galaxy-dev February 2010

galaxy-dev@lists.galaxyproject.org

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180 discussions

[hg] galaxy 3368: A slightly better closing icon for screencast ...
by Greg Von Kuster 11 Feb '10

11 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/773273b96ff4 changeset: 3368:773273b96ff4 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Wed Feb 10 15:13:46 2010 -0500 description: A slightly better closing icon for screencast overlays diffstat: static/images/closebox.png | 0 static/scripts/galaxy.panels.js | 2 +- 2 files changed, 1 insertions(+), 1 deletions(-) diffs (14 lines): diff -r 485d9f2c7627 -r 773273b96ff4 static/images/closebox.png Binary file static/images/closebox.png has changed diff -r 485d9f2c7627 -r 773273b96ff4 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Wed Feb 10 14:59:46 2010 -0500 +++ b/static/scripts/galaxy.panels.js Wed Feb 10 15:13:46 2010 -0500 @@ -210,7 +210,7 @@ hide_modal(); $("#overlay-background").unbind( "click.overlay" ); }); - show_modal( null, $("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-12px;top:-12px;' src='../images/delete_icon.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); + show_modal( null, $("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;' src='../images/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); $("#close_button").bind( "click", function() { hide_modal() } ); }

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[hg] galaxy 3367: Corrected some typos in DNA filtering tool
by Greg Von Kuster 11 Feb '10

11 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/485d9f2c7627 changeset: 3367:485d9f2c7627 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Feb 10 14:59:46 2010 -0500 description: Corrected some typos in DNA filtering tool diffstat: test-data/dna_filter_in1.bed | 49 ------------------------------------------- test-data/dna_filter_out1.bed | 4 --- test-data/dna_filter_out2.bed | 39 ---------------------------------- test-data/dna_filter_out3.bed | 41 ----------------------------------- test-data/dna_filter_out4.bed | 24 --------------------- tools/stats/dna_filtering.xml | 15 ++++++------- 6 files changed, 7 insertions(+), 165 deletions(-) diffs (230 lines): diff -r 1487502e7996 -r 485d9f2c7627 test-data/dna_filter_in1.bed --- a/test-data/dna_filter_in1.bed Wed Feb 10 14:42:42 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -chr1 256 257 A N M N - M N U N N A N D N G N N K N N N -chr1 468 469 C C C N M N N K . N C U N H N G N N M N S -chr1 582 583 G G G N G R N R N - N M N V K N N N G C R -chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R -chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N -chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N -chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S -chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N -chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y -chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N -chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K -chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A -chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y -chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N -chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C -chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N -chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N -chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N -chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N -chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R -chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N -chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N -chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N -chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R -chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y -chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N -chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N -chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N -chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N -chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N -chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N -chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N -chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N -chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N -chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N -chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T -chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A -chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R -chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N -chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N -chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W -chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N -chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K -chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N -chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N -chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y -chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N -chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M -chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N \ No newline at end of file diff -r 1487502e7996 -r 485d9f2c7627 test-data/dna_filter_out1.bed --- a/test-data/dna_filter_out1.bed Wed Feb 10 14:42:42 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -chr1 582 583 G G G N G R N R N - N M N V K N N N G C R -chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R -chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N -chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R diff -r 1487502e7996 -r 485d9f2c7627 test-data/dna_filter_out2.bed --- a/test-data/dna_filter_out2.bed Wed Feb 10 14:42:42 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -chr1 256 257 A N M N - M N U N N A N D N G N N K N N N -chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R -chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N -chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N -chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S -chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N -chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y -chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N -chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K -chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C -chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N -chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N -chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N -chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R -chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N -chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N -chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R -chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y -chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N -chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N -chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N -chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N -chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N -chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N -chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N -chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N -chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N -chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T -chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A -chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R -chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N -chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N -chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W -chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N -chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K -chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N -chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y -chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N -chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r 1487502e7996 -r 485d9f2c7627 test-data/dna_filter_out3.bed --- a/test-data/dna_filter_out3.bed Wed Feb 10 14:42:42 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -chr1 468 469 C C C N M N N K . N C U N H N G N N M N S -chr1 582 583 G G G N G R N R N - N M N V K N N N G C R -chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R -chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N -chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S -chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N -chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y -chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N -chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K -chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A -chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y -chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N -chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C -chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N -chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N -chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N -chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N -chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N -chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N -chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y -chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N -chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N -chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N -chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N -chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N -chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N -chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N -chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N -chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T -chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A -chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R -chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N -chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N -chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W -chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N -chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K -chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N -chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y -chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N -chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M -chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r 1487502e7996 -r 485d9f2c7627 test-data/dna_filter_out4.bed --- a/test-data/dna_filter_out4.bed Wed Feb 10 14:42:42 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -chr1 582 583 G G G N G R N R N - N M N V K N N N G C R -chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R -chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N -chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N -chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N -chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y -chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C -chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N -chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N -chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R -chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N -chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N -chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y -chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N -chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N -chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N -chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N -chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A -chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R -chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W -chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y -chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N -chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M -chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r 1487502e7996 -r 485d9f2c7627 tools/stats/dna_filtering.xml --- a/tools/stats/dna_filtering.xml Wed Feb 10 14:42:42 2010 -0500 +++ b/tools/stats/dna_filtering.xml Wed Feb 10 14:59:46 2010 -0500 @@ -56,7 +56,7 @@ .. class:: warningmark -**TIP:** This tool is intended primarily for comparing column values (such as "c5==c12"), although it is also possible to filter on specific values (like "c6!='G'"). Be aware that when searching for specific values, any possible match is considered. So if you search on "c6!='G'", rows will be excluded when c6 is G, K, R, S, B, V, or D (plus N or X if you set that to equal "Everything"), because it is possible those values could be G. +**TIP:** This tool is intended primarily for comparing column values (such as "c5==c12"), although it is also possible to filter on specific values (like "c6!='G'"). Be aware that when searching for specific values, any possible match is considered. So if you search on "c6!='G'", rows will be excluded when c6 is G, K, R, S, B, V, or D (plus N or X if you set that to equal "Everything"), because it is possible those values could indicate G. ----- @@ -69,7 +69,7 @@ chr1 100 101 A M C R chr1 200 201 T K C C -and your want to select all rows where patient1 has the same base as patient2. Unfortunately you cannot do this with the *Filter and Sort -> Filter* tool because it does not understant DNA ambiguity codes (see below). For example, at postion 100 patient1 is the same as patient2 because M is a mix of As and Cs. This tool is designed to make filtering on ambiguities possible. +and your want to select all rows where patient1 has the same base as patient2. Unfortunately you cannot do this with the *Filter and Sort -> Filter* tool because it does not understand DNA ambiguity codes (see below). For example, at position 100 patient1 is the same as patient2 because M is a mix of As and Cs. This tool is designed to make filtering on ambiguities possible. ----- @@ -88,14 +88,13 @@ The following types of filtering are allowed: -- Testing colums for eqality (e.g., c2 == c4 or c2 != c4) +- Testing columns for equality (e.g., c2 == c4 or c2 != c4) - Testing that a column contains a particular base (e.g., c4 == 'C'). Only bases listed in *DNA Codes* below are allowed. - Testing that a column represents a plus or a minus strand (e.g., c3 == '+' or c3 != '-') -- Testing that a column is a chromsomes (c1 == 'chrX') or a scaffold (c1 == 'scafford87976') +- Testing that a column is a chromosomes (c1 == 'chrX') or a scaffold (c1 == 'scaffold87976') All other types of filtering should be done with *Filter and Sort -> Filter* tool. - ----- **DNA Codes** @@ -128,10 +127,10 @@ **Example** -- **c8=='A'** selects lines in which the eighth column is A, M, R, W, V, H, D and N or X if appropriate +- **c8=='A'** selects lines in which the eighth column is A, M, R, W, V, H, or D, or N or X if appropriate - **c12==c15** selects lines where the value in the twelfth column could be the same as the fifteenth and the fifteenth column could be the same as the twelfth column (based on appropriate codes) -- **c9!=c19** selects lines where column nine could not be the same as column nineteen and column nineteen could not be the same as column nine (using appropriate codes) -- **c4 == 'A' and c4 == c5** selects lines where column 4 and 5 are both A, M, R, W, V, H, D and N or X if appropriate +- **c9!=c19** selects lines where column nine could not be the same as column nineteen or column nineteen could not be the same as column nine (using appropriate codes) +- **c4 == 'A' and c4 == c5** selects lines where column 4 and 5 are both A, M, R, W, V, H, D or N, or X if appropriate </help> </tool>

