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Basic Python Review

Basic Python Review. BCHB524 2009 Lecture 5. Outline. Revision of data-structures Class exercises Exercises. Python Data-Structures. Mutable and changeable storage of many items Lists - Access by index or iteration Dictionaries - Access by key or iteration

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Basic Python Review

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  1. Basic Python Review BCHB5242009Lecture 5 BCHB524 - 2009 - Edwards

  2. Outline • Revision of data-structures • Class exercises • Exercises BCHB524 - 2009 - Edwards

  3. Python Data-Structures • Mutable and changeable storage of many items • Lists - Access by index or iteration • Dictionaries - Access by key or iteration • Sets - Access by iteration, membership test • Files - Access by iteration, as string • Lists of numbers (range) • Strings → List (split), List → String (join) • Reading sequences, parsing codon table. BCHB524 - 2009 - Edwards

  4. Class Review Exercises • DNA sequence length • Are all DNA symbols valid? • DNA sequence composition • Read chunk format sequence from file • Parse and print NCBI taxonomy names • Compute codon usage BCHB524 - 2009 - Edwards

  5. DNA Sequence Length • Write a program to determine the length of a DNA sequence provided in a file. BCHB524 - 2009 - Edwards

  6. Valid DNA Symbols • Write a program to determine if a DNA sequence provided in a file contains any invalid symbols. BCHB524 - 2009 - Edwards

  7. DNA Composition • Write a program to count the proportion of each symbol in a DNA sequence, provided in a file. BCHB524 - 2009 - Edwards

  8. Chunk format sequence • Write a program to count the proportion of each symbol in a DNA sequence, provided in a file in "chunk" format. • Download these files from the data-directory • SwissProt_Format_Ns.seq • SwissProt_Format.seq • Check that your program correctly reads these sequences BCHB524 - 2009 - Edwards

  9. Codon usage • Write a program to compute the codon usage of gene whose DNA sequence provided in a file. • Assume translation starts with the first symbol of the provided gene sequence. BCHB524 - 2009 - Edwards

  10. Taxonomy names • Write a program to lists all the scientific names from a NCBI taxonomy file. • Download the names.dmp file from the data-directory • Look at the file and figure out how to parse it • Read the file, line by line, and print out only those names that represent scientific names of species. BCHB524 - 2009 - Edwards

  11. Lab Exercises • Modify your DNA translation program to translate in each forward frame (1,2,3) • Modify your translation program to translate in each reverse translation frame. • Modify your translation program to handle 'N' symbols in the DNA sequence • If all possible codons translate to the same amino-aicd, then output that amino-acid. • If the possible codons translate to different amino-acids, the output 'X'. BCHB524 - 2009 - Edwards

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