public class Genomes
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.lang.String |
HRGChromosome10Str |
static java.lang.String |
HRGChromosome11Str |
static java.lang.String |
HRGChromosome12Str |
static java.lang.String |
HRGChromosome13Str |
static java.lang.String |
HRGChromosome14Str |
static java.lang.String |
HRGChromosome15Str |
static java.lang.String |
HRGChromosome16Str |
static java.lang.String |
HRGChromosome17Str |
static java.lang.String |
HRGChromosome18Str |
static java.lang.String |
HRGChromosome19Str |
static java.lang.String |
HRGChromosome1Str |
static java.lang.String |
HRGChromosome20Str |
static java.lang.String |
HRGChromosome21Str |
static java.lang.String |
HRGChromosome22Str |
static java.lang.String |
HRGChromosome2Str |
static java.lang.String |
HRGChromosome3Str |
static java.lang.String |
HRGChromosome4Str |
static java.lang.String |
HRGChromosome5Str |
static java.lang.String |
HRGChromosome6Str |
static java.lang.String |
HRGChromosome7Str |
static java.lang.String |
HRGChromosome8Str |
static java.lang.String |
HRGChromosome9Str |
static java.lang.String |
HRGChromosomeXStr |
static java.lang.String |
HRGChromosomeYStr |
static java.util.logging.Logger |
logger |
Constructor and Description |
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Genomes() |
Modifier and Type | Method and Description |
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static void |
analyzeHumanReferenceGenome(java.lang.String humanReferenceGenomePath,
java.lang.String outputPath,
int lineDivisor)
Conduct an analysis of the human reference genome.
|
static java.lang.String[] |
createChromosomeArray()
Create an array of chromosome header strings.
|
static void |
generateToyGenome(java.lang.String outFilePath,
int length,
boolean printChromosomeLines,
int chromosomeLineIntervals)
Generate a toy genome.
|
static java.lang.String[] |
getChromosomeStartEndStrs(java.lang.String chromosomes)
Get the human reference genome sequence start and end strings for a set of chromsomes.
|
static boolean |
isNonBase(java.lang.String currentCharStr,
java.lang.String previousCharStr)
Check whether a human reference sequence file character is a base.
|
static java.lang.String |
makeCountProportionsString(double ACount,
double TCount,
double CCount,
double GCount,
double NCount,
double divisor)
Make a String containing summary statistics for a region of nucleobases in the human reference sequence file.
|
public static final java.lang.String HRGChromosome1Str
public static final java.lang.String HRGChromosome2Str
public static final java.lang.String HRGChromosome3Str
public static final java.lang.String HRGChromosome4Str
public static final java.lang.String HRGChromosome5Str
public static final java.lang.String HRGChromosome6Str
public static final java.lang.String HRGChromosome7Str
public static final java.lang.String HRGChromosome8Str
public static final java.lang.String HRGChromosome9Str
public static final java.lang.String HRGChromosome10Str
public static final java.lang.String HRGChromosome11Str
public static final java.lang.String HRGChromosome12Str
public static final java.lang.String HRGChromosome13Str
public static final java.lang.String HRGChromosome14Str
public static final java.lang.String HRGChromosome15Str
public static final java.lang.String HRGChromosome16Str
public static final java.lang.String HRGChromosome17Str
public static final java.lang.String HRGChromosome18Str
public static final java.lang.String HRGChromosome19Str
public static final java.lang.String HRGChromosome20Str
public static final java.lang.String HRGChromosome21Str
public static final java.lang.String HRGChromosome22Str
public static final java.lang.String HRGChromosomeXStr
public static final java.lang.String HRGChromosomeYStr
public static java.util.logging.Logger logger
public static void generateToyGenome(java.lang.String outFilePath, int length, boolean printChromosomeLines, int chromosomeLineIntervals)
outFilePath
- - the path for the outputted toy genome.length
- - the number of nucleobases to go into the toy genome.printChromosomeLines
- - Whether to write the header lines for each chromosome.chromosomeLineIntervals
- - the number of nucleobases to go into each chromosome in the toy genome.public static java.lang.String[] createChromosomeArray()
public static java.lang.String[] getChromosomeStartEndStrs(java.lang.String chromosomes)
chromosomes
- - the chromosomes for which we want the start and end strings.public static void analyzeHumanReferenceGenome(java.lang.String humanReferenceGenomePath, java.lang.String outputPath, int lineDivisor)
humanReferenceGenomePath
- - the path to the human reference genome file.outputPath
- - the path for the output.lineDivisor
- - the region size in # of nucleobases for which to provide summary statistics.public static boolean isNonBase(java.lang.String currentCharStr, java.lang.String previousCharStr)
currentCharStr
- - the current human reference sequence file character as a String.previousCharStr
- - the previous human reference sequence file character as a String.public static java.lang.String makeCountProportionsString(double ACount, double TCount, double CCount, double GCount, double NCount, double divisor)
ACount
- - number of A nucleobases in the region.TCount
- - number of T nucleobases in the region.CCount
- - number of C nucleobases in the region.GCount
- - number of G nucleobases in the region.NCount
- - number of N nucleobases in the region.divisor
- - size of the region in number of nucleobases.