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[hg] galaxy 3366: Edites to DNA ambig filter interface
by Greg Von Kuster 11 Feb '10

11 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1487502e7996 changeset: 3366:1487502e7996 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Wed Feb 10 14:42:42 2010 -0500 description: Edites to DNA ambig filter interface diffstat: tools/stats/dna_filtering.xml | 89 ++++++++++++++++++++++++++---------------- 1 files changed, 55 insertions(+), 34 deletions(-) diffs (131 lines): diff -r e85a213a347d -r 1487502e7996 tools/stats/dna_filtering.xml --- a/tools/stats/dna_filtering.xml Wed Feb 10 14:14:55 2010 -0500 +++ b/tools/stats/dna_filtering.xml Wed Feb 10 14:42:42 2010 -0500 @@ -1,5 +1,5 @@ -<tool id="dna_filter" name="DNA Filter" version="1.0.0"> - <description>filter column data on DNA ambiguity codes using simple expressions</description> +<tool id="dna_filter" name="Filter on ambiguities" version="1.0.0"> + <description>in polymorphism datasets</description> <command interpreter="python"> dna_filtering.py --input=$input @@ -14,9 +14,9 @@ <param name="cond" size="40" type="text" value="c4 == 'G'" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."> <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/> </param> - <param name="n_handling" type="select" label="Do you want N (and X) to match A or C or G or T OR nothing?"> - <option value="all">N = A or C or G or T</option> - <option value="none">N = nothing</option> + <param name="n_handling" type="select" label="What is the meaning of N" help="Everything matches everything, Unknown matches nothing"> + <option value="all">Everything (A, T, C, G)</option> + <option value="none">Unknown</option> </param> </inputs> <outputs> @@ -50,30 +50,51 @@ </tests> <help> -.. class:: warningmark - -Double equal signs, ==, must be used as *"equal to"* (e.g., **c1 == 'G'**) - .. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* -.. class:: infomark +.. class:: warningmark -**TIP:** This tool is intended primarily for comparing column values (such as "c5==c12"), although it is also possible to filter on specific values (like "c6!='G'"). Be aware that when searching for specific values, any possible match is considered. So if you search on "c6!='G'", rows will be excluded when c6 is G, K, R, S, B, V, or D (plus N or X if you set that to equal "all"), because it is possible those values could be G. +**TIP:** This tool is intended primarily for comparing column values (such as "c5==c12"), although it is also possible to filter on specific values (like "c6!='G'"). Be aware that when searching for specific values, any possible match is considered. So if you search on "c6!='G'", rows will be excluded when c6 is G, K, R, S, B, V, or D (plus N or X if you set that to equal "Everything"), because it is possible those values could be G. + +----- + +**What it does** + +This tool is written for a very specific case related to an analysis of polymorphism data. Suppose you have a table of SNP data that looks like this:: + + chromosome start end patient1 parient2 patient3 patient4 + -------------------------------------------------------- + chr1 100 101 A M C R + chr1 200 201 T K C C + +and your want to select all rows where patient1 has the same base as patient2. Unfortunately you cannot do this with the *Filter and Sort -> Filter* tool because it does not understant DNA ambiguity codes (see below). For example, at postion 100 patient1 is the same as patient2 because M is a mix of As and Cs. This tool is designed to make filtering on ambiguities possible. ----- **Syntax** -The filter tool allows you to restrict the dataset using simple conditional statements. +The filter tool allows you to restrict the dataset using simple conditional statements: -- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file -- Make sure that multi-character operators contain no white space ( e.g., **!=** is valid while **! =** is not valid ) +- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file (e.g., **c4 == c5**) - When using 'equal-to' operator **double equal sign '==' must be used** ( e.g., **c1=='chr1'** ) - Non-numerical values must be included in single or double quotes ( e.g., **c6=='C'** ) - Filtering condition can include logical operators, but **make sure operators are all lower case** ( e.g., **(c1!='chrX' and c1!='chrY') or c6=='+'** ) -- You can use spaces between the arguments and equality sign or not (e.g. both **c9 == c10** and **c9==c10** are valid) + +------ + +**Allowed types of filtering** + +The following types of filtering are allowed: + +- Testing colums for eqality (e.g., c2 == c4 or c2 != c4) +- Testing that a column contains a particular base (e.g., c4 == 'C'). Only bases listed in *DNA Codes* below are allowed. +- Testing that a column represents a plus or a minus strand (e.g., c3 == '+' or c3 != '-') +- Testing that a column is a chromsomes (c1 == 'chrX') or a scaffold (c1 == 'scafford87976') + +All other types of filtering should be done with *Filter and Sort -> Filter* tool. + ----- @@ -81,25 +102,25 @@ The following are the DNA codes used for filtering:: - Code Meaning - ---- --------------------------- - A A - T T - U T - G G - C C - K G or T - M A or C - R A or G - Y C or T - S C or G - W A or T - B C, G or T - V A, C or G - H A, C or T - D A, G or T - X A, C, G or T - N A, C, G or T + Code Meaning + ---- -------------------------- + A A + T T + U T + G G + C C + K G or T + M A or C + R A or G + Y C or T + S C or G + W A or T + B C, G or T + V A, C or G + H A, C or T + D A, G or T + X A, C, G or T + N A, C, G or T . not (A, C, G or T) - gap of indeterminate length

