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Appendix III - A short Perl reference

Published online by Cambridge University Press:  05 August 2012

Tore Samuelsson
Affiliation:
Göteborgs Universitet, Sweden
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Summary

In short, when the genome project was foundering in a sea of incompatible data formats, rapidly changing techniques, and monolithic data-analysis programs, Perl saved the day. Though it's not perfect, Perl seems to meet the needs of the genome centers remarkably well, and is usually the first tool we turn to when we have a problem to solve.

(Lincoln Stein, from ‘How Perl saved the genome project’)

The Perl programming language was invented by Larry Wall; his version 1.000 was presented in 1987. Perl is said not to be an acronym, but still you occasionally see it said to represent ‘Practical Extraction and Report Language’ or ‘Pathologically Eclectic Rubbish Lister’. The word ‘Perl’ (with a capital P) refers to the programming language as such, whereas ‘perl’ refers to the interpreter (implementation). Larry Wall originally invented the language to help out in system administration and in the analysis of huge text files, but through the years Perl has been continuously developed and has for many years been widely used in areas such as web programming and bioinformatics.

The information found in this appendix is very far from a complete description of Perl. The focus here is on the features of Perl that are mentioned in this book. There are certain important elements that are left out, such as variable references and object-oriented approaches. For more extensive information the reader is referred to other sources as listed towards the end of this appendix – for example, Perl Programming, for which Larry Wall is one of the coauthors.

Type
Chapter
Information
Genomics and Bioinformatics
An Introduction to Programming Tools for Life Scientists
, pp. 300 - 322
Publisher: Cambridge University Press
Print publication year: 2012

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References

Christiansen, T Torkington, N. 2003 Perl Cookbook O’Reilly Google Scholar
Schwartz, R. L Phoenix, T. Foy, B. D. 2008 Learning Perl O’Reilly Google Scholar
Tisdall, J. D 2001 Beginning Perl for Bioinformatics Sebastopol, CA O’Reilly Google Scholar
Wall, L Christiansen, T. Orwant, J. 2000 Programming Perl Cambridge, MA O’Reilly Google Scholar
Friedl, J. E. F 2006 Mastering Regular Expressions Sebastopol, CA O’Reilly Google Scholar
Schwartz, R. L Phoenix, T. 2003 Learning Perl Objects, References, and Modules Sebastopol, CA O’Reilly Google Scholar
Tisdall, J. D. 2003 Mastering Perl for Bioinformatics Sebastopol, CA O’Reilly Google Scholar

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  • A short Perl reference
  • Tore Samuelsson, Göteborgs Universitet, Sweden
  • Book: Genomics and Bioinformatics
  • Online publication: 05 August 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9781139022095.025
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  • A short Perl reference
  • Tore Samuelsson, Göteborgs Universitet, Sweden
  • Book: Genomics and Bioinformatics
  • Online publication: 05 August 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9781139022095.025
Available formats
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Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

  • A short Perl reference
  • Tore Samuelsson, Göteborgs Universitet, Sweden
  • Book: Genomics and Bioinformatics
  • Online publication: 05 August 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9781139022095.025
Available formats
×