net.maizegenetics.pangenome.processAssemblyGenomes

Class MummerScriptProcessing

java.lang.Object

net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

public class MummerScriptProcessing
extends Object

This class contains methods that run mummer4 scripts, e.g. nucmer, delta-filter, show-coords and show-snps. In addition, there are methods that process the output from these scripts. NOTE: processing here is relative to the needs of AssemblyHaplotypesPlugin.

Author:

lcj34

Constructor Summary

Constructors

Constructor and Description
MummerScriptProcessing()

Method Summary

Modifier and Type	Method and Description
static net.maizegenetics.util.Tuple<String,String>	adjustEntryForOverlap(String prevEntry, String currentEntry, int numOverlaps, com.google.common.collect.Multimap<Integer,String> snpByRefMap, com.google.common.collect.Multimap<Integer,String> snpByAsmMap)
static void	alignWithNucmer(String refFasta, String asmFasta, String outputDeltaFilePrefix, String outputDir, String mummer4Path, int clusterSize) Call mummer nucmer program to align the sequences Parameters are: -c 250: Set the minimum cluster length to 250 --mum: Use anchor matches that are unique in both the reference and query
static List<String>	checkForEmbedded(List<String> sortedList, boolean splitByRef) Check entries in a list of mummer4 coords file entries and removed those that are embedded
static net.maizegenetics.util.Tuple<Integer,Boolean>	checkForOverlap(net.maizegenetics.util.Tuple<Integer,Integer> prevStartEnd, net.maizegenetics.util.Tuple<Integer,Integer> curStartEnd) Returns a Tuple indicating THe original list was sorted, so prevStartEnd.x will be <= curStartEnd.x
static boolean	checkNoListEntriesInRange(HashSet<Integer> hashSet, List<Integer> testList) Method takes a RangeSet of Integers and a list of integers.
static void	filterCoordsOverlaps(String coordsNoEmbedded, String snpFile, String coordsFinal) Takes a mummer coords file and searches for overlaps.
static void	finalSnpFiltering(String outputSNPS, String deltaFilePrefix, String chrom)
static List<String>	findAlignmentsToReturn(List<String> removedList) Finds groups of 3 or more lines that have descending start values, and where the position of 1 is no more than .01 percent away from the start of the next value.
static String	getAdjustedMummerCoordEntry(String entry, int adjustLen)
static void	refilterCoordsFile(String outputDeltaFilePrefix, String coordsDelta, String coordsDeltaG, String coordsGNoEmbedded, String chrom) This method post-processes the filtered and original coords file.
static void	runDeltaFilter(String deltaFilePrefix, String outputDir, String mummer4Path) Call mummer4 delta-filter method with parameter: -g 1-to-1 global alignment not allowing rearrangements NOTE: the -g option filters out many alignments, including inversions.
static void	runShowCoords(String deltaFilePrefix, String outputDir, String mummer4Path) call mummer4 show-coords method
static void	runShowSNPs(String deltaFilePrefix, String outputDir, String mummer4Path, String chrom) This method calls show-snps using only a delta file as input
static void	runShowSNPsWithCat(String deltaFilePrefix, String coordsForShowSnps, String outputDir, String mummer4Path, String chrom) Fun the mummer4 show-snps entry against a delta file, using a coords file as additional input.
static List<String>	splitOverlappingCoordsEntries(List<String> sortedList, List<String> snpList, boolean splitByRef) Splits overlapping entries, The mummer4 coords file entries will have these tab-delimited columns: S1 E1 S2 E2 Len1 Len2 %ID refID asmID The files processed were sorted by ref-coordiates via the show-coords -r param, so S1/E1 is ref coords and S2/E2 are the assembly coordinates.
static List<String>	verifySNPEntries(List<String> deltaSNPs, String coordsFile, String chrom) This method takes a list of Mummer SNP file entries and verifies the SNP positions are represented in the filtered/overlap-merged coords file.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MummerScriptProcessing

public MummerScriptProcessing()

Method Detail

alignWithNucmer

public static void alignWithNucmer(String refFasta,
                                   String asmFasta,
                                   String outputDeltaFilePrefix,
                                   String outputDir,
                                   String mummer4Path,
                                   int clusterSize)

Call mummer nucmer program to align the sequences Parameters are: -c 250: Set the minimum cluster length to 250 --mum: Use anchor matches that are unique in both the reference and query

Parameters:

refFasta -

asmFasta -

outputDeltaFilePrefix -

outputDir -

runDeltaFilter

public static void runDeltaFilter(String deltaFilePrefix,
                                  String outputDir,
                                  String mummer4Path)

Call mummer4 delta-filter method with parameter: -g 1-to-1 global alignment not allowing rearrangements NOTE: the -g option filters out many alignments, including inversions. Some of these will be added back when the "refilterCoords" method is run later.

