From akarger at CGR.Harvard.edu Tue Jan 16 13:47:47 2007 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue Jan 16 14:00:45 2007 Subject: [Scriptome-announce] New tools, "expand view" of tools' Perl code, downloadable simple Scriptome programs Message-ID: Hello, Scriptomists, I'm happy to report a whole bunch of neat new stuff for the Scriptome, which can be found at its new-ish location, http://sysbio.harvard.edu/csb/resources/computational/scriptome/ A quick advertisment: I'll be giving a software demo at ECCB 06 next Wednesday, so please come by if you're there. New stuff: 1. Scriptome command-line programs - Change a FASTA file to tabular format by typing the following on the (UNIX, Mac or Windows) command line: Scriptome -t change_fasta_to_tab seqs.fasta > seqs.tab The program will retrieve tool code from the Scriptome website, then run it. (There's also a no-Internet version.) It will ask you for parameters, or you can give them on the command line. It's available as a download on the (NEW!) Resources page. Installation, if you're lucky, involves unzipping the files (and optionally moving them to a different directory). 2. New Tools: - change_transpose_table: Transpose a table, exchanging rows and columns - choose_lines_with_col_min: (like max equivalent) - choose_lines_with_min_per_name: (like max equivalent) - merge_lines_side_by_side: E.g., file A has ten rows, 3 columns, file B has ten rows, 4 columns. Create file AB with ten rows, 7 columns by putting tables side by side. 3. Expandable Perl code - one of our most popular requests. Click the "Expand code" button next to any tool's code for a much more readable, multi-line view. Also, if you cut & paste all but the first/last line into a text editor and save it, you should have a working Perl program you can edit and run on your own. 4. Tips Page - The Tips page features quick advice on using tools, writing protocols, and general data management. ("Start counting columns at zero!") Happy scripting! -Amir