NewSoftware

New Lab Software

 

This is an overview of what is newto the lab software archives.

 

If you add something here, please also add it to the SoftwareResources page. After a year or so, things will be deleted from here and will only be documented on the normal SoftwareResourcespage.

 April 2011

 

csvsql

  • Treats csv files as database tables, allowing you to perform arbitrary queries on those files/tables, including multi-file/table joins.  Examples:
 csvsql "select * from people.csv where age > 40"
  csvsql "select name,score from people.csv where age >40"
  csvsql "select name,score from people.csv where age <50 and score > 100
 csvsql "select sum(score) from people.csv where age < 40"
 csvsql "select people.name,children.child from people.csv,children.csv where people.name=children.name" 
    See "csvsql -h" for information.  

August 2007

 

New perl script: seqlogo in /projects/sysbio/apps/perl/weblogo/

  • seqlogo is the WebLogo sequence logo generator. Running the program with no arguments will generate help information. See http://weblogo.berkeley.edu/ for more information and a Web interface to WebLogo.
  • This directory also contains various example files and documentation.

 

December, 2006

 

November, 2006

 

New perl script: select_best_item.pl(Alex Williams)

  • This script is used for selecting the best experiment from a list of replicates. "Best" can mean either the highest numerical value, or the lowest numerical value.
  • This is useful when you want to compare the best runs of various settings.
  • Technical details: you specify a KEY and a VALUE column. The script goes through once and looks at all the KEY columns, remembering the values. It then makes a second pass, and only prints out each key ONE time (the one time with the best associated value). (Note that it prints out the ENTIRE line that the key was on, not just the key). In the case of multiple tied "best" values, we only print out the very first one found.
  • Note that if you use join or join.pl, if you have multiple items with the same key, it is not always clear which line will be used for the join (I think). So you might want to run this script first to make sure there is at least some systematic reason for which item was chosen.

 

New program: graphvizgraph layout suite

  • Used for making graphs to PNG (or PDF, or whatever) from the command line. Check the SoftwareResources page and scroll down for more information. Note that we don't really know any specifics about it, so you might want to check http://www.graphviz.org/ for more information.

 

October, 2006