# 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
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diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/circos.png
Binary file tmp2/circos/circos.png has changed
diff -r dc4c9490fac8 -r b56f47c58779 tmp2/circos/circos.svg
--- a/tmp2/circos/circos.svg Wed Mar 01 22:49:11 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4050 +0,0 @@
-
-
-
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 @@
-
-
-
-
-
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-
-
\ 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
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-
-
-
-
- radius = 1.0r
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-
- thickness = 2p
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-
-
- 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
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-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
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-ctgA 1501 1519 -0.801224790676895,-0.801224790676895
-ctgA 1601 1619 -0.387920558984219,-0.387920558984219
-ctgA 1701 1719 0.132202352755937,0.132202352755937
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-ctgA 1901 1919 0.930039504416137,0.930039504416137
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-ctgA 2101 2119 0.774005214886395,0.774005214886395
-ctgA 2201 2219 0.34681910129778,0.34681910129778
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-ctgA 2901 2919 0.219189974282818,0.219189974282818
-ctgA 3001 3019 0.683063594104854,0.683063594104854
-ctgA 3101 3119 0.958847282055722,0.958847282055722
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-ctgA 3401 3419 0.262665724548229,0.262665724548229
-ctgA 3501 3519 -0.262083959018097,-0.262083959018097
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-ctgA 4301 4319 0.980168039762288,0.980168039762288
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-ctgA 33501 33519 -0.618293718815172,-0.618293718815172
-ctgA 33601 33619 -0.13518972446219,-0.13518972446219
-ctgA 33701 33719 0.385140417328934,0.385140417328934
-ctgA 33801 33819 0.79941742514918,0.79941742514918
-ctgA 33901 33919 0.993565047754595,0.993565047754595
-ctgA 34001 34019 0.914122357899222,0.914122357899222
-ctgA 34101 34119 0.582964873838637,0.582964873838637
-ctgA 34201 34219 0.091280867284509,0.091280867284509
-ctgA 34301 34319 -0.425538444762198,-0.425538444762198
-ctgA 34401 34419 -0.825180530889296,-0.825180530889296
-ctgA 34501 34519 -0.997599044898223,-0.997599044898223
-ctgA 34601 34619 -0.895316435894515,-0.895316435894515
-ctgA 34701 34719 -0.546497473784151,-0.546497473784151
-ctgA 34801 34819 -0.0471937347087195,-0.0471937347087195
-ctgA 34901 34919 0.465105377598017,0.465105377598017
-ctgA 35001 35019 0.849332024119238,0.849332024119238
-ctgA 35101 35119 0.999684688874618,0.999684688874618
-ctgA 35201 35219 0.874761922988011,0.874761922988011
-ctgA 35301 35319 0.508962741027838,0.508962741027838
-ctgA 35401 35419 0.00301443077113541,0.00301443077113541
-ctgA 35501 35519 -0.503763939941528,-0.503763939941528
-ctgA 35601 35619 -0.871824735950293,-0.871824735950293
-ctgA 35701 35719 -0.999817906332802,-0.999817906332802
-ctgA 35801 35819 -0.852498963013576,-0.852498963013576
-ctgA 35901 35919 -0.470433982491772,-0.470433982491772
-ctgA 36001 36019 0.0411707604773582,0.0411707604773582
-ctgA 36101 36119 0.541438629983896,0.541438629983896
-ctgA 36201 36219 0.892614737164045,0.892614737164045
-ctgA 36301 36319 0.997998437093437,0.997998437093437
-ctgA 36401 36419 0.828571036474523,0.828571036474523
-ctgA 36501 36519 0.430986446472459,0.430986446472459
-ctgA 36601 36619 -0.0852755434877088,-0.0852755434877088
-ctgA 36701 36719 -0.57805586746054,-0.57805586746054
-ctgA 36801 36819 -0.911661424007995,-0.911661424007995
-ctgA 36901 36919 -0.994229834656976,-0.994229834656976
-ctgA 37001 37019 -0.803024875624353,-0.803024875624353
-ctgA 37101 37119 -0.390697175677724,-0.390697175677724
-ctgA 37201 37219 0.129213779751557,0.129213779751557
-ctgA 37301 37319 0.613544137356508,0.613544137356508
-ctgA 37401 37419 0.92892759749641,0.92892759749641
-ctgA 37501 37519 0.988519459263516,0.988519459263516
-ctgA 37601 37619 0.775910373196683,0.775910373196683
-ctgA 37701 37719 0.349644856759043,0.349644856759043
-ctgA 37801 37819 -0.17289965603339,-0.17289965603339
-ctgA 37901 37919 -0.647834129578325,-0.647834129578325
-ctgA 38001 38019 -0.944379536061519,-0.944379536061519
-ctgA 38101 38119 -0.980878463517946,-0.980878463517946
-ctgA 38201 38219 -0.747280484962623,-0.747280484962623
-ctgA 38301 38319 -0.30790966663318,-0.30790966663318
-ctgA 38401 38419 0.216247851967423,0.216247851967423
-ctgA 38501 38519 0.680858874319544,0.680858874319544
-ctgA 38601 38619 0.957987061413159,0.957987061413159
-ctgA 38701 38719 0.971321770608431,0.971321770608431
-ctgA 38801 38819 0.717191126305919,0.717191126305919
-ctgA 38901 38919 0.265573115893276,0.265573115893276
-ctgA 39001 39019 -0.259173706691886,-0.259173706691886
-ctgA 39101 39119 -0.712553872855609,-0.712553872855609
-ctgA 39201 39219 -0.969723597478254,-0.969723597478254
-ctgA 39301 39319 -0.959868045160799,-0.959868045160799
-ctgA 39401 39419 -0.685701063017834,-0.685701063017834
-ctgA 39501 39519 -0.22271788961521,-0.22271788961521
-ctgA 39601 39619 0.301593384195272,0.301593384195272
-ctgA 39701 39719 0.742857223512596,0.742857223512596
-ctgA 39801 39819 0.979566222305013,0.979566222305013
-ctgA 39901 39919 0.946539656785734,0.946539656785734
-ctgA 40001 40019 0.652871796525078,0.652871796525078
-ctgA 40101 40119 0.179427685870145,0.179427685870145
-ctgA 40201 40219 -0.343424037051613,-0.343424037051613
-ctgA 40301 40319 -0.771709742563807,-0.771709742563807
-ctgA 40401 40419 -0.987495712830468,-0.987495712830468
-ctgA 40501 40519 -0.931362636389977,-0.931362636389977
-ctgA 40601 40619 -0.618767443774911,-0.618767443774911
-ctgA 40701 40719 -0.13578705225865,-0.13578705225865
-ctgA 40801 40819 0.384583968225014,0.384583968225014
-ctgA 40901 40919 0.799055079818084,0.799055079818084
-ctgA 41001 41019 0.993496582423937,0.993496582423937
-ctgA 41101 41119 0.91436662533687,0.91436662533687
-ctgA 41201 41219 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')