1 0

[hg] galaxy 3365: Modified strand column assignment to the NiceR...
by Greg Von Kuster 11 Feb '10

11 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e85a213a347d changeset: 3365:e85a213a347d user: gua110 date: Wed Feb 10 14:14:55 2010 -0500 description: Modified strand column assignment to the NiceReaderWrapper object in basecoverage tool. Previously, if the input had no strand column declared, the object would have a default strand col of 5, and return a coverage of 0 as c5 might not have been a valid strand col. diffstat: tools/new_operations/gops_basecoverage.py | 8 +++----- 1 files changed, 3 insertions(+), 5 deletions(-) diffs (30 lines): diff -r 33b475ccc316 -r e85a213a347d tools/new_operations/gops_basecoverage.py --- a/tools/new_operations/gops_basecoverage.py Wed Feb 10 13:18:45 2010 -0500 +++ b/tools/new_operations/gops_basecoverage.py Wed Feb 10 14:14:55 2010 -0500 @@ -8,7 +8,6 @@ from galaxy import eggs import pkg_resources pkg_resources.require( "bx-python" ) - import sys, traceback, fileinput from warnings import warn from bx.intervals import * @@ -29,15 +28,14 @@ in_fname, out_fname = args except: doc_optparse.exception() - + g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), chrom_col=chr_col_1, start_col=start_col_1, end_col=end_col_1, + strand_col = strand_col_1, fix_strand=True ) - - if strand_col_1 >= 0: - g1.strand_col=strand_col_1 + try: bases = base_coverage(g1) except ParseError, exc:

1 0

[hg] galaxy 3364: Changed some of the filtering logic for DNA co...
by Greg Von Kuster 11 Feb '10

