Segway bigWig testcase

pyproject.toml

@@ -17,7 +17,7 @@ dependencies = [
   "autolog>=0.2.0",
   "colorbrewer>=0.2.0",
   "drmaa>=0.4a3",
-  "genomedata>=1.7",
+  "genomedata>=1.7.2",
   "numpy",
   "optbuild>=0.2.0",
   "optplus>=0.2.0",

segway/observations.py

@@ -794,12 +794,21 @@ def generate_coords_all(self, genomes):
                 for supercontig, continuous in chromosome.itercontinuous():
                     # If the the supercontig is not empty
                     if continuous is not None:
-                        attrs = supercontig.attrs
-
-                        starts = convert_windows(attrs, "chunk_starts")
-                        ends = convert_windows(attrs, "chunk_ends")
-
-                        chromosome_windows.extend(zip(starts, ends))
+                        # Attempt at getting starts and end coords from
+                        # PyTables / HDF5 metadata
+                        try:
+                            attrs = supercontig.attrs
+
+                            starts = convert_windows(attrs, "chunk_starts")
+                            ends = convert_windows(attrs, "chunk_ends")
+
+                            chromosome_windows.extend(zip(starts, ends))
+                        # Otherwise use the start and end coordinate from
+                        # the supercontig
+                        except NotImplementedError:
+                            chromosome_windows.append(
+                                [supercontig.start, supercontig.end]
+                            )
 
             # If at least 1 window exists
             if chromosome_windows:

test/simplebigwig/include-coords.bed

@@ -0,0 +1 @@
+chr1	0	8000

test/simplebigwig/run.sh

@@ -0,0 +1,37 @@
+#!/usr/bin/env bash
+
+## run.sh: test segway
+
+## $Revision: -1 $
+
+set -o nounset -o pipefail -o errexit
+
+if [ $# != 0 ]; then
+    echo usage: "$0"
+    exit 2
+fi
+
+testdir="$(mktemp -dp . "test-$(date +%Y%m%d).XXXXXX")"
+
+echo >&2 "entering directory $testdir"
+cd "$testdir"
+
+if [ "${SEGWAY_TEST_CLUSTER_OPT:-}" ]; then
+    cluster_arg="--cluster-opt=$SEGWAY_TEST_CLUSTER_OPT"
+else
+    cluster_arg="--cluster-opt="
+fi
+
+set -x
+
+SEGWAY_RAND_SEED=1498730685 segway "$cluster_arg" \
+    train --include-coords="../include-coords.bed" \
+    --tracks-from="../tracks.txt" --num-labels=4 \
+    "../testtrack1.bigWig" "../testtrack2.bigWig" traindir
+
+segway "$cluster_arg" identify --include-coords="../include-coords.bed" \
+    "../testtrack1.bigWig" "../testtrack2.bigWig" traindir identifydir
+
+cd ..
+
+python${SEGWAY_TEST_PYTHON_VERSION:-""} ../compare_directory.py ../simplebigwig/touchstone ../simplebigwig/${testdir#"./"}

test/simplebigwig/testtrack1.bedgraph

@@ -0,0 +1,8 @@
+chr1	0	1000	0
+chr1	1000	2000	0
+chr1	2000	3000	1
+chr1	3000	4000	1
+chr1	4000	5000	0
+chr1	5000	6000	0
+chr1	6000	7000	1
+chr1	7000	8000	1

test/simplebigwig/testtrack2.bedgraph

@@ -0,0 +1,8 @@
+chr1	0	1000	0
+chr1	1000	2000	1
+chr1	2000	3000	0
+chr1	3000	4000	1
+chr1	4000	5000	0
+chr1	5000	6000	1
+chr1	6000	7000	0
+chr1	7000	8000	1

