first

.gitignore

+*.fa
+*.sizes
+*.bb
+*_static*

LICENSE.md

+The MIT License (MIT)
+Copyright (c) 2016 Saulo Aflitos
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

+Uses github.com:sauloal/kentjs.git

exp_refineFinal1_merged_r.cmap.sh

+#!/bin/bash
+
+set -xeu
+
+DIR=/PWD/
+#${PWD}
+#DIR=http://localhost:8000
+
+FA=${DIR}S_lycopersicum_chromosomes.2.50.fa
+
+BED=${DIR}exp_refineFinal1_merged_r.cmap.bed
+
+BIGBED=${BED/.bed/.bb}
+
+SIZES=${FA}.sizes
+
+
+#if [[ ! -f "${SIZES}" ]]; then
+#    ./gen_sizes.py ${FA}
+#fi
+
+#./bedToBigBed_static -tab ${BED} ${SIZES} ${BIGBED}
+
+ENVIRONMENT=NONE node bedToBigBed_static.js -tab ${BED} ${SIZES} ${BIGBED}

gen_sizes.py

+#!/usr/bin/env python
+
+import os
+import sys
+
+def main():
+    infile = sys.argv[1]
+    oufile = infile + '.sizes'
+    
+    data   = []
+    with open(infile, 'r') as fhd:
+        for line in fhd:
+            line = line.strip()
+            if len(line) == 0:
+                continue
+
+            if line[0] == ">":
+                chrom_name = line[1:].split(" ")[0]
+                data.append([ chrom_name, 0 ])
+            else:
+                data[-1][1] += len(line)
+
+    with open(oufile, 'w') as fhd:
+        for chrom_name, chrom_len in data:
+            print chrom_name, chrom_len
+            fhd.write("%s %d\n"%(chrom_name, chrom_len))
+
+
+if __name__ == "__main__":
+    main()

s1.bed

+#browser position chr7:127471196-127495720
+#browser hide all
+#track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On"
+chr7    127471196   127472363   Pos1    0   +   127471196   127472363   255,0,0
+chr7    127472363   127473530   Pos2    0   +   127472363   127473530   255,0,0
+chr7    127473530   127474697   Pos3    0   +   127473530   127474697   255,0,0
+chr7    127474697   127475864   Pos4    0   +   127474697   127475864   255,0,0
+chr7    127475864   127477031   Neg1    0   -   127475864   127477031   0,0,255
+chr7    127477031   127478198   Neg2    0   -   127477031   127478198   0,0,255
+chr7    127478198   127479365   Neg3    0   -   127478198   127479365   0,0,255
+chr7    127479365   127480532   Pos5    0   +   127479365   127480532   255,0,0
+chr7    127480532   127481699   Neg4    0   -   127480532   127481699   0,0,255
+

s2.bed

+#browser position chr7:127471196-127495720
+#browser hide all
+#track name="ColorByStrandDemo" description="Color by strand demonstration" visibility=2 colorByStrand="255,0,0 0,0,255"
+chr7    127471196  127472363  Pos1  0  +
+chr7    127472363  127473530  Pos2  0  +
+chr7    127473530  127474697  Pos3  0  +
+chr7    127474697  127475864  Pos4  0  +
+chr7    127475864  127477031  Neg1  0  -
+chr7    127477031  127478198  Neg2  0  -
+chr7    127478198  127479365  Neg3  0  -
+chr7    127479365  127480532  Pos5  0  +
+chr7    127480532  127481699  Neg4  0  -