11 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/33b475ccc316 changeset: 3364:33b475ccc316 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Feb 10 13:18:45 2010 -0500 description: Changed some of the filtering logic for DNA code filter tool, and got tests working diffstat: test-data/dna_filter_in1.tabular | 49 +++++++++++++++++++++ test-data/dna_filter_out1.tabular | 35 +++++++++++++++ test-data/dna_filter_out2.tabular | 31 +++++++++++++ test-data/dna_filter_out3.tabular | 42 ++++++++++++++++++ test-data/dna_filter_out4.tabular | 6 ++ tools/stats/dna_filtering.py | 87 ++++++++++++++++++++++++-------------- tools/stats/dna_filtering.xml | 24 +++++---- 7 files changed, 230 insertions(+), 44 deletions(-) diffs (389 lines): diff -r 1fc06b260097 -r 33b475ccc316 test-data/dna_filter_in1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_in1.tabular Wed Feb 10 13:18:45 2010 -0500 @@ -0,0 +1,49 @@ +chr1 256 257 A N M N - M N U N N A N D N G N N K N N N + +chr1 468 469 C C C N M N N K . N C U N H N G N N M N S - +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R + +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R + +chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N + +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N + +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S - +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N + +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y + +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N + +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K - +chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A + +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y + +chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N + +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C - +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N + +chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N + +chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N + +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N + +chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R + +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N - +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N - +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N + +chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R + +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y + +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N + +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N + +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N + +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N + +chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N + +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N + +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N - +chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N + +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N + +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N + +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T + +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A - +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R + +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N + +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N + +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W + +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N - +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K + +chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N + +chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N + +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y + +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N + +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M + +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N - \ No newline at end of file diff -r 1fc06b260097 -r 33b475ccc316 test-data/dna_filter_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out1.tabular Wed Feb 10 13:18:45 2010 -0500 @@ -0,0 +1,35 @@ +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R + +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R + +chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N + +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N + +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S - +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N + +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y + +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K - +chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A + +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y + +chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N + +chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N + +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N + +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N - +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N - +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N + +chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R + +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y + +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N + +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N + +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N + +chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N + +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N + +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N + +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T + +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A - +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R + +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N + +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N + +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W + +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N - +chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N + +chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N + +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N + +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N - \ No newline at end of file diff -r 1fc06b260097 -r 33b475ccc316 test-data/dna_filter_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out2.tabular Wed Feb 10 13:18:45 2010 -0500 @@ -0,0 +1,31 @@ +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R + +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y + +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N + +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K - +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C - +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N + +chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N + +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N + +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N + +chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R + +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y + +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N + +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N + +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N + +chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N + +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N + +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N - +chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N + +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N + +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N + +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T + +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R + +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N + +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N + +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W + +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N - +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K + +chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N + +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y + +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N + +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N - \ No newline at end of file diff -r 1fc06b260097 -r 33b475ccc316 test-data/dna_filter_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out3.tabular Wed Feb 10 13:18:45 2010 -0500 @@ -0,0 +1,42 @@ +chr1 468 469 C C C N M N N K . N C U N H N G N N M N S - +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R + +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R + +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N + +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S - +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N + +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y + +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N + +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K - +chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A + +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y + +chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N + +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C - +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N + +chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N + +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N + +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N - +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N - +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N + +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y + +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N + +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N + +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N + +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N + +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N + +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N - +chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N + +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N + +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N + +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T + +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A - +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R + +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N + +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N + +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W + +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N - +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K + +chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N + +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y + +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N + +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M + +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N - \ No newline at end of file diff -r 1fc06b260097 -r 33b475ccc316 test-data/dna_filter_out4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out4.tabular Wed Feb 10 13:18:45 2010 -0500 @@ -0,0 +1,6 @@ +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C - +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N - +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N - +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N - +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A - +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N - \ No newline at end of file diff -r 1fc06b260097 -r 33b475ccc316 tools/stats/dna_filtering.py --- a/tools/stats/dna_filtering.py Wed Feb 10 12:17:38 2010 -0500 +++ b/tools/stats/dna_filtering.py Wed Feb 10 13:18:45 2010 -0500 @@ -14,7 +14,7 @@ """ #from __future__ import division -import os.path, re, string, sys +import os.path, re, string, string, sys from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.cookbook import doc_optparse @@ -62,28 +62,29 @@ orig_cond_text = cond_text # Expand to allow for DNA codes dot_letters = [ letter for letter in string.uppercase if letter not in \ - [ 'A', 'T', 'U', 'G', 'C', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] ] - codes = {'A': [ 'A', 'M', 'R', 'W', 'V', 'H', 'D' ], - 'T': [ 'T', 'U', 'K', 'Y', 'W', 'B', 'H', 'D' ], - 'G': [ 'G', 'K', 'R', 'S', 'B', 'V', 'D' ], - 'C': [ 'C', 'M', 'Y', 'S', 'B', 'V', 'H' ], - 'U': [ 'T', 'U', 'K', 'Y', 'W', 'B', 'H', 'D' ], - 'K': [ 'K', 'G', 'T' ], - 'M': [ 'M', 'A', 'C' ], - 'R': [ 'R', 'A', 'G' ], - 'Y': [ 'Y', 'C', 'T' ], - 'S': [ 'S', 'C', 'G' ], - 'W': [ 'W', 'A', 'T' ], - 'B': [ 'B', 'C', 'G', 'T' ], - 'V': [ 'V', 'A', 'C', 'G' ], - 'H': [ 'H', 'A', 'C', 'T' ], - 'D': [ 'D', 'A', 'G', 'T' ], + [ 'A', 'C', 'G', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'N', 'R', 'S', 'V', 'W', 'X', 'Y' ] ] + dot_letters.append( '.' ) + codes = {'A': [ 'A', 'D', 'H', 'M', 'R', 'V', 'W' ], + 'C': [ 'C', 'B', 'H', 'M', 'S', 'V', 'Y' ], + 'G': [ 'G', 'B', 'D', 'K', 'R', 'S', 'V' ], + 'T': [ 'T', 'U', 'B', 'D', 'H', 'K', 'W', 'Y' ], + 'U': [ 'T', 'U', 'B', 'D', 'H', 'K', 'W', 'Y' ], + 'K': [ 'G', 'T', 'U', 'B', 'D', 'H', 'K', 'R', 'S', 'V', 'W', 'Y' ], + 'M': [ 'A', 'C', 'B', 'D', 'H', 'M', 'R', 'S', 'V', 'W', 'Y' ], + 'R': [ 'A', 'G', 'B', 'D', 'H', 'K', 'M', 'R', 'S', 'V', 'W' ], + 'Y': [ 'C', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'S', 'V', 'W', 'Y' ], + 'S': [ 'C', 'G', 'B', 'D', 'H', 'K', 'M', 'R', 'S', 'V', 'Y' ], + 'W': [ 'A', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'R', 'V', 'W', 'Y' ], + 'B': [ 'C', 'G', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'R', 'S', 'V', 'W', 'Y' ], + 'V': [ 'A', 'C', 'G', 'B', 'D', 'H', 'K', 'M', 'R', 'S', 'V', 'W' ], + 'H': [ 'A', 'C', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'R', 'S', 'V', 'W', 'Y' ], + 'D': [ 'A', 'G', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'R', 'S', 'V', 'W', 'Y' ], '.': dot_letters, '-': [ '-' ]} # Add handling for N and X if n_handling == "all": - codes[ 'N' ] = [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] - codes[ 'X' ] = [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] + codes[ 'N' ] = [ 'A', 'C', 'G', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'N', 'R', 'S', 'V', 'W', 'X', 'Y' ] + codes[ 'X' ] = [ 'A', 'C', 'G', 'T', 'U', 'B', 'D', 'H', 'K', 'M', 'N', 'R', 'S', 'V', 'W', 'X', 'Y' ] for code in codes.keys(): if code != '.' and code != '-': codes[code].append( 'N' ) @@ -91,31 +92,51 @@ else: codes[ 'N' ] = dot_letters codes[ 'X' ] = dot_letters + codes[ '.' ].extend( [ 'N', 'X' ] ) # Expand conditions to allow for DNA codes try: match_replace = {} - pat = re.compile( "c\d+\s*[!=]=\s*[\w']+" ) + pat = re.compile( 'c\d+\s*[!=]=\s*[\w\d"\'+-.]+' ) matches = pat.findall( cond_text ) for match in matches: - if match.find( '==' ) > 0: + if match.find( 'chr' ) >= 0 or match.find( 'scaffold' ) >= 0 or match.find( '+' ) >= 0: + if match.find( '==' ) >= 0: + match_parts = match.split( '==' ) + elif match.find( '!=' ) >= 0: + match_parts = match.split( '!=' ) + else: + raise Exception, "The operators '==' and '!=' were not found." + left = match_parts[0].strip() + right = match_parts[1].strip() + new_match = "(%s)" % ( match ) + elif match.find( '==' ) > 0: match_parts = match.split( '==' ) - new_match = '(%s in codes[%s] and %s in codes[%s])' % ( match_parts[0], match_parts[1], match_parts[1], match_parts[0] ) + left = match_parts[0].strip() + right = match_parts[1].strip() + new_match = '(%s in codes[%s] and %s in codes[%s])' % ( left, right, right, left ) elif match.find( '!=' ) > 0 : match_parts = match.split( '!=' ) - new_match = '(%s not in codes[%s] or %s not in codes[%s])' % ( match_parts[0], match_parts[1], match_parts[1], match_parts[0] ) + left = match_parts[0].strip() + right = match_parts[1].strip() + new_match = '(%s not in codes[%s] or %s not in codes[%s])' % ( left, right, right, left ) else: - raise Exception - if match_parts[1].find( "'" ) >= 0: - assert match_parts[1].replace( "'", '' ) in [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X', '-', '.' ] + raise Exception, "The operators '==' and '!=' were not found." + assert left.startswith( 'c' ), 'The column names should start with c (lowercase)' + if right.find( "'" ) >= 0 or right.find( '"' ) >= 0: + test = right.replace( "'", '' ).replace( '"', '' ) + assert test in string.uppercase or test.find( '+' ) >= 0 or test.find( '.' ) >= 0 or test.find( '-' ) >= 0\ + or test.startswith( 'chr' ) or test.startswith( 'scaffold' ), \ + 'The value to search for should be a valid base, code, plus sign, chromosome (like "chr1") or scaffold (like "scaffold5"). ' \ + 'Use the general filter tool to filter on anything else first' else: - assert match_parts[1].startswith( 'c' ) + assert right.startswith( 'c' ), 'The column names should start with c (lowercase)' match_replace[match] = new_match + if len( match_replace.keys() ) == 0: + raise Exception, 'There do not appear to be any valid conditions' for match in match_replace.keys(): - cond_text = cond_text.replace(match, match_replace[match]) - if len( match_replace ) == 0: - raise Exception - except: - stop_err( "One of your conditions is invalid. Make sure to use only '!=' or '==', valid column numbers, and valid base values." ) + cond_text = cond_text.replace( match, match_replace[match] ) + except Exception, e: + stop_err( "At least one of your conditions is invalid. Make sure to use only '!=' or '==', valid column numbers, and valid base values.\n" + str(e) ) # Attempt to determine if the condition includes executable stuff and, if so, exit secured = dir() @@ -177,7 +198,7 @@ out.close() if str( e ).startswith( 'invalid syntax' ): valid_filter = False - stop_err( 'Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % orig_cond_text ) + stop_err( 'Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % orig_cond_text + ' '+str(e)) else: stop_err( str( e ) ) diff -r 1fc06b260097 -r 33b475ccc316 tools/stats/dna_filtering.xml --- a/tools/stats/dna_filtering.xml Wed Feb 10 12:17:38 2010 -0500 +++ b/tools/stats/dna_filtering.xml Wed Feb 10 13:18:45 2010 -0500 @@ -11,7 +11,7 @@ </command> <inputs> <param format="tabular" name="input" type="data" label="Filter" help="Query missing? See TIP below."/> - <param name="cond" size="40" type="text" value="c8=='G'" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."> + <param name="cond" size="40" type="text" value="c4 == 'G'" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."> <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/> </param> <param name="n_handling" type="select" label="Do you want N (and X) to match A or C or G or T OR nothing?"> @@ -24,28 +24,28 @@ </outputs> <tests> <test> - <param name="input" value="dna_filter_in1.bed" /> + <param name="input" ftype="tabular" value="dna_filter_in1.tabular" /> <param name="cond" value="c8=='G'" /> <param name="n_handling" value="all" /> - <output name="out_file1" file="dna_filter_out1.bed" /> + <output name="out_file1" ftype="tabular" file="dna_filter_out1.tabular" /> </test> <test> - <param name="input" value="dna_filter_in1.bed" /> - <param name="cond" value="(c10==c11 or c17==c18) and c6!='C' and c23=='R'" /> + <param name="input" value="dna_filter_in1.tabular" /> + <param name="cond" value="(c10 == c11 or c17 == c18) and c6 != 'C' and c23 == 'R'" /> <param name="n_handling" value="all" /> - <output name="out_file1" file="dna_filter_out2.bed" /> + <output name="out_file1" file="dna_filter_out2.tabular" /> </test> <test> - <param name="input" value="dna_filter_in1.bed" /> + <param name="input" value="dna_filter_in1.tabular" /> <param name="cond" value="c4=='B' or c9==c10" /> <param name="n_handling" value="none" /> - <output name="out_file1" file="dna_filter_out3.bed" /> + <output name="out_file1" file="dna_filter_out3.tabular" /> </test> <test> - <param name="input" value="dna_filter_in1.bed" /> - <param name="cond" value="c7!='Y' and c9!='U'" /> + <param name="input" value="dna_filter_in1.tabular" /> + <param name="cond" value="c1!='chr1' and c7!='Y' and c25!='+'" /> <param name="n_handling" value="none" /> - <output name="out_file1" file="dna_filter_out4.bed" /> + <output name="out_file1" file="dna_filter_out4.tabular" /> </test> </tests> <help> @@ -73,6 +73,7 @@ - When using 'equal-to' operator **double equal sign '==' must be used** ( e.g., **c1=='chr1'** ) - Non-numerical values must be included in single or double quotes ( e.g., **c6=='C'** ) - Filtering condition can include logical operators, but **make sure operators are all lower case** ( e.g., **(c1!='chrX' and c1!='chrY') or c6=='+'** ) +- You can use spaces between the arguments and equality sign or not (e.g. both **c9 == c10** and **c9==c10** are valid) ----- @@ -109,6 +110,7 @@ - **c8=='A'** selects lines in which the eighth column is A, M, R, W, V, H, D and N or X if appropriate - **c12==c15** selects lines where the value in the twelfth column could be the same as the fifteenth and the fifteenth column could be the same as the twelfth column (based on appropriate codes) - **c9!=c19** selects lines where column nine could not be the same as column nineteen and column nineteen could not be the same as column nine (using appropriate codes) +- **c4 == 'A' and c4 == c5** selects lines where column 4 and 5 are both A, M, R, W, V, H, D and N or X if appropriate </help> </tool>

