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Giovanni Marco Dall'Olio committed 8f74cab

SPACE: fixed region and parameters for genotype_space. Added the Gaps tracks, which is useful for filtering regions out

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Files changed (3)

 results/chr1.pdf: params/tracks_options/ibe.txt params/regions/all_chromosomes_hg18.txt
 	python fetch_ucsc.py -r params/regions/all_chromosomes_hg18.txt -t params/tracks_options/ibe.txt -u params/browser_config/ibe.txt
 
+genotype_space:
+	python fetch_ucsc.py -r params/regions/all_chromosomes_hg19.txt -t params/tracks_options/genotype_space.txt -u params/browser_config/genotypespace_ibe.txt -l 1x1  -s
+
 
 #all_chromosomes_report:
 #	python fetch_ucsc.py -r params/regions/all_chromosomes_hg18.txt -t params/tracks_options/default.txt -u params/browser_config/default.txt

params/regions/all_chromosomes_hg19.txt

-chr1 human hg19 1 0 249250621
-chr2 human hg19 2 0 243199373
-chr3 human hg19 3 0 198022430
-chr4 human hg19 4 0 191154276
-chr5 human hg19 5 0 180915260
-chr6 human hg19 6 0 171115067
-chr7 human hg19 7 0 159138663
-chr8 human hg19 9 0 146364022
-chr9 human hg19 10 0 141213431
-chr10 human hg19 11 0 135534747
-chr11 human hg19 12 0 135006516
-chr12 human hg19 13 0 133851895
-chr13 human hg19 14 0 115169878
-chr14 human hg19 15 0 107349540
-chr15 human hg19 16 0 102531392
-chr16 human hg19 17 0 90354753
-chr17 human hg19 18 0 81195210
-chr18 human hg19 19 0 78077248
-chr19 human hg19 22 0 59128983
-chr20 human hg19 20 0 63025520
-chr21 human hg19 24 0 48129895
-chr22 human hg19 23 0 51304566
+#label, organism, chromosome, start, end, description, upstream, downstream
+chr1, human, hg19, 1, 0, 249250621
+chr2, human, hg19, 2, 0, 243199373
+chr3, human, hg19, 3, 0, 198022430
+chr4, human, hg19, 4, 0, 191154276
+chr5, human, hg19, 5, 0, 180915260
+chr6, human, hg19, 6, 0, 171115067
+chr7, human, hg19, 7, 0, 159138663
+chr8, human, hg19, 8, 0, 146364022
+chr9, human, hg19, 9, 0, 141213431
+chr10, human, hg19, 10, 0, 135534747
+chr11, human, hg19, 11, 0, 135006516
+chr12, human, hg19, 12, 0, 133851895
+chr13, human, hg19, 13, 0, 115169878
+chr14, human, hg19, 14, 0, 107349540
+chr15, human, hg19, 15, 0, 102531392
+chr16, human, hg19, 16, 0, 90354753
+chr17, human, hg19, 17, 0, 81195210
+chr18, human, hg19, 18, 0, 78077248
+chr19, human, hg19, 19, 0, 59128983
+chr20, human, hg19, 20, 0, 63025520
+chr21, human, hg19, 21, 0, 48129895
+chr22, human, hg19, 22, 0, 51304566

params/tracks_options/genotype_space.txt

 # headers file as described http://genome.ucsc.edu/goldenPath/help/customTrack.html
 #track1 = http://pastebin.com/raw.php?i=Szua4x1L
 
-[track_hubs]
-track1 = http://bioevo.upf.edu/~gdallolio/genotype_space/hub.txt
+#[track_hubs]
+#track1 = http://bioevo.upf.edu/~gdallolio/genotype_space/hub.txt
 
 [tracks]
 # Define which tracks to show or hide. 
 cons44way               =       hide
 snp130                  =       hide
 snpArray                =       hide
-refGene                 =       pack
+refGene                 =       dense
 wgEncodeRegMarkPromoter =       hide
 knownGene               =       hide
 rmsk                    =       hide
 affyAllExonSuper        =       hide
 affyExonTissues         =       hide
 ntModernHumans          =       hide
+recombRate              =       dense
+Gap                     =       dense
 
 
 XPEHH_pvalues           =       hide
-XPEHH_stats             =       hide
+XPEHH_scores            =       hide
 FayWu_pvalues           =       hide
-FayWu_stats             =       hide
+FayWu_scores            =       hide
 TajD_pvalues            =       hide
-TajD_stats              =       full
+TajimasD_scores         =       full
 XPCLR_pvalues           =       hide
-XPCLR_stats             =       full
-iHS_stats             =       hide
-iHS_stats             =       hide
+XPCLR_scores            =       hide
+iHS_scores              =       hide
+iHS_scores              =       hide