Added the test case referenced in the documentation.

shendurelab · Feb 3, 2016 · c83fdeb · c83fdeb
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commit c83fdeb
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diff --git a/test_case/HiC/BV.H3.head.bmt.1.fq.bz2 b/test_case/HiC/BV.H3.head.bmt.1.fq.bz2
diff --git a/test_case/HiC/BV.H3.head.bmt.2.fq.bz2 b/test_case/HiC/BV.H3.head.bmt.2.fq.bz2
diff --git a/test_case/assembly/assembly.fasta b/test_case/assembly/assembly.fasta
diff --git a/test_case/assembly/assembly.fasta.FastaSize b/test_case/assembly/assembly.fasta.FastaSize
@@ -0,0 +1,21 @@
+      195410    contig-60_0
+       88900    contig-60_1
+       79479    contig-60_2
+       71616    contig-60_3
+       70179    contig-60_4
+       69509    contig-60_5
+       68412    contig-60_6
+       62869    contig-60_7
+       62447    contig-60_8
+       61662    contig-60_9
+       60868    contig-60_10
+       59750    contig-60_11
+       59052    contig-60_12
+       58381    contig-60_13
+       57485    contig-60_14
+       56288    contig-60_15
+       55960    contig-60_16
+       52072    contig-60_17
+       51439    contig-60_18
+       51126    contig-60_19
+     1392904    TOTAL LENGTH OF 20 CONTIGS	(N50 = 62869)
diff --git a/test_case/assembly/assembly.fasta.amb b/test_case/assembly/assembly.fasta.amb
@@ -0,0 +1 @@
+1392904 20 0
diff --git a/test_case/assembly/assembly.fasta.ann b/test_case/assembly/assembly.fasta.ann
@@ -0,0 +1,41 @@
+1392904 20 11
+0 contig-60_0 length_195410 read_count_41687719
+0 195410 0
+0 contig-60_1 length_88900 read_count_968576
+195410 88900 0
+0 contig-60_2 length_79479 read_count_24701224
+284310 79479 0
+0 contig-60_3 length_71616 read_count_22976997
+363789 71616 0
+0 contig-60_4 length_70179 read_count_658929
+435405 70179 0
+0 contig-60_5 length_69509 read_count_1190011
+505584 69509 0
+0 contig-60_6 length_68412 read_count_1056167
+575093 68412 0
+0 contig-60_7 length_62869 read_count_621228
+643505 62869 0
+0 contig-60_8 length_62447 read_count_3506109
+706374 62447 0
+0 contig-60_9 length_61662 read_count_668007
+768821 61662 0
+0 contig-60_10 length_60868 read_count_15911331
+830483 60868 0
+0 contig-60_11 length_59750 read_count_1106203
+891351 59750 0
+0 contig-60_12 length_59052 read_count_17128915
+951101 59052 0
+0 contig-60_13 length_58381 read_count_873648
+1010153 58381 0
+0 contig-60_14 length_57485 read_count_289143
+1068534 57485 0
+0 contig-60_15 length_56288 read_count_860062
+1126019 56288 0
+0 contig-60_16 length_55960 read_count_867299
+1182307 55960 0
+0 contig-60_17 length_52072 read_count_655955
+1238267 52072 0
+0 contig-60_18 length_51439 read_count_241823
+1290339 51439 0
+0 contig-60_19 length_51126 read_count_647817
+1341778 51126 0
diff --git a/test_case/assembly/assembly.fasta.bwt b/test_case/assembly/assembly.fasta.bwt
diff --git a/test_case/assembly/assembly.fasta.counts_AAGCTT.txt b/test_case/assembly/assembly.fasta.counts_AAGCTT.txt
@@ -0,0 +1,20 @@
+contig	189
+contig	27
+contig	89
+contig	86
+contig	22
+contig	52
+contig	40
+contig	20
+contig	1
+contig	14
+contig	58
+contig	42
+contig	57
+contig	47
+contig	12
+contig	48
+contig	49
+contig	14
+contig	8
+contig	12
diff --git a/test_case/assembly/assembly.fasta.names b/test_case/assembly/assembly.fasta.names
@@ -0,0 +1,20 @@
+contig-60_0 length_195410 read_count_41687719
+contig-60_1 length_88900 read_count_968576
+contig-60_2 length_79479 read_count_24701224
+contig-60_3 length_71616 read_count_22976997
+contig-60_4 length_70179 read_count_658929
+contig-60_5 length_69509 read_count_1190011
+contig-60_6 length_68412 read_count_1056167
+contig-60_7 length_62869 read_count_621228
+contig-60_8 length_62447 read_count_3506109
+contig-60_9 length_61662 read_count_668007
+contig-60_10 length_60868 read_count_15911331
+contig-60_11 length_59750 read_count_1106203
+contig-60_12 length_59052 read_count_17128915
+contig-60_13 length_58381 read_count_873648
+contig-60_14 length_57485 read_count_289143
+contig-60_15 length_56288 read_count_860062
+contig-60_16 length_55960 read_count_867299
+contig-60_17 length_52072 read_count_655955
+contig-60_18 length_51439 read_count_241823
+contig-60_19 length_51126 read_count_647817
diff --git a/test_case/assembly/assembly.fasta.pac b/test_case/assembly/assembly.fasta.pac
diff --git a/test_case/assembly/assembly.fasta.sa b/test_case/assembly/assembly.fasta.sa
diff --git a/test_case/refs/LI.fasta b/test_case/refs/LI.fasta
diff --git a/test_case/refs/LI.fasta.blastdb.nhr b/test_case/refs/LI.fasta.blastdb.nhr
diff --git a/test_case/refs/LI.fasta.blastdb.nin b/test_case/refs/LI.fasta.blastdb.nin
diff --git a/test_case/refs/LI.fasta.blastdb.nsq b/test_case/refs/LI.fasta.blastdb.nsq
diff --git a/test_case/tsvs/test_case.HiC_libs.tsv b/test_case/tsvs/test_case.HiC_libs.tsv
@@ -0,0 +1,8 @@
+# This file describes a set of Hi-C libraries and has the following format:
+# First non-commented line: A single token giving a directory, relative to the MetaPhase run directory
+# All other non-commented lines: 3 tokens:
+#    1. Library name (can be arbitrary)
+#    2. RE site sequence
+#    3. SAM/BAM file (in the directory on the first line) that contains the reads in that library aligned to the draft assembly
+test_case/HiC
+BV.HindIII	AAGCTT	BV.H3.head.bmt.bam
diff --git a/test_case/tsvs/test_case.refs.tsv b/test_case/tsvs/test_case.refs.tsv
@@ -0,0 +1,2 @@
+#species abbreviation	species reference fasta relative to refs_dir	species full name
+LI	LI.fasta	Lactobacillus iners