test/simplebigwig/touchstone/identifydir/auxiliary/segway.inc

@@ -0,0 +1,93 @@
+#ifndef SEG_INC
+#define SEG_INC
+
+% not used yet:
+% #define USE_MFSDG
+
+%% component types
+%% enumerated in tksrc/GMTK_Component.h:ComponentType
+#define COMPONENT_TYPE_DIAG_GAUSSIAN 0
+#define COMPONENT_TYPE_GAMMA 3
+#define COMPONENT_TYPE_MISSING_FEATURE_SCALED_DIAG_GAUSSIAN 5
+
+%% cardinalities
+
+% any boolean (such as alwaysTrue)
+#define CARD_BOOLEAN 2
+
+% data exists or is missing?
+
+#ifdef USE_MFSDG
+% only continues to exist for dinucleotide
+#define CARD_PRESENCE CARD_BOOLEAN
+#else /* USE_MFSDG */
+#define CARD_PRESENCE 2
+#endif /* USE_MFSDG */
+
+% transition or not?
+#define CARD_SEGTRANSITION 3
+
+% maximum number of frames
+#ifndef CARD_FRAMEINDEX
+#define CARD_FRAMEINDEX 2000000
+#endif
+
+% allow transition or not?
+#define CARD_RULER CARD_BOOLEAN
+
+% others
+#ifndef CARD_SEGCOUNTDOWN
+#define CARD_SEGCOUNTDOWN 2
+#endif
+
+% want to allow overriding this
+#ifndef CARD_SEG
+#define CARD_SEG 4
+#endif
+
+#ifndef CARD_SUBSEG
+#define CARD_SUBSEG 1
+#endif
+
+% supervision label
+#ifndef CARD_SUPERVISIONLABEL
+#define CARD_SUPERVISIONLABEL -1
+#endif
+
+% supervision label extension
+#ifndef SUPERVISIONLABEL_RANGE_SIZE
+#define SUPERVISIONLABEL_RANGE_SIZE 0
+#endif
+
+% AA .. TT
+#define CARD_DINUCLEOTIDE 16
+
+%% types
+
+#define TYPE_SEGCOUNTDOWN discrete hidden cardinality CARD_SEGCOUNTDOWN
+#define TYPE_SEG discrete hidden cardinality CARD_SEG
+#define TYPE_SUBSEG discrete hidden cardinality CARD_SUBSEG
+
+%% conditionalparents
+
+#define CONDITIONALPARENTS_NIL_CONTINUOUS nil using mixture("internal:UnityScore")
+#define CONDITIONALPARENTS_NIL_DISCRETE nil using DenseCPT("internal:UnityScore")
+#define CONDITIONALPARENTS_PRESENCE CONDITIONALPARENTS_NIL_DISCRETE
+
+#if CARD_SUBSEG <= 1
+#define CONDITIONALPARENTS_OBS seg(0)
+#define MAPPING_OBS mapping("internal:copyParent")
+#else /* CARD_SUBSEG > 1 */
+#define CONDITIONALPARENTS_OBS seg(0), subseg(0)
+#define MAPPING_OBS mapping("map_seg_subseg_obs")
+#endif /* CARD_SUBSEG == 1 */
+
+%% misc
+#define RULER_SCALE 10
+#define SUPERVISION_LABEL_OFFSET 1
+
+#ifndef SEGTRANSITION_WEIGHT_SCALE
+#define SEGTRANSITION_WEIGHT_SCALE 1.0
+#endif /* SEGTRANSITION_WEIGHT_SCALE */
+
+#endif

test/simplebigwig/touchstone/identifydir/cmdline/identify/vit0.identifydir.(%[0-9a-f]{32}%).sh

@@ -0,0 +1,2 @@
+#!/usr/bin/env bash
+(%[^ ]+%)/segway-task run viterbi identifydir/viterbi/viterbi0.bed chr1 0 8000 1 0 4 1 seg ../testtrack1.bigWig,../testtrack2.bigWig asinh_norm 0,0 False None None 1 -base 3 -cVitRegexFilter '^seg$' -cliqueTableNormalize 0.0 -componentCache F -cppCommandOptions (%'(?=.*-\bDCARD_SEG=4\b)()(?=.*-\bDCARD_FRAMEINDEX=2000000\b)(?=.*-\bDCARD_SUBSEG=1\b)(?=.*-\bDSEGTRANSITION_WEIGHT_SCALE=1\.0\b)(?=.*-\bDCARD_SUPERVISIONLABEL=-1\b)(?=.*-\bDINPUT_PARAMS_FILENAME=traindir/params/params\.params\b).*'%) -deterministicChildrenStore F -eVitRegexFilter '^seg$' -fmt1 binary -fmt2 binary -hashLoadFactor 0.98 -inputMasterFile traindir/params/input.master -island T -iswp1 F -iswp2 F -jtFile identifydir/log/jt_info.txt -lst 100000 -mVitValsFile - -nf1 2 -nf2 0 -ni1 0 -ni2 2 -obsNAN T -of1 identifydir/observations/float32.list -of2 identifydir/observations/int.list -pVitRegexFilter '^seg$' -strFile traindir/segway.str -triFile identifydir/triangulation/segway.str.4.1.trifile -verbosity 0 -vitCaseSensitiveRegexFilter T