Parameters:

deltaFilePrefix -

outputDir -

runShowCoords

public static void runShowCoords(String deltaFilePrefix,
                                 String outputDir,
                                 String mummer4Path)

call mummer4 show-coords method

Parameters:

deltaFilePrefix -

outputDir -

refilterCoordsFile

public static void refilterCoordsFile(String outputDeltaFilePrefix,
                                      String coordsDelta,
                                      String coordsDeltaG,
                                      String coordsGNoEmbedded,
                                      String chrom)

This method post-processes the filtered and original coords file. file. It will 1. create a list of entries to add back based on groups of ascending/descending entries of at least 3 adjacent alignments whose distance from each other is less than a specified amount 2. adds the entries above (in a sorted manner) to the filtered coords list

Parameters:

coordsDelta -

coordsDeltaG -

coordsFinal -

filterCoordsOverlaps

public static void filterCoordsOverlaps(String coordsNoEmbedded,
                                        String snpFile,
                                        String coordsFinal)

Takes a mummer coords file and searches for overlaps. All of the overlap goes to the first entry. If splitting in this manner results in a split in the middle or an assembly deletion, then split is adjusted so the deletion is contained in the first entry of the overlapped pair. The snpFile is used to determine indel positions. For now, assembly insertions may be split. This has not been a problem for variant context processing.

Parameters:

coordsNoEmbedded -

snpFile - SnpFIle used to determine assembly indels

coordsFinal -

splitOverlappingCoordsEntries

public static List<String> splitOverlappingCoordsEntries(List<String> sortedList,
                                                         List<String> snpList,
                                                         boolean splitByRef)

Splits overlapping entries, The mummer4 coords file entries will have these tab-delimited columns: S1 E1 S2 E2 Len1 Len2 %ID refID asmID The files processed were sorted by ref-coordiates via the show-coords -r param, so S1/E1 is ref coords and S2/E2 are the assembly coordinates. When 2 entries are found to overlap, the first entry keeps its coordinates. The second will be truncated by the amount of the overlap. It is understood this may not be completely accurate as the position of indels is not considered.

Parameters:

sortedFile - File to be filtered

Returns:

checkForEmbedded

public static List<String> checkForEmbedded(List<String> sortedList,
                                            boolean splitByRef)

Check entries in a list of mummer4 coords file entries and removed those that are embedded

Parameters:

sortedList - List of sorted mummer coords file entries. Should be sorted by ref start

splitByRef - Boolean - if true, check ref embedded. Otherwise check if assembly coordinates are embedded

Returns:

adjustEntryForOverlap

public static net.maizegenetics.util.Tuple<String,String> adjustEntryForOverlap(String prevEntry,
                                                                                String currentEntry,
                                                                                int numOverlaps,
                                                                                com.google.common.collect.Multimap<Integer,String> snpByRefMap,
                                                                                com.google.common.collect.Multimap<Integer,String> snpByAsmMap)

getAdjustedMummerCoordEntry

public static String getAdjustedMummerCoordEntry(String entry,
                                                 int adjustLen)

checkForOverlap

public static net.maizegenetics.util.Tuple<Integer,Boolean> checkForOverlap(net.maizegenetics.util.Tuple<Integer,Integer> prevStartEnd,
                                                                            net.maizegenetics.util.Tuple<Integer,Integer> curStartEnd)

Returns a Tuple indicating THe original list was sorted, so prevStartEnd.x will be <= curStartEnd.x

Parameters:

prevStartEnd -

curStartEnd -

Returns:

Tuple indicating (x) number of overlaps between the 2, and (y) was one embedded in the other?

findAlignmentsToReturn

public static List<String> findAlignmentsToReturn(List<String> removedList)

Finds groups of 3 or more lines that have descending start values, and where the position of 1 is no more than .01 percent away from the start of the next value.

Parameters:

removedList -

Returns:

runShowSNPsWithCat

public static void runShowSNPsWithCat(String deltaFilePrefix,
                                      String coordsForShowSnps,
                                      String outputDir,
                                      String mummer4Path,
                                      String chrom)

Fun the mummer4 show-snps entry against a delta file, using a coords file as additional input. From the command line, this would look like: cat coords_file | show-snps -T -r -H -S deltaFile

Parameters:

deltaFilePrefix -

coordsForShowSnps -

outputDir -

finalSnpFiltering

public static void finalSnpFiltering(String outputSNPS,
                                     String deltaFilePrefix,
                                     String chrom)

runShowSNPs

public static void runShowSNPs(String deltaFilePrefix,
                               String outputDir,
                               String mummer4Path,
                               String chrom)

This method calls show-snps using only a delta file as input

Parameters:

deltaFilePrefix -

outputDir -

verifySNPEntries

public static List<String> verifySNPEntries(List<String> deltaSNPs,
                                            String coordsFile,
                                            String chrom)

This method takes a list of Mummer SNP file entries and verifies the SNP positions are represented in the filtered/overlap-merged coords file. Additional filtering is performed to remove SNPs that occurred in overlapped coordinates entries, resulting in duplicate SNPs with differing assembly positions for the same reference position. A list of "represented" SNPs is returned. NOTE: Snp entries must be added in order.

Parameters:

deltaSNPs - - list of SNPs from a Mummer filtered delta file

coordsFile - - coordinates file to use when checking for positions.

Returns:

checkNoListEntriesInRange

public static boolean checkNoListEntriesInRange(HashSet<Integer> hashSet,
                                                List<Integer> testList)

Method takes a RangeSet of Integers and a list of integers. It returns "false" if any value from the list is present in the RangeSet It returns "true" if no value from the list is present in the RangeSet

Parameters:

rangeSet -

testList -

Returns: