From 4642a149fad27264b2751e8288fffdfb4493e7ba Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Wed, 9 Apr 2014 10:02:47 -0400
Subject: [PATCH] [ENH] all shuffle with -incl to follow data distribution
---
Makefile | 2 +-
src/shuffleBed/shuffleBed.cpp | 51 +-
src/shuffleBed/shuffleBedMain.cpp | 2 -
src/utils/bedFile/bedFile.cpp | 14 +
src/utils/bedFile/bedFile.h | 4 +
test/shuffle/excl.bed | 9 +
test/shuffle/incl.bed | 9 +
test/shuffle/simrep.bed | 1000 +++++++++++++++++++++++++++++
test/shuffle/test-shuffle.sh | 127 ++++
9 files changed, 1189 insertions(+), 29 deletions(-)
create mode 100644 test/shuffle/excl.bed
create mode 100644 test/shuffle/incl.bed
create mode 100644 test/shuffle/simrep.bed
create mode 100644 test/shuffle/test-shuffle.sh
diff --git a/Makefile b/Makefile
index 26767488..1890fa26 100644
--- a/Makefile
+++ b/Makefile
@@ -138,7 +138,7 @@ clean:
.PHONY: clean
test: all
- @cd test; sh test.sh
+ @cd test; bash test.sh
.PHONY: test
diff --git a/src/shuffleBed/shuffleBed.cpp b/src/shuffleBed/shuffleBed.cpp
index 518e2378..9d6a2d1e 100644
--- a/src/shuffleBed/shuffleBed.cpp
+++ b/src/shuffleBed/shuffleBed.cpp
@@ -74,15 +74,24 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
if (_haveInclude) {
_include = new BedFile(includeFile);
- _include->loadBedFileIntoMapNoBin();
-
- _numIncludeChroms = 0;
- masterBedMapNoBin::const_iterator it = _include->bedMapNoBin.begin();
- masterBedMapNoBin::const_iterator itEnd = _include->bedMapNoBin.end();
- for(; it != itEnd; ++it) {
- _includeChroms.push_back(it->first);
- _numIncludeChroms++;
+
+ // the user wants to choose the chromosome randomly first
+ if (_chooseChrom) {
+ _include->loadBedFileIntoMapNoBin();
+ _numIncludeChroms = 0;
+ masterBedMapNoBin::const_iterator it = _include->bedMapNoBin.begin();
+ masterBedMapNoBin::const_iterator itEnd = _include->bedMapNoBin.end();
+ for(; it != itEnd; ++it) {
+ _includeChroms.push_back(it->first);
+ _numIncludeChroms++;
+ }
}
+ // thue user wants the intervals shuffled accordingly to the
+ // chrom distribution in the -incl file.
+ else
+ {
+ _include->loadBedFileIntoVector();
+ }
}
if (_haveExclude == true && _haveInclude == false)
@@ -449,8 +458,14 @@ void BedShuffle::ChooseLocusFromInclusionFile(BED &bedEntry) {
CHRPOS randomStart;
BED includeInterval;
- if (_sameChrom == false) {
-
+ // choose an -incl interval randomly.
+ if (_chooseChrom == false) {
+ includeInterval = _include->bedList[rand() % _include->bedList.size()];
+ bedEntry.chrom = includeInterval.chrom;
+ }
+ // choose a chromosome randomly from the -incl file. then choose an
+ // interval from that chrom randomly.
+ else {
// grab a random chromosome from the inclusion file.
randomChrom = _includeChroms[rand() % _numIncludeChroms];
// get the number of inclusion intervals for that chrom
@@ -462,22 +477,6 @@ void BedShuffle::ChooseLocusFromInclusionFile(BED &bedEntry) {
bedEntry.chrom = randomChrom;
}
- else {
- if ( _include->bedMapNoBin.find(chrom) != _include->bedMapNoBin.end() )
- {
- // get the number of inclusion intervals for the original chrom
- size_t size = _include->bedMapNoBin[chrom].size();
- // grab a random interval on the chosen chromosome.