test/simplebigwig/touchstone/identifydir/identify.tab

@@ -0,0 +1,3 @@
+name	value
+exclude_coords_filename	
+include_coords_filename	../include-coords.bed

test/simplebigwig/touchstone/identifydir/log/details.sh

@@ -0,0 +1,3 @@
+## segway (%[^ ]+%) run (%[0-9a-f]{32}%) at (%[0-9]{4}%)-(%[0-9]{2}%)-(%[0-9]{2}%) (%[0-9]{2}%):(%[0-9]{2}%):(%[0-9]{2}%).(%[0-9]{1,}%)
+(%[^ ]+%)/gmtkTriangulate -cppCommandOptions (%'(?=.*-\bDCARD_SEG=4\b)(?=.*-\bDCARD_FRAMEINDEX=2000000\b)(?=.*-\bDCARD_SUBSEG=1\b)(?=.*-\bDSEGTRANSITION_WEIGHT_SCALE=1\.0\b)(?=.*-\bDCARD_SUPERVISIONLABEL=-1\b).*'%) -outputTriangulatedFile identifydir/triangulation/segway.str.4.1.trifile -strFile traindir/segway.str -verbosity 0
+(%[^ ]+%)/segway-task run viterbi identifydir/viterbi/viterbi0.bed chr1 0 8000 1 0 4 1 seg ../testtrack1.bigWig,../testtrack2.bigWig asinh_norm 0,0 False None None 1 -base 3 -cVitRegexFilter '^seg$' -cliqueTableNormalize 0.0 -componentCache F -cppCommandOptions (%'(?=.*-\bDCARD_SEG=4\b)(?=.*-\bDCARD_FRAMEINDEX=2000000\b)(?=.*-\bDCARD_SUBSEG=1\b)(?=.*-\bDSEGTRANSITION_WEIGHT_SCALE=1\.0\b)(?=.*-\bDCARD_SUPERVISIONLABEL=-1\b)(?=.*-\bDINPUT_PARAMS_FILENAME=traindir/params/params\.params\b).*'%) -deterministicChildrenStore F -eVitRegexFilter '^seg$' -fmt1 binary -fmt2 binary -hashLoadFactor 0.98 -inputMasterFile traindir/params/input.master -island T -iswp1 F -iswp2 F -jtFile identifydir/log/jt_info.txt -lst 100000 -mVitValsFile - -nf1 2 -nf2 0 -ni1 0 -ni2 2 -obsNAN T -of1 identifydir/observations/float32.list -of2 identifydir/observations/int.list -pVitRegexFilter '^seg$' -strFile traindir/segway.str -triFile identifydir/triangulation/segway.str.4.1.trifile -verbosity 0 -vitCaseSensitiveRegexFilter T

test/simplebigwig/touchstone/identifydir/log/jobs.identify.tab

@@ -0,0 +1,2 @@
+jobid	jobname	prog	num_segs	num_frames	maxvmem	cpu	exit_status
+(%[0-9]+(?:\.[a-zA-Z0-9-]+)?%)	vit0.identifydir.(%[0-9a-f]{32}%)	gmtkViterbi	4	8000	(%[0-9]+(?:\.[0-9]+)?%)	(%[0-9]+(?:\.[0-9]+)?%)	0

