Topics

• Indexing and Slicing
• Parsing Command Line arguments
• setup.py
• tempfile NamedTemporaryFile
• BLAST
• Basic Samtools

Examples

• Create (and write to a) known, persistant temporary file
• Adding command line scripts to your python package
• Create a DNA blastdb
• Extract fasta sequences from a nucl blastdb
• Install blast on ubuntu
• Count number of records per reference in bamfile
• Convert sam into bam (and back again)
• Extract GI and taxid from blastdb