almost-release-candidate' is at
>ftp://bioperl.org/pub/jason/bioperl-20010228.tar.gz
>
>I can continue to update this as we make progress today.
>
>Cross-platform people, if you run this and have any problems, run the
>tests that break like
>% perl -w -I. t/BROKENTEST.t >& BROKENTEST.testoutput
>
>and mail out these files to the list.
>
>Thanks.
>
>Jason Stajich
>jason@chg.mc.duke.edu
>Center for Human Genetics
>Duke University Medical Center
>http://www.chg.duke.edu/
>
>
>
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>Bioperl-l mailing list
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