2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d91e253734e/ Changeset: 1d91e253734e Branch: sort User: ghuls Date: 2013-05-28 15:48:45 Summary: Fix sorting of numbers in scientific notation. The -n option of sort can't handle numbers in scientific notation. The -g option of sort can handle those numbers correctly. Affected #: 3 files diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 1d91e253734edaaafa8f97bb4382ce18fd02371d test-data/sort_in2.bed --- /dev/null +++ b/test-data/sort_in2.bed @@ -0,0 +1,6 @@ +chr10 100 200 feature1 100.01 + +chr20 800 900 feature2 1.1 + +chr2 500 600 feature3 1000.1 + +chr1 300 400 feature4 1.1e-05 + +chr21 300 500 feature5 1.1e2 + +chr15 700 800 feature6 1.1e4 + diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 1d91e253734edaaafa8f97bb4382ce18fd02371d test-data/sort_out3.bed --- /dev/null +++ b/test-data/sort_out3.bed @@ -0,0 +1,6 @@ +chr1 300 400 feature4 1.1e-05 + +chr20 800 900 feature2 1.1 + +chr10 100 200 feature1 100.01 + +chr21 300 500 feature5 1.1e2 + +chr2 500 600 feature3 1000.1 + +chr15 700 800 feature6 1.1e4 + diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 1d91e253734edaaafa8f97bb4382ce18fd02371d tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -1,19 +1,37 @@ -<tool id="sort1" name="Sort" version="1.0.2"> +<tool id="sort1" name="Sort" version="1.0.3"><description>data in ascending or descending order</description><command interpreter="python"> sorter.py - --input=$input - --output=$out_file1 - #set $style = '' if (str($style) == 'alpha') else 'n' + --input=${input} + --output=${out_file1} + + #if (str($style) == 'num'): + #set $style = 'n' + #elif (str($style) == 'gennum'): + #set $style = 'g' + #else: + #set $style = '' + #end if + #set $order = '' if (str($order) == 'ASC') else 'r' - --key=$column,$column$style$order + + --key=${column},${column}${style}${order} + #for $col in $column_set: - #set $other_column = str($col.other_column) - #set $other_style = '' if (str($col.other_style) == "alpha") else 'n' - #set $other_order = '' if (str($col.other_order) == "ASC") else 'r' - --key=$other_column,$other_column$other_style$other_order + #set $other_column = str($col.other_column) + + #if (str($col.other_style) == 'num'): + #set $other_style = 'n' + #elif (str($col.other_style) == 'gennum'): + #set $other_style = 'g' + #else: + #set $other_style = '' + #end if + + #set $other_order = '' if (str($col.other_order) == "ASC") else 'r' + --key=${other_column},${other_column}${other_style}${other_order} #end for </command><inputs> @@ -21,6 +39,7 @@ <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/><param name="style" type="select" label="with flavor"><option value="num">Numerical sort</option> + <option value="gennum">General numeric sort</option><option value="alpha">Alphabetical sort</option></param><param name="order" type="select" label="everything in"> @@ -31,6 +50,7 @@ <param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" /><param name="other_style" type="select" label="with flavor"><option value="num">Numerical sort</option> + <option value="gennum">General numeric sort</option><option value="alpha">Alphabetical sort</option></param><param name="other_order" type="select" label="everything in"> @@ -63,6 +83,13 @@ <param name="other_order" value="ASC"/><output name="out_file1" file="sort_out2.bed"/></test> + <test> + <param name="input" value="sort_in2.bed"/> + <param name="column" value="5"/> + <param name="style" value="gennum"/> + <param name="order" value="ASC"/> + <output name="out_file1" file="sort_out3.bed"/> + </test></tests><help> .. class:: infomark @@ -75,8 +102,9 @@ This tool sorts the dataset on any number of columns in either ascending or descending order. -* Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. -* Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2). +* **Numerical sort** orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. +* **General numeric sort** orders numbers by their general numerical value. Unlike the numerical sort option, it can handle numbers in scientific notation too. +* **Alphabetical sort** is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2). ----- @@ -106,7 +134,7 @@ A g 10 H h 43 A g 4 I h 500 -on columns 1 (alpha), 3 (num), and 6 (num) in ascending order will yield:: +on columns 1 (alphabetical), 3 (numerical), and 6 (numerical) in ascending order will yield:: A kk 4 I h 111 A edf 4 tw b 234 @@ -127,5 +155,34 @@ Pd gf 7 Gthe de 567 Q d 7 II jhu 45 rS hty 90 YY LOp 89 + + +Sorting the following:: + + chr10 100 200 feature1 100.01 + + chr20 800 900 feature2 1.1 + + chr2 500 600 feature3 1000.1 + + chr1 300 400 feature4 1.1e-05 + + chr21 300 500 feature5 1.1e2 + + chr15 700 800 feature6 1.1e4 + + +on column 5 (numerical) in ascending order will yield:: + + chr1 300 400 feature4 1.1e-05 + + chr15 700 800 feature6 1.1e4 + + chr20 800 900 feature2 1.1 + + chr21 300 500 feature5 1.1e2 + + chr10 100 200 feature1 100.01 + + chr2 500 600 feature3 1000.1 + + +on column 5 (general numeric) in ascending order will yield:: + + chr1 300 400 feature4 1.1e-05 + + chr20 800 900 feature2 1.1 + + chr10 100 200 feature1 100.01 + + chr21 300 500 feature5 1.1e2 + + chr2 500 600 feature3 1000.1 + + chr15 700 800 feature6 1.1e4 + + </help></tool> https://bitbucket.org/galaxy/galaxy-central/commits/f54e602ca233/ Changeset: f54e602ca233 User: dannon Date: 2013-08-07 19:33:27 Summary: Merged in ghuls/galaxy-central/sort (pull request #172) Fix sorting of numbers in scientific notation. Affected #: 3 files diff -r 3e6f22a221eb521dddcb13bb7c1a07b4b9551932 -r f54e602ca23310b8a237af1388d7bc2a37047d34 test-data/sort_in2.bed --- /dev/null +++ b/test-data/sort_in2.bed @@ -0,0 +1,6 @@ +chr10 100 200 feature1 100.01 + +chr20 800 900 feature2 1.1 + +chr2 500 600 feature3 1000.1 + +chr1 300 400 feature4 1.1e-05 + +chr21 300 500 feature5 1.1e2 + +chr15 700 800 feature6 1.1e4 + diff -r 3e6f22a221eb521dddcb13bb7c1a07b4b9551932 -r f54e602ca23310b8a237af1388d7bc2a37047d34 test-data/sort_out3.bed --- /dev/null +++ b/test-data/sort_out3.bed @@ -0,0 +1,6 @@ +chr1 300 400 feature4 1.1e-05 + +chr20 800 900 feature2 1.1 + +chr10 100 200 feature1 100.01 + +chr21 300 500 feature5 1.1e2 + +chr2 500 600 feature3 1000.1 + +chr15 700 800 feature6 1.1e4 + diff -r 3e6f22a221eb521dddcb13bb7c1a07b4b9551932 -r f54e602ca23310b8a237af1388d7bc2a37047d34 tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -1,19 +1,37 @@ -<tool id="sort1" name="Sort" version="1.0.2"> +<tool id="sort1" name="Sort" version="1.0.3"><description>data in ascending or descending order</description><command interpreter="python"> sorter.py - --input=$input - --output=$out_file1 - #set $style = '' if (str($style) == 'alpha') else 'n' + --input=${input} + --output=${out_file1} + + #if (str($style) == 'num'): + #set $style = 'n' + #elif (str($style) == 'gennum'): + #set $style = 'g' + #else: + #set $style = '' + #end if + #set $order = '' if (str($order) == 'ASC') else 'r' - --key=$column,$column$style$order + + --key=${column},${column}${style}${order} + #for $col in $column_set: - #set $other_column = str($col.other_column) - #set $other_style = '' if (str($col.other_style) == "alpha") else 'n' - #set $other_order = '' if (str($col.other_order) == "ASC") else 'r' - --key=$other_column,$other_column$other_style$other_order + #set $other_column = str($col.other_column) + + #if (str($col.other_style) == 'num'): + #set $other_style = 'n' + #elif (str($col.other_style) == 'gennum'): + #set $other_style = 'g' + #else: + #set $other_style = '' + #end if + + #set $other_order = '' if (str($col.other_order) == "ASC") else 'r' + --key=${other_column},${other_column}${other_style}${other_order} #end for </command><inputs> @@ -21,6 +39,7 @@ <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/><param name="style" type="select" label="with flavor"><option value="num">Numerical sort</option> + <option value="gennum">General numeric sort</option><option value="alpha">Alphabetical sort</option></param><param name="order" type="select" label="everything in"> @@ -31,6 +50,7 @@ <param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" /><param name="other_style" type="select" label="with flavor"><option value="num">Numerical sort</option> + <option value="gennum">General numeric sort</option><option value="alpha">Alphabetical sort</option></param><param name="other_order" type="select" label="everything in"> @@ -63,6 +83,13 @@ <param name="other_order" value="ASC"/><output name="out_file1" file="sort_out2.bed"/></test> + <test> + <param name="input" value="sort_in2.bed"/> + <param name="column" value="5"/> + <param name="style" value="gennum"/> + <param name="order" value="ASC"/> + <output name="out_file1" file="sort_out3.bed"/> + </test></tests><help> .. class:: infomark @@ -75,8 +102,9 @@ This tool sorts the dataset on any number of columns in either ascending or descending order. -* Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. -* Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2). +* **Numerical sort** orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. +* **General numeric sort** orders numbers by their general numerical value. Unlike the numerical sort option, it can handle numbers in scientific notation too. +* **Alphabetical sort** is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2). ----- @@ -106,7 +134,7 @@ A g 10 H h 43 A g 4 I h 500 -on columns 1 (alpha), 3 (num), and 6 (num) in ascending order will yield:: +on columns 1 (alphabetical), 3 (numerical), and 6 (numerical) in ascending order will yield:: A kk 4 I h 111 A edf 4 tw b 234 @@ -127,5 +155,34 @@ Pd gf 7 Gthe de 567 Q d 7 II jhu 45 rS hty 90 YY LOp 89 + + +Sorting the following:: + + chr10 100 200 feature1 100.01 + + chr20 800 900 feature2 1.1 + + chr2 500 600 feature3 1000.1 + + chr1 300 400 feature4 1.1e-05 + + chr21 300 500 feature5 1.1e2 + + chr15 700 800 feature6 1.1e4 + + +on column 5 (numerical) in ascending order will yield:: + + chr1 300 400 feature4 1.1e-05 + + chr15 700 800 feature6 1.1e4 + + chr20 800 900 feature2 1.1 + + chr21 300 500 feature5 1.1e2 + + chr10 100 200 feature1 100.01 + + chr2 500 600 feature3 1000.1 + + +on column 5 (general numeric) in ascending order will yield:: + + chr1 300 400 feature4 1.1e-05 + + chr20 800 900 feature2 1.1 + + chr10 100 200 feature1 100.01 + + chr21 300 500 feature5 1.1e2 + + chr2 500 600 feature3 1000.1 + + chr15 700 800 feature6 1.1e4 + + </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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