- includeInterval = _include->bedMapNoBin[chrom][rand() % size];
- }
- else {
- cerr << "Error, line " << _bed->_lineNum
- << ": the requested chromosome ("
- << chrom
- << ") cannot "
- << "be found in the -incl file " << endl;
- }
- }
randomStart = includeInterval.start + rand() % (includeInterval.size());
bedEntry.start = randomStart;
bedEntry.end = randomStart + length;
diff --git a/src/shuffleBed/shuffleBedMain.cpp b/src/shuffleBed/shuffleBedMain.cpp
index c53dad50..fe49049d 100644
--- a/src/shuffleBed/shuffleBedMain.cpp
+++ b/src/shuffleBed/shuffleBedMain.cpp
@@ -89,7 +89,6 @@ int shuffle_main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-incl", 5, parameterLength)) {
if ((i+1) < argc) {
haveInclude = true;
- chooseChrom = true;
includeFile = argv[i + 1];
i++;
}
@@ -173,7 +172,6 @@ void shuffle_help(void) {
cerr << "\t-incl\t" << "Instead of randomly placing features in a genome, the -incl" << endl;
cerr << "\t\toptions defines a BED/GFF/VCF file of coordinates in which " << endl;
cerr << "\t\tfeatures in -i should be randomly placed (e.g. genes.bed). " << endl;
- cerr << "\t\t- NOTE: Forces use of -chromFirst (see below)." << endl << endl;
cerr << "\t-chrom\t" << "Keep features in -i on the same chromosome."<< endl;
cerr << "\t\t- By default, the chrom and position are randomly chosen." << endl;
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index ea993aff..7c1ae8dc 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -748,3 +748,17 @@ void BedFile::loadBedFileIntoMapNoBin() {
sort(m->second.begin(), m->second.end(), sortByStart);
}
}
+
+void BedFile::loadBedFileIntoVector() {
+
+ BED bedEntry;
+
+ Open();
+ while (GetNextBed(bedEntry)) {
+ if (_status == BED_VALID) {
+ bedList.push_back(bedEntry);
+ }
+ }
+ Close();
+}
+
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 37d8dda7..440986c0 100644
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -433,6 +433,9 @@ public:
// load a BED file into a map keyed by chrom. value is vector of BEDs
void loadBedFileIntoMapNoBin();
+ // load a BED file into a vector of BEDs
+ void loadBedFileIntoVector();
+
// Given a chrom, start, end and strand for a single feature,
// search for all overlapping features in another BED file.
// Searches through each relevant genome bin on the same chromosome
@@ -487,6 +490,7 @@ public:
masterBedCovMap bedCovMap;
masterBedCovListMap bedCovListMap;
masterBedMap bedMap;
+ bedVector bedList;
masterBedMapNoBin bedMapNoBin;
BedLineStatus _status;
diff --git a/test/shuffle/excl.bed b/test/shuffle/excl.bed
new file mode 100644
index 00000000..c9300e65
--- /dev/null
+++ b/test/shuffle/excl.bed
@@ -0,0 +1,9 @@
+chr1 0 10000000
+chr1 10000000 20000000
+chr1 20000000 30000000
+chr1 30000000 400000000
+chr1 40000000 500000000
+chr2 0 100000000
+chr3 0 100000000
+chr4 0 100000000
+chr5 0 100000000
diff --git a/test/shuffle/incl.bed b/test/shuffle/incl.bed
new file mode 100644
index 00000000..68f76c33
--- /dev/null
+++ b/test/shuffle/incl.bed
@@ -0,0 +1,9 @@
+chr1 0 1000000
+chr1 1000000 2000000
+chr1 2000000 3000000
+chr1 3000000 4000000
+chr1 4000000 5000000
+chr2 0 1000000
+chr3 0 1000000
+chr4 0 1000000
+chr5 0 1000000
diff --git a/test/shuffle/simrep.bed b/test/shuffle/simrep.bed
new file mode 100644
index 00000000..7d620fcd
--- /dev/null
+++ b/test/shuffle/simrep.bed
@@ -0,0 +1,1000 @@
+chr1 10000 10468 trf 789
+chr1 10627 10800 trf 346
+chr1 10757 10997 trf 434
+chr1 11225 11447 trf 273
+chr1 11271 11448 trf 187
+chr1 11283 11448 trf 199
+chr1 19305 19443 trf 242
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+chr1 1822049 1822099 trf 50
+chr1 1826194 1826271 trf 129
+chr1 1828155 1828487 trf 452
+chr1 1829604 1829693 trf 79
+chr1 1829656 1829713 trf 80
+chr1 1829745 1829936 trf 109
diff --git a/test/shuffle/test-shuffle.sh b/test/shuffle/test-shuffle.sh
