sanchit-saini / rtracklayer-improvements-test

Solution of tests for rtracklayer improvements proposed project for R Project for Statistical Computing GSoC 2020

rtracklayer-improvements-test

Solutions

• Write a test for the track hub export feature (create_track_hub function) in the PeakSegPipeline package.

  PeakSeg Pipeline create_track_hub Test

• Identify some of the functions in the Kent library that would need to be called to read and write BigBed files. Explain (possibly with pseudocode that mentions those functions) how you plan to implement the read/write features.

  Function	task	Return
  bigBedFileOpen	Open bigBed/bigWig File	struct bbiFile*
  bigBedIntervalQuery	Get data for interval	struct bigBedInterval*
  bbiChromList	Return list of chromosomes	struct bbiChromInfo*
  mustOpen	Open a file or squawk and die	FILE*
  repeatCharOut	Write character to file repeatedly	void
  mustWrite	Write to a file or squawk and die	void
  bbiWriteDummyHeader	Write out all-zero header, just to reserve space for it	void
  bbiWriteDummyZooms	Write out zeroes to reserve space for ten zoom levels	void
  bbiSummaryElementWrite	Write out summary element to file	void
  bbiWriteChromInfo	Write out information on chromosomes to file	void
  bbiWriteZoomLevels	Write out all the zoom levels and return the number of levels written	int
  bigBedFileClose	Close down a big wig/big bed file	void

  bigBed File Layout

  

  Examples

  Read bigBed

  1. Open bigBed file with the help of bigBedFileOpen
  2. Retrive list of chromosomes from file using bbiChromList
  3. Select chromosome infomation i.e name, start and end from list of chromosomes
  4. Query data for particular Interval with the help of bigBedIntervalQuery
  5. Do something involving chrom, el->start, el->end
  6. Clean Up with the help of bigBedFileClose, bbiChromInfoFreeList

  struct bbiFile *bbi = bigBedFileOpen(fileName);
  struct bbiChromInfo *chromList = bbiChromList(bbi);
  struct bbiChromInfo *chrom = chromList;
  char *chromName = chrom->name;
  int start = 0, end = chrom->size;
  struct lm *lm = lmInit(0); // Memory pool to hold returned list
  struct bigBedInterval *list = bigBedIntervalQuery(bbi, chromName, start, end, 0, lm);
  struct bigBedInterval *el;
  for (el = list; el != NULL; el = el->next){
      // do something involving chrom, el->start, el->end
  }
  lmCleanup(&lm);         // typically do this after each query
  bigBedFileClose(&bbi);  // typically only do this when finished all queries
  bbiChromInfoFreeList(&chromList);

  Write bigBed

  1. Read bed file line by line with lineFileOpen and chrom.sizes with twoBitChromHash if file is 2 bit file else with bbiChromSizesFromFile
  2. If extra fields are present read autoSql file and parse it with asParseText, Check Is it a valid autosql file with asCompareObjAgainstStandardBed if not throw an error and stop execution
  3. Go through bed file and collect chromosomes and statistics with bbiChromUsageFromBedFile
  4. Open bigBed file with the help of mustOpen
  5. Write out dummy headers to reserve space for later with bbiWriteDummyHeader and bbiWriteDummyZooms on bigBed file
  6. If extra fields are present write out autoSql string with mustWrite on bigBed file
  7. Write out dummy total summary with bbiSummaryElementWrite
  8. If extra fields are present write out extra fields header and index
  9. Calculate number of zoom levels with bbiCalcResScalesAndSizes
  10. Write out primary full resolution data in sections, collect stats to use for reductions.
  11. Write out primary data index inside the tree
  12. Write out zoom levels on bigbed file.
  13. If extra fields are present write out extra fields index
  14. Go back and rewrite header
  15. Write end signature and free used memory

• Use the restfulr package to retrieve the list of available UCSC genomes from their REST API. Provide a link to a web page with your R code and results/output (possibly using Rmd/Rpubs, http://rpubs.com/).

  Link for Compiled Markdown Hosted on Rpubs

  # Checking requirements are installed if not, then install the required packages
  if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
  
  if(!require(S4Vectors))
  BiocManager::install("S4Vectors")
  
  if(!require(restfulr))
  install.packages("restfulr")
  
  library(restfulr)
  
  # Solution: Fetch list of available UCSC genomes 
  api_genome <- RestUri("http://api.genome.ucsc.edu/list")
  response <- read(api_genome$ucscGenomes)
  genomes_list <-do.call(rbind.data.frame, response$ucscGenomes)
  knitr::kable(genomes_list, caption = "List of UCSC genomes")