WIBR Bioinformatics and Research Computing

Unix, Perl, and Python (2012)

Previous course: Unix, Perl, and BioPerl (2006)

Unix

An introduction to the Unix shell environment. Including navigating, file manipulation, biology tools, and the LSF cluster.

Lecture

• Slides [for print]

Exercises

1. Exercise 1: BLASTing ESTs against a RefSeq database       [seq.fa]
2. Exercise 2: Create a shell script to automate the above BLASTing excercise (starting with script at /home/byuan/unix_2012/blast_seqs.sh)       [solution]
3. Exercise 3 (optional) : Check Illumina Data quality and clean up reads       [H3K36me3.fastq.gz]
4. Exercise 4 : Manipulate genomic features with bedtools.       [H3K36me3_peaks.bed]

Resources

General Unix

• Introduction to Unix
  (University of Wisconsin-Milwaukee)
• Rule the World with 13 UNIX Commands
• UNIX Tutorial for Beginners
• Unix Cheat sheet
• Demo commands from WIBR "Applied Bioinformatics for Biologists" class (October 2003)

Unix at Whitehead (Bioinformatics on tak)

• Applying for a WIBR Bioinformatics account
• Connecting to tak and transferring files
  (including sources of software to do this)
• Using X windows on tak
• Using Cygwin/X for X Windows on tak
• Local biological tools
  program list and help pages
• Local BLAST database list
• BLAST documentation
  details about running NCBI's blastall, formatdb, and fastacmdh
• Whitehead LSF help
• EMBOSS
  The European Molecular Biology Open Software Suite
• Image Magick
  free software suite to create, edit and compose bitmap images

Perl

An introduction to Perl programming for bioinformatics

Lecture

• Slides [for print]

Exercises

1. Converting a SAM file into a BED file
   [starting script] [SAM file] [solution] [BED file]
2. Retrieving and aligning a list of human-mouse orthologs
   [starting script] [human-mouse pairs] [solution] [alignment-all.txt]

Resources

General Perl

• Comprehensive Perl Archive Network
  (CPAN modules and documentation)
• Perl.com
  O'Reilly's Perl resources
• ActivePerl
  Perl for Windows (download and documentation)
• Perl Frequently Asked Questions
• Installing Perl modules
  (but check first - the module may already be installed) - and you'll need to specify the PREFIX when running Makefile.PL
• O'Reilly Perl books (Whitehead and MIT only)
• Perl modules on tak (Whitehead only)

BioPerl

• BioPerl home
• BioPerl tutorial
• BioPerl "HOWTOs": tutorials about some specific modules
• BioPerl documentation on CPAN
• BioPerl documentation on BioPerl

Sample Perl Scripts

• BaRC's Perl Scripts (Whitehead only)

Python

An introduction to Python programming. Essential syntax and script writing.

Lecture

• Slides [for print]

Exercises

1. Parsing a FASTA file and producing its reverse compliment
2. FASTQ Deduping by quality

Resources

General Python

• The Python Wiki
  Start here!
• A Gentle Introduction to Programming Using Python
  MIT Open Courseware
• Python Documentation

Scientific Python

• Numeric And Scientific libraries
• A Primer on Python for Life Science Researchers
  PLoS Collections

Libraries

• PyPI - the Python Package Index
• SciPy
  Scientific Tools
• Biopython
  Biological Computation Tools
• PyCogent
  Genomic Biology