new file mode 100644
index 00000000..606d60ce
--- /dev/null
+++ b/test/shuffle/test-shuffle.sh
@@ -0,0 +1,127 @@
+BT=${BT-../../bin/bedtools}
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ return 1
+ else
+ echo fail
+ return 0
+ fi
+}
+
+
+###########################################################
+# test basic shuffle
+###########################################################
+echo " shuffle.t1...\c"
+echo \
+"chr9 108600879 108601347 trf 789
+chr12 9186177 9186350 trf 346
+chr8 89726287 89726527 trf 434
+chr8 40323278 40323500 trf 273
+chr8 69904335 69904512 trf 187
+chr5 138240459 138240624 trf 199
+chr11 96382483 96382621 trf 242
+chr8 105834146 105834181 trf 70
+chrX 105921488 105921585 trf 79
+chrX 125331456 125331497 trf 73" > exp
+$BT shuffle -seed 42 -i simrep.bed \
+ -g ../../genomes/human.hg19.genome | head > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# test basic shuffle with -incl (choose intervals randomly)
+###########################################################
+echo " shuffle.t2...\c"
+echo \
+"chr3 542223 542691 trf 789
+chr5 444343 444516 trf 346
+chr1 2520601 2520841 trf 434
+chr5 194760 194982 trf 273
+chr1 2121545 2121722 trf 187
+chr1 2246343 2246508 trf 199
+chr1 2724117 2724255 trf 242
+chr4 304892 304927 trf 70
+chr2 332618 332715 trf 79
+chr5 822410 822451 trf 73
+chr1 1450982 1451014 trf 64
+chr1 3218361 3218466 trf 149
+chr4 338952 338990 trf 58
+chr3 713207 713677 trf 278
+chr1 4378307 4378777 trf 339
+chr1 4451988 4452416 trf 202
+chr1 1545567 1545610 trf 59
+chr1 573175 573215 trf 62
+chr4 931201 931236 trf 52
+chr1 4215777 4215954 trf 302" > exp
+$BT shuffle -incl incl.bed -seed 42 -i simrep.bed \
+ -g ../../genomes/human.hg19.genome | head -20 > obs
+check obs exp
+rm obs exp
+
+##############################################################
+# test basic shuffle with -incl (choose chroms randomly first)
+##############################################################
+echo " shuffle.t3...\c"
+echo \
+"chr5 310009 310477 trf 789
+chr4 520601 520774 trf 346
+chr2 130650 130890 trf 434
+chr1 3246343 3246565 trf 273
+chr2 968160 968337 trf 187
+chr3 332618 332783 trf 199
+chr4 638727 638865 trf 242
+chr3 218361 218396 trf 70
+chr1 2259217 2259314 trf 79
+chr3 378307 378348 trf 73
+chr4 447387 447419 trf 64
+chr3 573175 573280 trf 149
+chr2 106791 106829 trf 58
+chr3 618697 619167 trf 278
+chr2 211901 212371 trf 339
+chr5 656883 657311 trf 202
+chr2 993338 993381 trf 59
+chr2 713531 713571 trf 62
+chr2 428268 428303 trf 52
+chr4 590632 590809 trf 302" > exp
+$BT shuffle -incl incl.bed -chromFirst -seed 42 -i simrep.bed \
+ -g ../../genomes/human.hg19.genome | head -20 > obs
+check obs exp
+rm obs exp
+
+
+##############################################################
+# test basic shuffle with -excl
+##############################################################
+echo " shuffle.t4...\c"
+echo -n "" > exp
+$BT shuffle -seed 42 -i simrep.bed \
+ -g ../../genomes/human.hg19.genome \
+ -excl excl.bed \
+| $BT intersect -a - -b excl.bed > obs
+check obs exp
+rm obs exp
+
+##############################################################
+# test basic shuffle with
+##############################################################
+echo " shuffle.t5...\c"
+echo \
+"chr1 150415830 150415862 trf 64
+chr1 150415830 150415862 trf 64
+chr5 78078743 78079213 trf 339
+chr4 84711820 84712248 trf 202
+chr4 61777751 61777794 trf 59
+chr3 28583223 28583400 trf 302
+chr1 55933709 55934092 trf 712
+chr1 55933709 55934092 trf 712
+chr1 39686691 39686725 trf 68
+chr2 2555287 2555330 trf 86" > exp
+$BT shuffle -seed 42 -i simrep.bed \
+ -g ../../genomes/human.hg19.genome \
+| $BT intersect -a - -b excl.bed | head > obs
+check obs exp
+rm obs exp
\ No newline at end of file
--
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