1 0

[hg] galaxy 3363: trackster:
by Greg Von Kuster 11 Feb '10

11 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1fc06b260097 changeset: 3363:1fc06b260097 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Feb 10 12:17:38 2010 -0500 description: trackster: - Refactor element creation code - Can delete tracks - Can reorder tracks diffstat: static/june_2007_style/history.css.tmpl | 2 +- static/scripts/trackster.js | 19 ++++++++++-- templates/tracks/browser.mako | 49 ++++++++++++++++---------------- 3 files changed, 41 insertions(+), 29 deletions(-) diffs (142 lines): diff -r 445986a09dbb -r 1fc06b260097 static/june_2007_style/history.css.tmpl --- a/static/june_2007_style/history.css.tmpl Tue Feb 09 15:05:39 2010 -0500 +++ b/static/june_2007_style/history.css.tmpl Wed Feb 10 12:17:38 2010 -0500 @@ -19,7 +19,7 @@ margin: 5px 0 5px 0; } -## Default history item appearend +## Default history item appearance div.historyItem { margin: 5px -5px 5px 0px; padding: 5px 11px 5px 5px; diff -r 445986a09dbb -r 1fc06b260097 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Feb 09 15:05:39 2010 -0500 +++ b/static/scripts/trackster.js Wed Feb 10 12:17:38 2010 -0500 @@ -89,21 +89,34 @@ this.center = (this.max_high - this.max_low) / 2; this.zoom_factor = 3; this.zoom_level = 0; + this.track_id_counter = 0; }; $.extend( View.prototype, { add_track: function ( track ) { track.view = this; + track.track_id = this.track_id_counter; this.tracks.push( track ); if (track.init) { track.init(); } + track.container_div.attr('id', 'track_' + track.track_id); + this.track_id_counter += 1; }, add_label_track: function ( label_track ) { label_track.view = this; this.label_tracks.push( label_track ); }, remove_track: function( track ) { + track.container_div.fadeOut('slow', function() { $(this).remove(); }); delete this.tracks[track]; }, update_options: function() { + var sorted = $("ul#sortable-ul").sortable('toArray'); + var payload = []; + + var divs = $("#viewport > div").sort(function (a, b) { + return sorted.indexOf( $(a).attr('id') ) > sorted.indexOf( $(b).attr('id') ); + }); + $("#viewport > div").remove(); + $("#viewport").html(divs); for (var track_id in view.tracks) { var track = view.tracks[track_id]; if (track.update_options) { @@ -177,13 +190,13 @@ var Track = function ( name, parent_element ) { this.name = name; this.parent_element = parent_element; - this.make_container(); + this.init_global(); }; $.extend( Track.prototype, { - make_container: function () { + init_global: function () { this.header_div = $("<div class='track-header'>").text( this.name ); this.content_div = $("<div class='track-content'>"); - this.container_div = $("<div class='track'></div>").append( this.header_div ).append( this.content_div ); + this.container_div = $("<div></div>").addClass('track').append( this.header_div ).append( this.content_div ); this.parent_element.append( this.container_div ); } }); diff -r 445986a09dbb -r 1fc06b260097 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Feb 09 15:05:39 2010 -0500 +++ b/templates/tracks/browser.mako Wed Feb 10 12:17:38 2010 -0500 @@ -25,15 +25,6 @@ margin: 5px 0; background: #eee; } - .delete-button { - background: transparent url(history-buttons.png) no-repeat scroll 0 -104px; - height: 20px; - width: 20px; - } - .delete-button:hover { - background-position: 0 -130px; - } - </style> </%def> @@ -231,7 +222,6 @@ }); }); - hide_modal(); }, "Cancel": function() { @@ -307,23 +297,32 @@ function sidebar_box(track) { if (!track.hidden) { - var track_id = view.tracks.length -1; // Track was just added to view, so index is current length -1 - var label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'); - var title = $('<div class="historyItemTitle"></div>'); - var del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />'); - var body = $('<div class="historyItemBody"></div>'); - // var checkbox = $('<input type="checkbox" checked="checked"></input>').attr("id", "track_" + track_id + "title"); - var li = $('<li class="sortable"></li>').attr("id", "track_" + track_id); - var div = $('<div class="historyItemContainer historyItem"></div>'); - del_icon.prependTo(title); - label.appendTo(title); - // checkbox.prependTo(title); + var track_id = track.track_id, + label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'), + title = $('<div class="historyItemTitle"></div>'), + del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />'), + edit_icon = $('<a style="display:block; float:right" href="#" class="icon-button edit" />'), + body = $('<div class="historyItemBody"></div>'), + checkbox = $('<input type="checkbox" checked="checked"></input>').attr("id", "track_" + track_id + "title"), + li = $('<li class="sortable"></li>').attr("id", "track_" + track_id), + div = $('<div class="historyItemContainer historyItem"></div>'), + editable = $('<div style="display:none"></div>'); + + edit_icon.bind("click", function() { + editable.toggle(); + }); + + del_icon.bind("click", function() { + li.fadeOut('slow', function() { $(this).remove(); }); + view.remove_track(track); + view.update_options(); + }); + + title.append(label).append(del_icon).append(edit_icon); if (track.gen_options) { - body.append(track.gen_options(track_id)); + editable.append(track.gen_options(track_id)).appendTo(body); } - title.prependTo(div); - body.appendTo(div); - li.append(div); + div.append(title).append(body).appendTo(li) $("ul#sortable-ul").append(li); } };

1 0

[hg] galaxy 3362: Removed NumberField from form_builder
by Greg Von Kuster 11 Feb '10

11 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/445986a09dbb changeset: 3362:445986a09dbb user: rc date: Tue Feb 09 15:05:39 2010 -0500 description: Removed NumberField from form_builder diffstat: lib/galaxy/model/__init__.py | 3 --- lib/galaxy/web/form_builder.py | 21 +-------------------- templates/admin/requests/show_request.mako | 2 -- templates/requests/show_request.mako | 2 -- 4 files changed, 1 insertions(+), 27 deletions(-) diffs (75 lines): diff -r 606686b073f3 -r 445986a09dbb lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Feb 09 13:40:01 2010 -0500 +++ b/lib/galaxy/model/__init__.py Tue Feb 09 15:05:39 2010 -0500 @@ -1267,9 +1267,6 @@ if field[ 'type' ] == 'TextField': field_widget.set_size( 40 ) field_widget.value = value - if field[ 'type' ] == 'NumberField': - field_widget.set_size( 40 ) - field_widget.value = value elif field[ 'type' ] == 'TextArea': field_widget.set_size( 3, 40 ) field_widget.value = value diff -r 606686b073f3 -r 445986a09dbb lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Tue Feb 09 13:40:01 2010 -0500 +++ b/lib/galaxy/web/form_builder.py Tue Feb 09 15:05:39 2010 -0500 @@ -12,7 +12,7 @@ raise TypeError( "Abstract Method" ) @staticmethod def form_field_types(): - return ['TextField', 'NumberField', 'TextArea', 'SelectField', 'CheckboxField', 'AddressField'] + return ['TextField', 'TextArea', 'SelectField', 'CheckboxField', 'AddressField'] class TextField(BaseField): """ @@ -51,25 +51,6 @@ % ( prefix, self.name, self.size, escape(str(self.value), quote=True) ) def set_size(self, size): self.size = int( size ) - -class NumberField(BaseField): - """ - A number input box. - - >>> print NumberField( "foo" ).get_html() - <input type="int" name="foo" size="10" value=""> - >>> print NumberField( "bins", size=4, value="12345" ).get_html() - <input type="int" name="bins" size="4" value="12345"> - """ - def __init__( self, name, size=None, value=None ): - self.name = name - self.size = int( size or 10 ) - self.value = value or "" - def get_html( self, prefix="" ): - return '<input type="int" name="%s%s" size="%d" value="%s">' \ - % ( prefix, self.name, self.size, escape(str(self.value), quote=True) ) - def set_size(self, size): - self.size = int( size ) class TextArea(BaseField): """ diff -r 606686b073f3 -r 445986a09dbb templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Tue Feb 09 13:40:01 2010 -0500 +++ b/templates/admin/requests/show_request.mako Tue Feb 09 15:05:39 2010 -0500 @@ -226,8 +226,6 @@ </select> %elif field['type'] == 'CheckboxField': <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> - %elif field['type'] == 'NumberField': - <input type="int" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> %endif <div class="toolParamHelp" style="clear: both;"> <i>${'('+field['required']+')' }</i> diff -r 606686b073f3 -r 445986a09dbb templates/requests/show_request.mako --- a/templates/requests/show_request.mako Tue Feb 09 13:40:01 2010 -0500 +++ b/templates/requests/show_request.mako Tue Feb 09 15:05:39 2010 -0500 @@ -214,8 +214,6 @@ </select> %elif field['type'] == 'CheckboxField': <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> - %elif field['type'] == 'NumberField': - <input type="int" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> %endif <div class="toolParamHelp" style="clear: both;"> <i>${'('+field['required']+')' }</i>

1 0

Map of Heavens + Galaxy Dev Conf
by Anton Nekrutenko 10 Feb '10

10 Feb '10

Dear Galaxy Devs: two things: 1. MAP of HEAVENS ----------------- We would like to create a little map of the starry sky by painting locations of existing galaxies on a map. All we need is a URL of your instance. This is, of course, completely voluntary = we will not give this info to Google ;) and galaxy will always be free. 2. Galaxy Dev Conf ------------------ We are running the First Galaxy Developer Conference. Deadline for registration = April 1st. Where and When ============== May 15 - 17 Cold Spring Harbor Laboratory, NY http://www.galaxyproject.org/dev2010 What is Galaxy (well, you probably already know ) ================================================= Galaxy (http://usegalaxy.org) makes it easy to perform analysis interactively through the web, on arbitrarily large datasets. With hundreds of tools there are few limits on what can be done. Now with NGS analysis workflows (including numerous Illumina-, SOLiD-, and 454- specific tools), trackster browser, and collaborative pages you can do more in the Cloud. Galaxy is distributed under BSD-like license. What is Galaxy Developer Conference =================================== The goal of this meeting is to bring together developers, data producers, and tool creators to discuss and implement new way for integration of NGS analysis practices and to create a seamless user experience. We will cover the following aspects of Galaxy framework: The hitchhiker's guide to Galaxy architecture Integration of tools (including NGS analysis tools) and distributed job management Deployment of private Galaxy instances on local resources and on the Cloud Management of large datasets with the Galaxy Library System Using the Galaxy LIMS functionality at NGS sequencing facilities LET US KNOW! THANK YOU! anton + the team Anton Nekrutenko http://usegalaxy.org

