Added initial chromHMM workflow

daisybio · Dec 7, 2023 · 8820918 · 8820918
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commit 8820918
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diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+*.swp
diff --git a/assets/chromhmm/ANCHORFILES/ce10/RefSeqTES.ce10.txt.gz b/assets/chromhmm/ANCHORFILES/ce10/RefSeqTES.ce10.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/ce10/RefSeqTSS.ce10.txt.gz b/assets/chromhmm/ANCHORFILES/ce10/RefSeqTSS.ce10.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/ce11/RefSeqTES.ce11.txt.gz b/assets/chromhmm/ANCHORFILES/ce11/RefSeqTES.ce11.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/ce11/RefSeqTSS.ce11.txt.gz b/assets/chromhmm/ANCHORFILES/ce11/RefSeqTSS.ce11.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/ce6/RefSeqTES.ce6.txt.gz b/assets/chromhmm/ANCHORFILES/ce6/RefSeqTES.ce6.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/ce6/RefSeqTSS.ce6.txt.gz b/assets/chromhmm/ANCHORFILES/ce6/RefSeqTSS.ce6.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/danRer10/RefSeqTES.danRer10.txt.gz b/assets/chromhmm/ANCHORFILES/danRer10/RefSeqTES.danRer10.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/danRer10/RefSeqTSS.danRer10.txt.gz b/assets/chromhmm/ANCHORFILES/danRer10/RefSeqTSS.danRer10.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/danRer11/RefSeqTES.danRer11.txt.gz b/assets/chromhmm/ANCHORFILES/danRer11/RefSeqTES.danRer11.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/danRer11/RefSeqTSS.danRer11.txt.gz b/assets/chromhmm/ANCHORFILES/danRer11/RefSeqTSS.danRer11.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/danRer7/RefSeqTES.danRer7.txt.gz b/assets/chromhmm/ANCHORFILES/danRer7/RefSeqTES.danRer7.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/danRer7/RefSeqTSS.danRer7.txt.gz b/assets/chromhmm/ANCHORFILES/danRer7/RefSeqTSS.danRer7.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/dm3/RefSeqTES.dm3.txt.gz b/assets/chromhmm/ANCHORFILES/dm3/RefSeqTES.dm3.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/dm3/RefSeqTSS.dm3.txt.gz b/assets/chromhmm/ANCHORFILES/dm3/RefSeqTSS.dm3.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/dm6/RefSeqTES.dm6.txt.gz b/assets/chromhmm/ANCHORFILES/dm6/RefSeqTES.dm6.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/dm6/RefSeqTSS.dm6.txt.gz b/assets/chromhmm/ANCHORFILES/dm6/RefSeqTSS.dm6.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hg18/RefSeqTES.hg18.txt.gz b/assets/chromhmm/ANCHORFILES/hg18/RefSeqTES.hg18.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hg18/RefSeqTSS.hg18.txt.gz b/assets/chromhmm/ANCHORFILES/hg18/RefSeqTSS.hg18.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hg19/RefSeqTES.hg19.txt.gz b/assets/chromhmm/ANCHORFILES/hg19/RefSeqTES.hg19.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hg19/RefSeqTSS.hg19.txt.gz b/assets/chromhmm/ANCHORFILES/hg19/RefSeqTSS.hg19.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hg38/RefSeqTES.hg38.txt.gz b/assets/chromhmm/ANCHORFILES/hg38/RefSeqTES.hg38.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hg38/RefSeqTSS.hg38.txt.gz b/assets/chromhmm/ANCHORFILES/hg38/RefSeqTSS.hg38.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hs1/RefSeqTES.hs1.txt.gz b/assets/chromhmm/ANCHORFILES/hs1/RefSeqTES.hs1.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/hs1/RefSeqTSS.hs1.txt.gz b/assets/chromhmm/ANCHORFILES/hs1/RefSeqTSS.hs1.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/mm10/RefSeqTES.mm10.txt.gz b/assets/chromhmm/ANCHORFILES/mm10/RefSeqTES.mm10.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/mm10/RefSeqTSS.mm10.txt.gz b/assets/chromhmm/ANCHORFILES/mm10/RefSeqTSS.mm10.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/mm39/RefSeqTES.mm39.txt.gz b/assets/chromhmm/ANCHORFILES/mm39/RefSeqTES.mm39.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/mm39/RefSeqTSS.mm39.txt.gz b/assets/chromhmm/ANCHORFILES/mm39/RefSeqTSS.mm39.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/mm9/RefSeqTES.mm9.txt.gz b/assets/chromhmm/ANCHORFILES/mm9/RefSeqTES.mm9.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/mm9/RefSeqTSS.mm9.txt.gz b/assets/chromhmm/ANCHORFILES/mm9/RefSeqTSS.mm9.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/rn5/RefSeqTES.rn5.txt.gz b/assets/chromhmm/ANCHORFILES/rn5/RefSeqTES.rn5.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/rn5/RefSeqTSS.rn5.txt.gz b/assets/chromhmm/ANCHORFILES/rn5/RefSeqTSS.rn5.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/rn6/RefSeqTES.rn6.txt.gz b/assets/chromhmm/ANCHORFILES/rn6/RefSeqTES.rn6.txt.gz
diff --git a/assets/chromhmm/ANCHORFILES/rn6/RefSeqTSS.rn6.txt.gz b/assets/chromhmm/ANCHORFILES/rn6/RefSeqTSS.rn6.txt.gz
diff --git a/assets/chromhmm/CHROMSIZES/ce10.txt b/assets/chromhmm/CHROMSIZES/ce10.txt
@@ -0,0 +1,7 @@
+chrV	20924149
+chrX	17718866
+chrIV	17493793
+chrII	15279345
+chrI	15072423
+chrIII	13783700
+chrM	13794
diff --git a/assets/chromhmm/CHROMSIZES/ce11.txt b/assets/chromhmm/CHROMSIZES/ce11.txt
@@ -0,0 +1,7 @@
+chrV	20924180
+chrX	17718942
+chrIV	17493829
+chrII	15279421
+chrI	15072434
+chrIII	13783801
+chrM	13794
diff --git a/assets/chromhmm/CHROMSIZES/ce6.txt b/assets/chromhmm/CHROMSIZES/ce6.txt
@@ -0,0 +1,7 @@
+chrV	20919568
+chrX	17718854
+chrIV	17493785
+chrII	15279323
+chrI	15072421
+chrIII	13783681
+chrM	13794
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,3 +6,4 @@ results/ @@
     testing/
     testing*
     *.pyc
+    *.swp