University:
Boston University
Course:
MET CS 201 | Introduction to Programming
Academic year:

2024
Views:

165

Pages:

20
Author:

Brooklyn Nelson

Perl for Pipeline Part I HuRI - A Real Bioinformatical Pipeline Example HuRI – Human Reference Interactome Map Project Summary: map high-quality binary protein-protein interactions (PPIs) is based on using yeast two-hybrid (Y2H) as the primary screening method followed by validation of subsets of PPIs in multiple orthogonal assays for binary PPI detection. Three Stages: HI-I-05: space of ~7,000 human genes, ~2,700 PPIs HI-II-14: space of ~13,000 human genes , ~14,000 PPIs HI-III: space of ~ 18,000 human genes, ~50,000+ PPIs up to 2015 HuRI – Human Reference Interactome Map The HI-III space is huge, AD 18k x DB 18k = ~320m binary pairs Way to tackle : divide and conquer –> divided entire space to 9 AD groups and 9 DB groups, that gives 9 x 9 = 81 matrices What is the computational challenge by this design: - more demanding in experiment design - more complicated in algorithms - more detail-oriented data storage and maintenance -… HuRI – Human Reference Interactome Map Project Scope: Total sequence batches: 35 Total PCR plates processed: 6528 Total Read count: ~1.3x109 Total Sequence File Size: ~3.5x1011 With each plate be the result of colony pick of PCR product of thousands of AD and DB mating HuRI – Human Reference Interactome Map Y2H screen PCR plates NGS Sequence Analysis Report Preprocess Align Sequence Identify IST QC Packaging Present result in excel, pdf, text, etc plate content plate layout Batch name . . . Reference Sequences HuRI – Human Reference Interactome Map HuRI – Human Reference Interactome Map HuRI – Human Reference Interactome Map HuRI – Human Reference Interactome Map HuRI – Human Reference Interactome Map OutputSummary : HuRI – Human Reference Interactome Map OutputDetail : So how do we achieve this ?? Pipeline code: Huri_pipeline.pl We will come back later Perl Language Fundamentals Language Design Philosophy • “There's more than one way to do it“ design philosophy and multiparadigm, dynamically typed language features leads to great degree of flexibility in program design. • CPAN and Perl Modules (191,032 available modules in CPAN in 35,637 distributions, written by 13,218 authors, mirrored on 250 servers over 60 countries) Perl Classification Perl 5 and 6 are considered a family of high-level, generalpurpose, interpreted, dynamic programming languages. • High-level – syntax/semantics close to natural language • General purpose – not limited to specific tasks in a particular application domain • Interpreted – relative to compiled language (prepared/checked vs realtime/interactive) • Dynamic – not strict in predefined data type constraints, etc. Borrowed Features Perl Borrows many features from other programming languages • From C: procedural, variables, expression, assignment (=), bracedelimited blocks ({}, ;), control flow (if, while, for, do, etc ), subroutine • From shell: ‘$’ sign, system command • From Lisp: lists data structure; implicit return value • From AWK: hash • From sed: regular expression Authentic Features Perl’s most authentic features of its own: • auto data-typing • auto memory management • It’s all handled by Perl interpreter These are very powerful features and contribute a lot to the wide adoption of Perl language Where Perl is used • • • • • • • • System administration Configuration management Web sites/web application Small scripts Bioinformatics Scientific calculations Test automation … (the riches lie in CPAN)