See below for Installation instructions.
A simple script to search for a motif in a FASTA file. Specified amino acids or X for any amino acid are allowed.
Grab a PDB file by code from the internet
Grab a SwissProt or FASTA file from UniProtKB by specifying accession or identifier. Can also download the DNA if there is a link to an ENA entry.
Index a FASTA file such that an entry can be grabbed quickly
Index a SwissProt file such that an entry can be grabbed quickly
Converts a Weka ARFF file to CSV format
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
Checks the nesting of environments and curly brackets in a LaTeX file. Also checks cross-references to tables, figures, etc and reports those that haven't been reference or have been referenced out of order.
Intelligently lean up intermediate files when using LaTeX.
A powerful script for mirroring FTP sites
Installation places the scripts in a specified directory and then makes links in a binary directory with no extension (so you can just type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)
The defaults are sensible
Type:
make install
to install the scripts.
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
You need to install the following Perl modules:
LWP::UserAgent
Fedora/RedHat/CentOS installs this automatically. Otherwise (as root) do:
perl -MCPAN -e shell
install LWP::UserAgent