[galaxy-dev] [hg] galaxy 3367: Corrected some typos in DNA filtering tool

details: http://www.bx.psu.edu/hg/galaxy/rev/485d9f2c7627 changeset: 3367:485d9f2c7627 user: Kelly Vincent <kpvincent@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>