test/simplebigwig/touchstone/identifydir/log/jt_info.txt

@@ -0,0 +1,109 @@
+===============================
+   P1 partition information: JT_weight = 1.000000
+=== Clique Information ===
+Number of cliques = 1
+== Clique number: 0, root/right-interface clique, root/right-interface clique, leaf
+Clique information: 9 packed bits, 1 unsigned words (0 splits), weight = 1.982271, jt_weight = 1.000000
+10 Nodes: (%((segCountDown\(0\)\[2\],?)|(seg\(0\)\[4\],?)|(presence__x___2E_2E_2Ftesttrack1_2EbigWig\(0\)\[2\],?)|(x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(presence__x___2E_2E_2Ftesttrack2_2EbigWig\(0\)\[2\],?)|(x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(ruler\(1\)\[2\],?)|(segCountDown\(1\)\[2\],?)|(segTransition\(1\)\[3\],?)|(seg\(1\)\[4\],?)){10}%)
+10 Assigned: (%((segCountDown\(0\),?)|(seg\(0\),?)|(presence__x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(presence__x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(ruler\(1\),?)|(segCountDown\(1\),?)|(segTransition\(1\),?)|(seg\(1\),?)){10}%)
+10 Assigned Sorted: (%((seg\(0\)\[4\],?)|(presence__x___2E_2E_2Ftesttrack1_2EbigWig\(0\)\[2\],?)|(x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(presence__x___2E_2E_2Ftesttrack2_2EbigWig\(0\)\[2\],?)|(x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(segCountDown\(0\)\[2\],?)|(ruler\(1\)\[2\],?)|(segTransition\(1\)\[3\],?)|(seg\(1\)\[4\],?)|(segCountDown\(1\)\[2\],?)){10}%)
+10 Dispositions: 0 0 0 0 0 0 0 0 0 0
+10 Assigned Prob: (%((segCountDown\(0\),?)|(seg\(0\),?)|(presence__x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(presence__x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(ruler\(1\),?)|(segCountDown\(1\),?)|(segTransition\(1\),?)|(seg\(1\),?)){10}%)
+0 Cum Assigned Prob: 
+0 Union Incomming Seps: 
+0 Unassigned Iterated: 
+0 Cumulative Unassigned: 
+6 Hidden/Hashable: (%((segCountDown\(0\)\[2\],?)|(seg\(0\)\[4\],?)|(ruler\(1\)\[2\],?)|(segCountDown\(1\)\[2\],?)|(segTransition\(1\)\[3\],?)|(seg\(1\)\[4\],?)){6}%)
+0 Clique Neighbors: 
+0 Clique Children: 
+0 Receive Seps: 
+0 incomming VE Separators
+Send Sep: -1
+
+=== Separator Information ===
+Number of separators = 0
+
+
+===============================
+   Co partition information: JT_weight = 1.000000
+=== Clique Information ===
+Number of cliques = 1
+== Clique number: 0, root/right-interface clique, root/right-interface clique, leaf/left-interface clique
+Clique information: 9 packed bits, 1 unsigned words (0 splits), weight = 2.283301, jt_weight = 1.000000
+11 Nodes: frameIndex(1)[2000000],segCountDown(1)[2],seg(1)[4],presence__x___2E_2E_2Ftesttrack1_2EbigWig(1)[2],x___2E_2E_2Ftesttrack1_2EbigWig(1),presence__x___2E_2E_2Ftesttrack2_2EbigWig(1)[2],x___2E_2E_2Ftesttrack2_2EbigWig(1),ruler(2)[2],segCountDown(2)[2],segTransition(2)[3],seg(2)[4]
+9 Assigned: frameIndex(1),presence__x___2E_2E_2Ftesttrack1_2EbigWig(1),x___2E_2E_2Ftesttrack1_2EbigWig(1),presence__x___2E_2E_2Ftesttrack2_2EbigWig(1),x___2E_2E_2Ftesttrack2_2EbigWig(1),ruler(2),segCountDown(2),segTransition(2),seg(2)
+9 Assigned Sorted: presence__x___2E_2E_2Ftesttrack1_2EbigWig(1)[2],x___2E_2E_2Ftesttrack1_2EbigWig(1),presence__x___2E_2E_2Ftesttrack2_2EbigWig(1)[2],x___2E_2E_2Ftesttrack2_2EbigWig(1),frameIndex(1)[2000000],ruler(2)[2],segTransition(2)[3],seg(2)[4],segCountDown(2)[2]
+9 Dispositions: 0 0 0 0 0 0 0 0 0
+9 Assigned Prob: frameIndex(1),presence__x___2E_2E_2Ftesttrack1_2EbigWig(1),x___2E_2E_2Ftesttrack1_2EbigWig(1),presence__x___2E_2E_2Ftesttrack2_2EbigWig(1),x___2E_2E_2Ftesttrack2_2EbigWig(1),ruler(2),segCountDown(2),segTransition(2),seg(2)