1 0

Problem with job & database
by Dijk, F van 10 Feb '10

10 Feb '10

Hi, I have a problem with Galaxy which we're running locally. Somehow we overloaded Galaxy with the jobs which resulted in the database server going down. Now when I try to restart Galaxy the following error is displayed: galaxy.jobs DEBUG 2010-02-08 17:14:08,705 recovering job 1050 in local runner Traceback (most recent call last): File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py ", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/app.py", line 67, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 42, in __init__ self.job_queue = JobQueue( app, self.dispatcher ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 120, in __init__ self.__check_jobs_at_startup() File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 148, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 785, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/runners/lo cal.py", line 179, in recover job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 460, in change_state dataset.state = state File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/model/__init__. py", line 478, in set_dataset_state object_session( self ).flush() #flush here, because hda.flush() won't flush the Dataset object File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush self._flush(objects) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1434, in _flush flush_context.execute() File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute UOWExecutor().execute(self, tasks) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute self.execute_save_steps(trans, task) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps self.save_objects(trans, task) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj c = connection.execute(statement.values(value_params), params) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) unable to open database file u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2010-02-08 16:14:08.738227', 'error', 1084] Do you know how to solve this problem? I hope to hear from you soon. Regards, Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

2 1

QueuePool error
by SHAUN WEBB 10 Feb '10

10 Feb '10

Hi, our Galaxy server is showing a timeout error: TimeoutError: QueuePool limit of size 10 overflow 20 reached, connection timed out, timeout 30 I assume this is due to overuse as it is consistent with the database settings in the universe.wsgi file. First of all, is there anyway to view and cancel queued jobs? I usually use the admin page but this is not accessible at the moment. Secondly, we plan for Galaxy to be used on a large scale, is there anyway of preventing this type of error in future? I've included the full traceback below. Thanks in advance for any help Shaun Webb URL: http://bifx3.bio.ed.ac.uk:8080/admin Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred >> environ, self.app) Module paste.wsgilib:539 in intercept_output << data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter)>> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ << environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware(>> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ << []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response)>> return self.application(environ, start_response) Module galaxy.web.framework.base:99 in __call__ << rc.environ = environ # Setup the transaction trans = self.transaction_factory( environ ) rc.redirect = trans.response.send_redirect # Get the controller class >> trans = self.transaction_factory( environ ) Module galaxy.web.framework:110 in <lambda> << def __init__( self, galaxy_app, session_cookie='galaxysession' ): base.WebApplication.__init__( self ) self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) # Mako support self.mako_template_lookup = mako.lookup.TemplateLookup(>> self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) Module galaxy.web.framework:150 in __init__ << self.workflow_building_mode = False # Always have a valid galaxy session self.__ensure_valid_session( session_cookie ) # Prevent deleted users from accessing Galaxy if self.app.config.use_remote_user and self.galaxy_session.user.deleted:>> self.__ensure_valid_session( session_cookie ) Module galaxy.web.framework:279 in __ensure_valid_session << galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, self.app.model.GalaxySession.table.c.is_valid==True ) ) \ .first() # If remote user is in use it can invalidate the session, so we need to to check some things now. >> self.app.model.GalaxySession.table.c.is_valid==True ) ) Module sqlalchemy.orm.query:1300 in first << ret = list(self)[0:1] else: ret = list(self[0:1]) if len(ret) > 0: return ret[0]>> ret = list(self[0:1]) Module sqlalchemy.orm.query:1221 in __getitem__ << return list(res)[None:None:item.step] else: return list(res) else: return list(self[item:item+1])[0]>> return list(res) Module sqlalchemy.orm.query:1361 in __iter__ << if self._autoflush and not self._populate_existing: self.session._autoflush() return self._execute_and_instances(context) def _execute_and_instances(self, querycontext):>> return self._execute_and_instances(context) Module sqlalchemy.orm.query:1364 in _execute_and_instances << def _execute_and_instances(self, querycontext): result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) return self.instances(result, querycontext)>> result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) Module sqlalchemy.orm.session:754 in execute << engine = self.get_bind(mapper, clause=clause, **kw) return self.__connection(engine, close_with_result=True).execute( clause, params or {})>> return self.__connection(engine, close_with_result=True).execute( Module sqlalchemy.orm.session:721 in __connection << return self.transaction._connection_for_bind(engine) else: return engine.contextual_connect(**kwargs) def execute(self, clause, params=None, mapper=None, **kw):>> return engine.contextual_connect(**kwargs) Module sqlalchemy.engine.base:1229 in contextual_connect << """ return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs) def table_names(self, schema=None, connection=None):>> return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs) Module sqlalchemy.pool:142 in connect << def connect(self): if not self._use_threadlocal: return _ConnectionFairy(self).checkout() try:>> return _ConnectionFairy(self).checkout() Module sqlalchemy.pool:304 in __init__ << self.__counter = 0 try: rec = self._connection_record = pool.get() conn = self.connection = self._connection_record.get_connection() self._connection_record.backref = weakref.ref(self, lambda ref:_finalize_fairy(conn, rec, pool, ref))>> rec = self._connection_record = pool.get() Module sqlalchemy.pool:161 in get << def get(self): return self.do_get() def do_get(self):>> return self.do_get() Module sqlalchemy.pool:628 in do_get << return self.do_get() else: raise exc.TimeoutError("QueuePool limit of size %d overflow %d reached, connection timed out, timeout %d" % (self.size(), self.overflow(), self._timeout)) if self._overflow_lock is not None:>> raise exc.TimeoutError("QueuePool limit of size %d overflow %d reached, connection timed out, timeout %d" % (self.size(), self.overflow(), self._timeout)) TimeoutError: QueuePool limit of size 10 overflow 20 reached, connection timed out, timeout 30 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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galaxy-dev February 2010