NAME

snpParser.pl -- All the sub-routines for SNV (sometimes denoted interchangeably as SNP) handling in the ASARP pipeline.

SYNOPSIS

	use Statistics::R; #interact with R
	require "fileParser.pl"; #sub's for input annotation files
	require "snpParser.pl"; #sub's for snps
	...

... get all configs, input files (see fileParser)

	# read and parse SNVs
	my ($snpRef, $pRef) = initSnp($snpF, $POWCUTOFF);
        # suggested, get the Chi-Squared Test p-value cutoff from FDR ($FDRCUTOFF)
	($SNVPCUTOFF) = fdrControl($pRef, $FDRCUTOFF, 0); #1--verbose
	# match SNVs with gene transcript annotations
	my $geneSnpRef = setGeneSnps($snpRef, $transRef);
	# match gene SNVs with AI/AT and alternative splicing (AS) events
	my ($snpEventsRef) = 
	setSnpEvents($geneSnpRef, $altRef, $splicingRef);

	# calculate NEV and filter the matched gene SNVs with AI/AT/AS events
	my ($snpsNevRef) = 
	filterSnpEventsWithNev($snpRef, $geneSnpRef, $snpEventsRef, $bedF, 
	$allEventsListRef, $NEVCUTOFFLOWER, $NEVCUTOFFUPPER); 

	# process ASE and ASARP
	my ($allAsarpsRef) = 
	processASEWithNev($snpRef, $geneSnpRef, $snpsNevRef, $SNVPCUTOFF, 
	$ASARPPCUTOFF, $ALRATIOCUTOFF);

	# format results to output
	my $outputGene = $outputFile.'.gene.prediction';
	outputRawASARP($allAsarpsRef, 'ASARPgene', $outputGene);
	my $allNarOutput = formatOutputVerNAR($allAsarpsRef);

REQUIREMENT

Statistics::R: has to be installed. See search.cpan.org

DESCRIPTION

This perl file contains all the sub-routines for SNV handling and ASARP processing, as well as result formatting. They are quite procedural and one should first get the input files such as annotations and events using the sub-routines in fileParser.

Basically there are 3 steps:

1. read and parse the individual SNVs

2. match the SNVs to transcripts, and then events, and then filter them based on the PSI like Normalized Expression Value (NEV) calculation

3. process the SNVs with ASE patterns and SNV pairs with other ASARP patterns: AI/AT/AS, and output the formatted results

AI/AT/AS categories are briefly illustrated below (where the red dots represent SNVs with ASARP patterns):

SNV List Format

The SNV list input file contains the list of all SNVs covered by RNA-Seq in the genes of interest, with the read counts of the reference (Ref) and alternative (Alt) alleles.

This file is space delimited with the following fields for each SNV:

	chromosome
	coordinate
	alleles (reference allele>alternative allele)
	dbsnpID
	RNA-Seq counts 
	(# reads for 
	reference allele:alternative allele:wrong nucleotide)

Example file: data/snp.list.fig3

Sub-routines (major)

• initSnp

read and parse SNVs

  input: ($snpF, $POWCUTOFF) --SNV file path, powerful SNV cutoff

  output ($snpRef, $pRef) 
  --reference to SNVs, categorized into powerful/non-powerful internally
  --reference to the p-value list, which will be used to control FDR

• setGeneSnps

match SNVs with gene transcript annotations

  input: ($snpRef, $transRef);
  --reference to SNVs, reference to gene transcripts
  
  output: $geneSnpRef 
  --reference to SNVs matching gene transcripts

• setSnpEvents

match gene SNVs with AI/AT and alternative splicing (AS) events

  input: ($geneSnpRef, $altRef, $splicingRef)
  --reference to gene SNVs ($geneSnpRef), 
  --reference to AI/AT events ($altRef)
  --reference to AS events ($splicingRef)

  output: ($snpEventsRef) --gene SNVs matching AI/AT/AS events

• filterSnpEventsWithNev

calculate NEV and filter the matched gene SNVs with AI/AT/AS events

  input: ($snpRef, $geneSnpRef, $snpEventsRef, $bedF, 
  $allEventsListRef, $NEVCUTOFFLOWER, $NEVCUTOFFUPPER)
  --reference to SNVs ($snpRef),
  --reference to gene SNVs ($geneSnpRef),
  --reference to SNVs matching AI/AT/AS events ($snpEventsRef),
  --reference to bed folder for mapped reads ($bedF),
  --reference to all parsed events ($allEvetnsListRef),
  --lower and upper cutoffs (excl.) for NEV ($NEVCUTOFFLOWER/UPPER)

  output: ($snpsNevRef) --gene SNVs matching NEV and AI/AT/AS events 

• processASEWithNev

process ASE and ASARP

  intput: ($snpRef, $geneSnpRef, $snpsNevRef, 
  $SNVPCUTOFF, $ASARPPCUTOFF, $ALRATIOCUTOFF)
  --see above for $snpRef, $geneSnpRef, $snpsNevRef
  --Chi-Squared Test p-value cutoff on individual SNVs for ASE ($SNVPCUTOFF)
  --Fisher's Exact Test p-value cutoff on target-control SNV pairs for
  ASARP ($ASARPPCUTOFF)
  --allelic ratio difference cutoff for target-control SNV pairs for
  ASARP ($ALRATIOCUTOFF)

  output: ($allAsarpsRef) --reference to all ASE and ASARP results 

• outputRawASARP

format results to output

  input: ($allAsarpsRef, $key, $outputFile)
  --reference to ASARP results ($allAsarpsRef)
  --result type to output ($key) with choices: 
  'ASEgene'--ASE results arranged by genes,
  'ASARPgene'--ASARP results arranged by genes
  'ASARPsnp' --ASARP results arranged by SNVs
  --the output file for the results ($outputFile)

  output: corresponding ASE/ASARP results written to $outputGene

• formatOutputVerNAR

format results to be like the old version for NAR

  input: $allAsarpsRef --see above
  
  output: ($allNarOutput) 
  --text formatted according to the old version

SEE ALSO

asarp, fileParser, MyConstants

COPYRIGHT

This pipeline is free software; you can redistribute it and/or modify it given that the related works and authors are cited and acknowledged.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.

AUTHOR

Cyrus Tak-Ming CHAN

Xiao Lab, Department of Integrative Biology & Physiology, UCLA