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Top Forums Shell Programming and Scripting Help making simple perl or bash script to create a simple matrix Post 302630193 by neutronscott on Wednesday 25th of April 2012 01:24:46 PM
Old 04-25-2012
Code:
$ ./gene  input
gene      1         2         3         4         5
a         @
b                   #
c                             @         @
d                                                 %,*

it's an awk script.
Code:
#!/usr/bin/awk -f

# keep list of unique genes, in order
!($1 in genes_uniq) { genes_uniq[$1]; genes[gene_idx++]=$1; }

{
        split($2, cols, /,/)
        for (col in cols) {
                if (cols[col] > max_col) max_col=cols[col]
                matrix[$1,cols[col]] = matrix[$1,cols[col]] "," $3
        }
}

END {
        # print header
        printf("%-9s ", "gene")
        for (col = 1; col <= max_col; col++)
                printf("%-9d ", col);
        printf("\n")

        for (i = 0; i < gene_idx; i++) {
                printf("%-9s ", genes[i]);
                for (col = 1; col <= max_col; col++)
                        printf("%-9s ", substr(matrix[genes[i],col],2));
                printf("\n");
        }
}

 

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Template::Plugin::Table(3)				User Contributed Perl Documentation				Template::Plugin::Table(3)

NAME
Template::Plugin::Table - Plugin to present data in a table SYNOPSIS
[% USE table(list, rows=n, cols=n, overlap=n, pad=0) %] [% FOREACH item IN table.row(n) %] [% item %] [% END %] [% FOREACH item IN table.col(n) %] [% item %] [% END %] [% FOREACH row IN table.rows %] [% FOREACH item IN row %] [% item %] [% END %] [% END %] [% FOREACH col IN table.cols %] [% col.first %] - [% col.last %] ([% col.size %] entries) [% END %] DESCRIPTION
The "Table" plugin allows you to format a list of data items into a virtual table. When you create a "Table" plugin via the "USE" directive, simply pass a list reference as the first parameter and then specify a fixed number of rows or columns. [% USE Table(list, rows=5) %] [% USE table(list, cols=5) %] The "Table" plugin name can also be specified in lower case as shown in the second example above. You can also specify an alternative variable name for the plugin as per regular Template Toolkit syntax. [% USE mydata = table(list, rows=5) %] The plugin then presents a table based view on the data set. The data isn't actually reorganised in any way but is available via the "row()", "col()", "rows()" and "cols()" as if formatted into a simple two dimensional table of "n" rows x "n" columns. So if we had a sample "alphabet" list contained the letters '"a"' to '"z"', the above "USE" directives would create plugins that represented the following views of the alphabet. [% USE table(alphabet, ... %] rows=5 cols=5 a f k p u z a g m s y b g l q v b h n t z c h m r w c i o u d i n s x d j p v e j o t y e k q w f l r x We can request a particular row or column using the "row()" and "col()" methods. [% USE table(alphabet, rows=5) %] [% FOREACH item = table.row(0) %] # [% item %] set to each of [ a f k p u z ] in turn [% END %] [% FOREACH item = table.col(2) %] # [% item %] set to each of [ m n o p q r ] in turn [% END %] Data in rows is returned from left to right, columns from top to bottom. The first row/column is 0. By default, rows or columns that contain empty values will be padded with the undefined value to fill it to the same size as all other rows or columns. For example, the last row (row 4) in the first example would contain the values "[ e j o t y undef ]". The Template Toolkit will safely accept these undefined values and print a empty string. You can also use the IF directive to test if the value is set. [% FOREACH item = table.row(4) %] [% IF item %] Item: [% item %] [% END %] [% END %] You can explicitly disable the "pad" option when creating the plugin to returned shortened rows/columns where the data is empty. [% USE table(alphabet, cols=5, pad=0) %] [% FOREACH item = table.col(4) %] # [% item %] set to each of 'y z' [% END %] The "rows()" method returns all rows/columns in the table as a reference to a list of rows (themselves list references). The "row()" methods when called without any arguments calls "rows()" to return all rows in the table. Ditto for "cols()" and "col()". [% USE table(alphabet, cols=5) %] [% FOREACH row = table.rows %] [% FOREACH item = row %] [% item %] [% END %] [% END %] The Template Toolkit provides the "first", "last" and "size" virtual methods that can be called on list references to return the first/last entry or the number of entries in a list. The following example shows how we might use this to provide an alphabetical index split into 3 even parts. [% USE table(alphabet, cols=3, pad=0) %] [% FOREACH group = table.col %] [ [% group.first %] - [% group.last %] ([% group.size %] letters) ] [% END %] This produces the following output: [ a - i (9 letters) ] [ j - r (9 letters) ] [ s - z (8 letters) ] We can also use the general purpose "join" virtual method which joins the items of the list using the connecting string specified. [% USE table(alphabet, cols=5) %] [% FOREACH row = table.rows %] [% row.join(' - ') %] [% END %] Data in the table is ordered downwards rather than across but can easily be transformed on output. For example, to format our data in 5 columns with data ordered across rather than down, we specify "rows=5" to order the data as such: a f . . b g . c h d i e j and then iterate down through each column (a-e, f-j, etc.) printing the data across. a b c d e f g h i j . . . Example code to do so would be much like the following: [% USE table(alphabet, rows=3) %] [% FOREACH cols = table.cols %] [% FOREACH item = cols %] [% item %] [% END %] [% END %] Output: a b c d e f g h i j . . . In addition to a list reference, the "Table" plugin constructor may be passed a reference to a Template::Iterator object or subclass thereof. The Template::Iterator get_all() method is first called on the iterator to return all remaining items. These are then available via the usual Table interface. [% USE DBI(dsn,user,pass) -%] # query() returns an iterator [% results = DBI.query('SELECT * FROM alphabet ORDER BY letter') %] # pass into Table plugin [% USE table(results, rows=8 overlap=1 pad=0) -%] [% FOREACH row = table.cols -%] [% row.first.letter %] - [% row.last.letter %]: [% row.join(', ') %] [% END %] AUTHOR
Andy Wardley <abw@wardley.org> <http://wardley.org/> COPYRIGHT
Copyright (C) 1996-2007 Andy Wardley. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. SEE ALSO
Template::Plugin perl v5.12.1 2009-05-20 Template::Plugin::Table(3)
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