Perl scripts

Make sure that your system has the following basic packages installed A compiler for the c programming language (such as gcc), the Perl scripting language, and tel / tk. Currently, all common distributions include these features in their standard setup. 

We thank Dr. J. Gong for noting Ref. 5, Prof. A. Kidera, Prof. S. Okazaki, Prof. J. L. Skinner, Prof. D. Coker, Prof. D. M. Leitner, Prof. Y. Mizutani, Dr. T. Takami, Dr. T. Miyadera, Dr. Y. Kawashima, Dr. S. Fuchigami, Mr. H. Teramoto for useful discussions, Prof. A. Stuchebrukhov for sending reprints, and Dr. M. Shigemori for providing perl scripts used in this work. We thank the National Science Foundation (CFiE-0316551) and Boston University s Center for Computational Science for generous support of our research. 

Zhang, Y Cocklin, R.R. Bidasee, K.R. Wang, M. Rapid Determination of Advanced Glycation End Products of Proteins Using MALDI-TOF-MS and PERL Script Peptide Searching Algorithm, J. Biomol. Tech. 14(3), 224-230 (2003). 

Below (Figure 1.15) is a perl script for searching the SWISS-PROT database for the entry with ID C931 SOYBN . A set of entries is returned, this time with just one entry in it. The entry can be retrieved using the getEntry method of the set class, and the fieldToString method of the entry class is... 

To use standalone BLAST to generate a BugView genome comparison file it is necessary to perform successive comparisons of protein sequences. A Perl script to automate this, gcfprep, can be downloaded from http //www.gla.ac.uk/ dplln/BugView/bvdownload.html. This script has only been tested on standalone BLAST running under Solaris, and may need modification to run on other platforms. 

The ROOT/code/helpers/preproc.pl Perl script uses an external library called bioperl, that is not included with the PhyME distribution. This library may be downloaded from http //bio.perl.org/, the user should install it at some location, say BIOPERLDIR, and add the line use lib BIOPERLDIR in preproc.pl. Alternatively, the user may use the program ROOT/code/helpers/preproc nobioperl.pl that does not use bioperl. 

Before running a QRNA search, the BLAST output file must be converted to a QRNA input file. To do this, drag and drop the blastn2qrnadepth.pl Perl file from the scripts directory followed by the BLAST output file (see Note 10) into the terminal window. These Perl scripts will create three new files in the scripts directory. The file with .q extension will serve as the input file for QRNA. 

Some of the supplied Perl scripts use the Tk library and Perl bindings for visualization purposes, the Perl/Tk module is available from CPAN. It can be installed by typing... 

Most Perl scripts carry embedded documentation that is displayed by typing, e.g.,... 

Running the Perl programs. Although RNAalifold itself is installed in /usr/local/bin by default, the Perl scripts are installed to /usr/local/ share/ViennaRNA/bin. This location is usually not in the search PATH of the shell. To avoid typing long pathnames such as /usr/local/share/ ViennaRNA/bin/colorrna.pl the user can either copy all files to a directory, which is included in the PATH, e.g. ... 

Biopipe [OS2] is a framework for running bioinformatics workflows and is deployable as an extension to the Bioperl project library [OS4]. It borrows heavily from the Ensembl pipeline project [OS7]. Potential users of the system should be comfortable coding Perl scripts and actually reconfiguring a Perl installation to add the necessary prerequisites. The user also needs to deal with coding raw XML to compose and configure a workflow and setting up the mySQL database that is required for the system to function. 

Once these modules are installed, the following perl script will select some rows and columns from a PostgreSQL database. 

The column structure.id is a unique integer relating the structure, sdf and property tables. The sdf.molfile column contains the molfile for each structure as defined by the vendor. The structure.name and structure.cansmiles columns contain the name and canonical smiles parsed and computed from the molfile. The structure.coord column will contain an array of atomic coordinates. The structure, atom column will contain an array of atom numbers from the file in canonical order to correspond to the atom order in the canonical SMILES. The OpenBabel/plpythonu extension functions molfile mol and molfile properties will be used to parse the vendor SDF molfiles and populate these tables. The molfile column of the sdf table is first populated from the SDF file, using the following perl script. 

A SMILES files is readily imported into the database using the following perl script smiloader. The output of this command is a set of SQL commands interspersed with lines in the input SMILES file. The file is minimally processed. The script expects the name of a schema in which the tables will be created. The entire perl script is shown in the Appendix. It is used at the linux command line as follows. The schema name here is drugs, the first argument to smiloader. 

The process of writing and rimning a Perl script is similar on Windows and UNIX systems but slightly different for Macintosh users. The basic steps are described below. 

This newly created file contains two lines. The first line is a comment that identifies the file as a Perl script (indicated by the at the beginning of the line). The second line is a print statement that tells Perl to print out the text... 

The name of the file ends in the extension. pi, which is a standard naming convention for Perl scripts. 

Perl script. The script can also be run directly through the MacPerl application by choosing Run Script from the Script pull-down menu. 

Life is full of decisions, however, and so are Perl scripts. Often, there should be different paths followed if a particular condition is true, another if the condition is false. Considering the dog years calculator shown above, what would happen if the user had entered a negative number for the age or a number that s imreasonably large It would be desirable to reject the input outright, rather than produce and output a preposterous answer. This simple modification to the original script achieves this goal. 

When a Perl script reads a line from <> and prints without using a specified file-handle, it instead uses two automatic filehandles called STDIN and STDOUT. The statements... 

The names STDIN and STDOUT are derived from standard input and standard output, an idea popularized by the UNIX operating system. Standard input and standard output are abstract files from which a script can accept input and send output, respectively. When a script is first launched, standard input corresponds to the keyboard and standard output corresponds to the computer screen. On Windows and UNIX systems, standard output appears in the command interpreter window. On Macs, the output appears in a small scrolling window that MacPerl creates specifically for this pmpose. When a Perl script is laimched, the user has the option of changing where standard input and output come from and go to. The user can also arrange for the standard output of one script to be sent to the standard input of another script in assembly-line fashion. This is actually a very powerful facility, but one that is beyond the scope of this chapter. 

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