# HG changeset patch # User eric-rasche # Date 1488430616 18000 # Node ID b56f47c587793eafe7f66c5d81c47addc447bac2 # Parent dc4c9490fac8b9d8e00e70101f74b1692aaa4f8a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 4503a4ca99e65aa821e2c953f2f18eaadeed170a diff -r dc4c9490fac8 -r b56f47c58779 fasta-to-karyotype.py --- a/fasta-to-karyotype.py Wed Mar 01 22:49:11 2017 -0500 +++ b/fasta-to-karyotype.py Wed Mar 01 23:56:56 2017 -0500 @@ -3,9 +3,9 @@ import sys for idx, seq in enumerate(SeqIO.parse(sys.argv[1], 'fasta')): - print "chr - {seq_id} {idx} 0 {length} set3-12-qual-{color}".format( + sys.stdout.write("chr - {seq_id} {idx} 0 {length} set3-12-qual-{color}\n".format( seq_id=seq.id, idx=idx, length=len(seq), color=((idx + 1) % 12) - ) + )) if len(sys.argv) > 2: # band hs1 p36.32 p36.32 2200000 5100000 gpos25 @@ -16,7 +16,7 @@ with open(sys.argv[2], 'r') as handle: for line in handle: lineData = dict(zip(COLS, line.split())) - print "band {chrom} {name} {name} {chromStart} {chromEnd} {color}".format( + sys.stdout.write("band {chrom} {name} {name} {chromStart} {chromEnd} {color}\n".format( # Can access name because requiring >bed3 name=lineData['name'], chrom=lineData['chrom'], @@ -24,7 +24,7 @@ chromEnd=lineData['chromEnd'], # ???? color=lineData.get('itemRgb', 'gpos50'), - ) + )) # band # ID # parentChr diff -r dc4c9490fac8 -r b56f47c58779 tmp --- a/tmp Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,206 +0,0 @@ -H4sIAOlNaVcAA+19a3MdR5KdPvNXXGtiI+ywQHa9q9bSRMzErtdfPN6Y9XcEBFySsPAaANSIDv14 -n5NVmX3xuJfNEUR5YrolQSQ6b3VVVmXWOZlZt0/Pb0+v79589WteE65SEv/vSpp2/6/XV86X4H3M -8nuH2/GrTfpVezWuD3f3J7ebzVf3tyc/nt/tl/vU/b/T67TP/+n11dtfbRF8/vz7Mrl1/r/EtTv/ -P5zcfry+/3izfX3/0/0LPoMTnHPcO/9uKo/mP+EPX22mF+zD3usfff7f326ONqf37/6wmfBP4nRs -7rb34cj5o798OLk4cq9M5o8bB5k8lfZQxL/6rYexXn/jtWv//c+v+ecXfYbYf9xv/zHl2f5jpv1P -0a/2/yWuV99+e351evHhbLs5vb64vr07fnt9dX93fHNyf7+9veqr4fe/3xF7f/3hbvvDdntzfvVO 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/2d.conf --- a/tmp2/circos/conf/2d.conf Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ - - - - type = histogram - file = data/data-0.txt - - r1 = 0.89r - r0 = 0.8r - orientation = out - - extend_bin = no - fill_color = purples-13-seq - - - - - - - - - - \ No newline at end of file diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/circos.conf --- a/tmp2/circos/conf/circos.conf Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ - -<> -<> -karyotype = karyotype.txt - - - <> - - -<> -<> - - <> - <> - - - <> - - -<> - \ No newline at end of file diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/galaxy_test_case.xml --- a/tmp2/circos/conf/galaxy_test_case.xml Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/highlight.conf --- a/tmp2/circos/conf/highlight.conf Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ - - \ No newline at end of file diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/ideogram.conf --- a/tmp2/circos/conf/ideogram.conf Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - - - - - - default = 0.005r - - - # ideogram position, thickness and fill - radius = 0.9r - thickness = 10.0p - fill = yes - - show_label = no - label_radius = dims(ideogram,radius) + 0.075r - label_size = 24 - label_parallel = no - - show_bands = yes - fill_bands = yes - band_transparency = 4 - - diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/karyotype.txt --- a/tmp2/circos/conf/karyotype.txt Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -chr - ctgA 0 0 50001 set3-12-qual-1 -chr - ctgB 1 0 6079 set3-12-qual-2 diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/links.conf --- a/tmp2/circos/conf/links.conf Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ - - - - file = data/links-0.txt - - radius = 0.8r - ribbon = no - color = 141, 179, 226 - - bezier_radius = 0.1r - thickness = 15.0 - crest = 0.5 - bezier_radius_purity = 0.75 - - - - - - - \ No newline at end of file diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/plot_highlight.conf --- a/tmp2/circos/conf/plot_highlight.conf Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ - - \ No newline at end of file diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/conf/ticks.conf --- a/tmp2/circos/conf/ticks.conf Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ - -show_ticks = yes -show_tick_labels = yes - - - - - radius = 1.0r - color = 0, 0, 0 - - thickness = 2p - multiplier = 0.001 - - - spacing = 5000.0 - size = 10.0p - show_label = no - label_size = 20.0p - label_offset = 10.0p - format = %d kb - - - - \ No newline at end of file diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/data/data-0.txt --- a/tmp2/circos/data/data-0.txt Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,499 +0,0 @@ -ctgA 1 19 -0.506365641109759,-0.506365641109759 -ctgA 101 119 -0.873297297213995,-0.873297297213995 -ctgA 201 219 -0.999755839901149,-0.999755839901149 -ctgA 301 319 -0.850919359639177,-0.850919359639177 -ctgA 401 419 -0.467771805322476,-0.467771805322476 -ctgA 501 519 0.0441824483318732,0.0441824483318732 -ctgA 601 619 0.543970523363376,0.543970523363376 -ctgA 701 719 0.893969648197021,0.893969648197021 -ctgA 801 819 0.99780327442197,0.99780327442197 -ctgA 901 919 0.826879540532003,0.826879540532003 -ctgA 1001 1019 0.428264391396659,0.428264391396659 -ctgA 1101 1119 -0.0882786064717262,-0.0882786064717262 -ctgA 1201 1219 -0.580513008156313,-0.580513008156313 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0.583454612012034,0.583454612012034 -ctgA 41301 41319 0.0918812207856598,0.0918812207856598 -ctgA 41401 41419 -0.424992790627422,-0.424992790627422 -ctgA 41501 41519 -0.824839828674128,-0.824839828674128 -ctgA 41601 41619 -0.997557111133059,-0.997557111133059 -ctgA 41701 41719 -0.895584817555511,-0.895584817555511 -ctgA 41801 41819 -0.547002268691819,-0.547002268691819 -ctgA 41901 41919 -0.0477959413987577,-0.0477959413987577 -ctgA 42001 42019 0.464571584118009,0.464571584118009 -ctgA 42101 42119 0.849013630425847,0.849013630425847 -ctgA 42201 42219 0.999669368573369,0.999669368573369 -ctgA 42301 42319 0.87505389471161,0.87505389471161 -ctgA 42401 42419 0.509481606783953,0.509481606783953 -ctgA 42501 42519 0.0036173145149015,0.0036173145149015 -ctgA 42601 42619 -0.503243049637554,-0.503243049637554 -ctgA 42701 42719 -0.871529272615042,-0.871529272615042 -ctgA 42801 42819 -0.999829229416663,-0.999829229416663 -ctgA 42901 42919 -0.85281395456664,-0.85281395456664 -ctgA 43001 43019 -0.470965905729547,-0.470965905729547 -ctgA 43101 43119 0.0405683771373384,0.0405683771373384 -ctgA 43201 43219 0.540931660176769,0.540931660176769 -ctgA 43301 43319 0.892342781239334,0.892342781239334 -ctgA 43401 43419 0.998036381447947,0.998036381447947 -ctgA 43501 43519 0.828908432665215,0.828908432665215 -ctgA 43601 43619 0.431530388323292,0.431530388323292 -ctgA 43701 43719 -0.0846748370315997,-0.0846748370315997 -ctgA 43801 43819 -0.577563808283757,-0.577563808283757 -ctgA 43901 43919 -0.911413506635259,-0.911413506635259 -ctgA 44001 44019 -0.994294326175203,-0.994294326175203 -ctgA 44101 44119 -0.803384017503629,-0.803384017503629 -ctgA 44201 44219 -0.391252073800153,-0.391252073800153 -ctgA 44301 44319 0.128615923384498,0.128615923384498 -ctgA 44401 44419 0.613067949822471,0.613067949822471 -ctgA 44501 44519 0.928704202868774,0.928704202868774 -ctgA 44601 44619 0.988610371990796,0.988610371990796 -ctgA 44701 44719 0.776290559345248,0.776290559345248 -ctgA 44801 44819 0.350209627413543,0.350209627413543 -ctgA 44901 44919 -0.172305817394175,-0.172305817394175 -ctgA 45001 45019 -0.647374743701449,-0.647374743701449 -ctgA 45101 45119 -0.944181100478148,-0.944181100478148 -ctgA 45201 45219 -0.980995619897873,-0.980995619897873 -ctgA 45301 45319 -0.747680972860835,-0.747680972860835 -ctgA 45401 45419 -0.308483206798754,-0.308483206798754 -ctgA 45501 45519 0.215659190848055,0.215659190848055 -ctgA 45601 45619 0.680417187299892,0.680417187299892 -ctgA 45701 45719 0.957813972427147,0.957813972427147 -ctgA 45801 45819 0.971464941829636,0.971464941829636 -ctgA 45901 45919 0.717611133783957,0.717611133783957 -ctgA 46001 46019 0.266154305421701,0.266154305421701 -ctgA 46101 46119 -0.258591372772452,-0.258591372772452 -ctgA 46201 46219 -0.71213074732663,-0.71213074732663 -ctgA 46301 46319 -0.969576193139719,-0.969576193139719 -ctgA 46401 46419 -0.960036951603826,-0.960036951603826 -ctgA 46501 46519 -0.686139769783315,-0.686139769783315 -ctgA 46601 46619 -0.223305593418733,-0.223305593418733 -ctgA 46701 46719 0.301018514798568,0.301018514798568 -ctgA 46801 46819 0.742453485856362,0.742453485856362 -ctgA 46901 46919 0.979444790500868,0.979444790500868 -ctgA 47001 47019 0.946733968569148,0.946733968569148 -ctgA 47101 47119 0.653328345765115,0.653328345765115 -ctgA 47201 47219 0.180020756138357,0.180020756138357 -ctgA 47301 47319 -0.342857754921908,-0.342857754921908 -ctgA 47401 47419 -0.77132618129705,-0.77132618129705 -ctgA 47501 47519 -0.987400490722168,-0.987400490722168 -ctgA 47601 47619 -0.931581974014641,-0.931581974014641 -ctgA 47701 47719 -0.619240943829511,-0.619240943829511 -ctgA 47801 47819 -0.13638433070021,-0.13638433070021 -ctgA 47901 47919 0.38402737933528,0.38402737933528 -ctgA 48001 48019 0.798692444052197,0.798692444052197 -ctgA 48101 48119 0.993427755984289,0.993427755984289 -ctgA 48201 48219 0.914610560427116,0.914610560427116 -ctgA 48301 48319 0.583944138115545,0.583944138115545 -ctgA 48401 48419 0.0924815408904855,0.0924815408904855 -ctgA 48501 48519 -0.424446982019324,-0.424446982019324 -ctgA 48601 48619 -0.824498826652114,-0.824498826652114 -ctgA 48701 48719 -0.997514814783015,-0.997514814783015 -ctgA 48801 48819 -0.895852873695781,-0.895852873695781 -ctgA 48901 48919 -0.547506864779039,-0.547506864779039 -ctgA 49001 49019 -0.048398130716271,-0.048398130716271 -ctgA 49101 49119 0.464037621778865,0.464037621778865 -ctgA 49201 49219 0.848694928139091,0.848694928139091 -ctgA 49301 49319 0.99965368491949,0.99965368491949 -ctgA 49401 49419 0.875345548376914,0.875345548376914 -ctgA 49501 49519 0.51000028735736,0.51000028735736 -ctgA 49601 49619 0.00422019694387214,0.00422019694387214 -ctgA 49701 49719 -0.502721976418416,-0.502721976418416 -ctgA 49801 49819 -0.871233492502601,-0.871233492502601 diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/data/links-0.txt --- a/tmp2/circos/data/links-0.txt Wed Mar 01 22:49:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -ctgA 0 500 ctgA 1000 1500 -ctgA 2500 3000 ctgA 3500 4000 -ctgA 5000 5500 ctgA 6000 6500 -ctgA 7500 8000 ctgA 8500 9000 -ctgA 10000 10500 ctgA 11000 11500 -ctgA 12500 13000 ctgA 13500 14000 -ctgA 15000 15500 ctgA 16000 16500 -ctgA 17500 18000 ctgA 18500 19000 -ctgA 20000 20500 ctgA 21000 21500 -ctgA 22500 23000 ctgA 23500 24000 -ctgA 25000 25500 ctgA 26000 26500 -ctgA 27500 28000 ctgA 28500 29000 -ctgA 30000 30500 ctgA 31000 31500 -ctgA 32500 33000 ctgA 33500 34000 -ctgA 35000 35500 ctgA 36000 36500 -ctgA 37500 38000 ctgA 38500 39000 -ctgA 40000 40500 ctgA 41000 41500 -ctgA 42500 43000 ctgA 43500 44000 -ctgA 45000 45500 ctgA 46000 46500 -ctgA 47500 48000 ctgA 48500 49000 -ctgA 50000 50500 ctgA 51000 51500 diff -r dc4c9490fac8 -r b56f47c58779 unified-histogram.py --- a/unified-histogram.py Wed Mar 01 22:49:11 2017 -0500 +++ b/unified-histogram.py Wed Mar 01 23:56:56 2017 -0500 @@ -115,7 +115,9 @@ if MODE == 'histogram': # histogram # hs4 0 1999999 5.0000,3.0000,1.0000,19.0000 - print genome, region_start, region_end, ','.join(values) + sys.stdout.write(' '.join( + (genome, region_start, region_end, ','.join(values)) + ) + '\n') elif MODE == 'heatmap': # heatmap # hs1 2000000 3999999 0.0000 id=hs4 @@ -126,15 +128,23 @@ # hs1 6000000 7999999 4.0000 id=hs2 for x in max_idx: if x in data[genome][position]: - print genome, region_start, region_end, data[genome][position][x], 'id=hm%s' % x + sys.stdout.write(' '.join( + (genome, region_start, region_end, data[genome][position][x], 'id=hm%s' % x) + ) + '\n') else: - print genome, region_start, region_end, 0.0, 'id=hm%s' % x + sys.stdout.write(' '.join( + (genome, region_start, region_end, 0.0, 'id=hm%s' % x) + ) + '\n') elif MODE == 'line': # multiple=False - print genome, region_start, region_end, data[genome][position][0] + sys.stdout.write(' '.join( + (genome, region_start, region_end, data[genome][position][0]) + ) + '\n') elif MODE == 'scatter': # multiple=False - print genome, region_start, region_end, data[genome][position][0] + sys.stdout.write(' '.join( + (genome, region_start, region_end, data[genome][position][0]) + ) + '\n') # Update start of next array region_start = position diff -r dc4c9490fac8 -r b56f47c58779 unified-tiles.py --- a/unified-tiles.py Wed Mar 01 22:49:11 2017 -0500 +++ b/unified-tiles.py Wed Mar 01 23:56:56 2017 -0500 @@ -68,4 +68,4 @@ if item[6] is not None: lineExtra.append('color=%s' % item[6]) - print item[0], item[1], item[2], ','.join(lineExtra) + sys.stdout.write(' '.join((item[0], item[1], item[2], ','.join(lineExtra))) + '\n')