+10 Cum Assigned Prob: (%((segCountDown\(0\),?)|(seg\(0\),?)|(presence__x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(presence__x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(ruler\(1\),?)|(segCountDown\(1\),?)|(segTransition\(1\),?)|(seg\(1\),?)){10}%)
+2 Union Incomming Seps: segCountDown(1),seg(1)
+0 Unassigned Iterated: 
+0 Cumulative Unassigned: 
+6 Hidden/Hashable: segCountDown(1)[2],seg(1)[4],ruler(2)[2],segCountDown(2)[2],segTransition(2)[3],seg(2)[4]
+0 Clique Neighbors: 
+0 Clique Children: 
+1 Receive Seps: 0,
+0 incomming VE Separators
+Send Sep: -1
+
+=== Separator Information ===
+Number of separators = 1
+== Separator number: 0
+Separator information: 0 acc packed bits (0 words, 0 splits), 3 rem packed bits (1 words, 0 splits)
+2 Nodes: segCountDown(1)[2],seg(1)[4]
+0 Acc Inter: 
+0 Hid Acc Inter: 
+2 remainder: segCountDown(1),seg(1)
+2 hRemainder: segCountDown(1),seg(1)
+
+
+===============================
+   E1 partition information: JT_weight = 1.000000
+=== Clique Information ===
+Number of cliques = 1
+== Clique number: 0, root/right-interface clique, root clique, leaf/left-interface clique
+Clique information: 3 packed bits, 1 unsigned words (0 splits), weight = 0.903090, jt_weight = 1.000000
+7 Nodes: frameIndex(2)[2000000],segCountDown(2)[2],seg(2)[4],presence__x___2E_2E_2Ftesttrack1_2EbigWig(2)[2],x___2E_2E_2Ftesttrack1_2EbigWig(2),presence__x___2E_2E_2Ftesttrack2_2EbigWig(2)[2],x___2E_2E_2Ftesttrack2_2EbigWig(2)
+5 Assigned: frameIndex(2),presence__x___2E_2E_2Ftesttrack1_2EbigWig(2),x___2E_2E_2Ftesttrack1_2EbigWig(2),presence__x___2E_2E_2Ftesttrack2_2EbigWig(2),x___2E_2E_2Ftesttrack2_2EbigWig(2)
+5 Assigned Sorted: presence__x___2E_2E_2Ftesttrack1_2EbigWig(2)[2],x___2E_2E_2Ftesttrack1_2EbigWig(2),presence__x___2E_2E_2Ftesttrack2_2EbigWig(2)[2],x___2E_2E_2Ftesttrack2_2EbigWig(2),frameIndex(2)[2000000]
+5 Dispositions: 0 0 0 0 0
+5 Assigned Prob: frameIndex(2),presence__x___2E_2E_2Ftesttrack1_2EbigWig(2),x___2E_2E_2Ftesttrack1_2EbigWig(2),presence__x___2E_2E_2Ftesttrack2_2EbigWig(2),x___2E_2E_2Ftesttrack2_2EbigWig(2)
+19 Cum Assigned Prob: (%((segCountDown\(0\),?)|(seg\(0\),?)|(presence__x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack1_2EbigWig\(0\),?)|(presence__x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(x___2E_2E_2Ftesttrack2_2EbigWig\(0\),?)|(frameIndex\(1\),?)|(ruler\(1\),?)|(segCountDown\(1\),?)|(segTransition\(1\),?)|(seg\(1\),?)|(presence__x___2E_2E_2Ftesttrack1_2EbigWig\(1\),?)|(x___2E_2E_2Ftesttrack1_2EbigWig\(1\),?)|(presence__x___2E_2E_2Ftesttrack2_2EbigWig\(1\),?)|(x___2E_2E_2Ftesttrack2_2EbigWig\(1\),?)|(ruler\(2\),?)|(segCountDown\(2\),?)|(segTransition\(2\),?)|(seg\(2\),?)){19}%)
+2 Union Incomming Seps: segCountDown(2),seg(2)
+0 Unassigned Iterated: 
+0 Cumulative Unassigned: 
+2 Hidden/Hashable: segCountDown(2)[2],seg(2)[4]
+0 Clique Neighbors: 
+0 Clique Children: 
+1 Receive Seps: 0,
+0 incomming VE Separators
+Send Sep: -1
+
+=== Separator Information ===
+Number of separators = 1
+== Separator number: 0
+Separator information: 0 acc packed bits (0 words, 0 splits), 3 rem packed bits (1 words, 0 splits)
+2 Nodes: segCountDown(2)[2],seg(2)[4]
+0 Acc Inter: 
+0 Hid Acc Inter: 
+2 remainder: segCountDown(2),seg(2)
+2 hRemainder: segCountDown(2),seg(2)
+
+
+===============================
+
+===============================
+   P1 message order
+Number of messages: 0
+
+
+===============================
+   Co message order
+Number of messages: 0
+
+
+===============================
+   E1 message order
+Number of messages: 0
+
+

test/simplebigwig/touchstone/identifydir/log/run.sh

@@ -0,0 +1,3 @@
+## segway (%[^ ]+%) run (%[0-9a-f]{32}%) at (%[0-9]{4}%)-(%[0-9]{2}%)-(%[0-9]{2}%) (%[0-9]{2}%):(%[0-9]{2}%):(%[0-9]{2}%).(%[0-9]{1,}%)
+(%[^ ]+%)/gmtkTriangulate -cppCommandOptions (%'(?=.*-\bDCARD_SEG=4\b)(?=.*-\bDCARD_FRAMEINDEX=2000000\b)(?=.*-\bDCARD_SUBSEG=1\b)(?=.*-\bDSEGTRANSITION_WEIGHT_SCALE=1\.0\b)(?=.*-\bDCARD_SUPERVISIONLABEL=-1\b).*'%) -outputTriangulatedFile identifydir/triangulation/segway.str.4.1.trifile -strFile traindir/segway.str -verbosity 0
+(%[^ ]+%)/gmtkViterbi -base 3 -cVitRegexFilter '^seg$' -cliqueTableNormalize 0.0 -componentCache F -cppCommandOptions (%'(?=.*-\bDCARD_SEG=4\b)(?=.*-\bDCARD_FRAMEINDEX=2000000\b)(?=.*-\bDCARD_SUBSEG=1\b)(?=.*-\bDSEGTRANSITION_WEIGHT_SCALE=1\.0\b)(?=.*-\bDCARD_SUPERVISIONLABEL=-1\b)(?=.*-\bDINPUT_PARAMS_FILENAME=traindir/params/params\.params\b).*'%) -deterministicChildrenStore F -eVitRegexFilter '^seg$' -fmt1 binary -fmt2 binary -hashLoadFactor 0.98 -inputMasterFile traindir/params/input.master -island T -iswp1 F -iswp2 F -jtFile identifydir/log/jt_info.txt -lst 100000 -mVitValsFile - -nf1 2 -nf2 0 -ni1 0 -ni2 2 -obsNAN T -of1 identifydir/observations/float32.list -of2 identifydir/observations/int.list -pVitRegexFilter '^seg$' -strFile traindir/segway.str -triFile identifydir/triangulation/segway.str.4.1.trifile -verbosity 0 -vitCaseSensitiveRegexFilter T

test/simplebigwig/touchstone/identifydir/log/segway.sh

@@ -0,0 +1,4 @@
+## segway (%[^ ]+%) run (%[0-9a-f]{32}%) at (%[0-9]{4}%)-(%[0-9]{2}%)-(%[0-9]{2}%) (%[0-9]{2}%):(%[0-9]{2}%):(%[0-9]{2}%).(%[0-9]{1,}%)
+
+cd "(%[^"]+%)/test-(%\d{8}%).(%[0-9a-zA-Z]{6}%)"
+"(%[^"]+%)/segway" "--cluster-opt=(%[^\"]*%)" "identify" "--include-coords=(%[^"]+%)/include-coords.bed" "(%[^"]+%)/testtrack1.bigWig" "(%[^"]+%)/testtrack2.bigWig" "traindir" "identifydir"