# HG changeset patch
# User fubar2
# Date 1702025256 0
# Node ID aff6409d16d126e461e029c0bf9691e12cc1572f
# Parent 551c076a635c0b9f9efdcbf0ff45acfb50b8a2ed
Uploaded
diff -r 551c076a635c -r aff6409d16d1 abslen_bed/.shed.yml
--- a/abslen_bed/.shed.yml Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-category: ToolFactory generated Tools
-description: ToolFactory autogenerated tool
-name: abslen_bed
-owner: fubar2
-synopsis: Add the contig length to the end of each row of a bed file
-type: unrestricted
diff -r 551c076a635c -r aff6409d16d1 abslen_bed/abslen_bed.python.txt
--- a/abslen_bed/abslen_bed.python.txt Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-#raw
-import sys
-inp = []
-for line in sys.stdin:
- if line.strip() > '':
- ls = line.split()
- if len(ls) > 3:
- x = abs(int(ls[2]) - int(ls[1]))
- ls.append((str(x)))
- inp.append('\t'.join(ls))
- else:
- break
-sys.stdout.write('\n'.join(inp))
-#end raw
diff -r 551c076a635c -r aff6409d16d1 abslen_bed/abslen_bed.xml
--- a/abslen_bed/abslen_bed.xml Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-
-
-
- Add the contig length to the end of each row of a bed file
-
- python
-
-
-
-$absout]]>
-
- '':
- ls = line.split()
- if len(ls) > 3:
- x = abs(int(ls[2]) - int(ls[1]))
- ls.append((str(x)))
- inp.append('\t'.join(ls))
- else:
- break
-sys.stdout.write('\n'.join(inp))
-#end raw]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1093/bioinformatics/bts573
-
-
-
diff -r 551c076a635c -r aff6409d16d1 abslen_bed/test-data/absin_sample
--- a/abslen_bed/test-data/absin_sample Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
-chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
-chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
-chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
-chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
-chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
-chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
-chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
-chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
-chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
-chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
-chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
-chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
-chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
-chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
-chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
-chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
-chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
-chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
-chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
-chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
-chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
-chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
-chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
-chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
-chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
-chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
-chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
-chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
-chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
-chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
-chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
-chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
-chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
-chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
-chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
-chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
-chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
-chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
-chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
-chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
-chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
-chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
-chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
-chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
-chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
-chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
-chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
-chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
diff -r 551c076a635c -r aff6409d16d1 abslen_bed/test-data/absout_sample
--- a/abslen_bed/test-data/absout_sample Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-chr1 147962192 147962580 region_0 0 - 388
-chr1 147984545 147984630 region_1 0 + 85
-chr1 148078400 148078582 region_2 0 - 182
-chr1 148185136 148185276 region_3 0 + 140
-chr10 55251623 55253124 region_4 0 - 1501
-chr11 116124407 116124501 region_5 0 - 94
-chr11 116206508 116206563 region_6 0 + 55
-chr11 116211733 116212337 region_7 0 - 604
-chr12 38440094 38440321 region_8 0 - 227
-chr13 112381694 112381953 region_9 0 + 259
-chr14 98710240 98712285 region_10 0 - 2045
-chr15 41486872 41487060 region_11 0 - 188
-chr15 41673708 41673857 region_12 0 + 149
-chr15 41679161 41679250 region_13 0 - 89
-chr16 142908 143003 region_14 0 + 95
-chr16 244413 244681 region_15 0 + 268
-chr16 259268 259383 region_16 0 - 115
-chr18 23786114 23786321 region_17 0 - 207
-chr18 59406881 59407046 region_18 0 + 165
-chr18 59455932 59456337 region_19 0 - 405
-chr19 59068595 59069564 region_20 0 + 969
-chr19 59236026 59236146 region_21 0 - 120
-chr19 59297998 59298008 region_22 0 + 10
-chr2 118288583 118288668 region_23 0 + 85
-chr2 220229609 220230869 region_24 0 - 1260
-chr20 33330413 33330423 region_25 0 - 10
-chr20 33513606 33513792 region_26 0 + 186
-chr21 32869641 32870022 region_27 0 - 381
-chr21 33321040 33322012 region_28 0 + 972
-chr22 30120223 30120265 region_29 0 + 42
-chr22 30160419 30160661 region_30 0 - 242
-chr5 131424298 131424460 region_31 0 + 162
-chr5 131556601 131556672 region_32 0 - 71
-chr5 131621326 131621419 region_33 0 + 93
-chr6 108299600 108299744 region_34 0 - 144
-chr6 108594662 108594687 region_35 0 + 25
-chr6 108640045 108640151 region_36 0 - 106
-chr6 108722976 108723115 region_37 0 + 139
-chr7 113660517 113660685 region_38 0 + 168
-chr7 116512159 116512389 region_39 0 - 230
-chr7 116714099 116714152 region_40 0 + 53
-chr7 116945541 116945787 region_41 0 - 246
-chr8 118881131 118881317 region_42 0 - 186
-chr9 128764156 128764189 region_43 0 + 33
-chr9 128787519 128789136 region_44 0 - 1617
-chrX 122745047 122745924 region_45 0 + 877
-chrX 152648964 152649196 region_46 0 - 232
-chrX 152691446 152691471 region_47 0 + 25
-chrX 152694029 152694263 region_48 0 - 234
\ No newline at end of file
diff -r 551c076a635c -r aff6409d16d1 absval/.shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/absval/.shed.yml Fri Dec 08 08:47:36 2023 +0000
@@ -0,0 +1,6 @@
+category: ToolFactory generated Tools
+description: ToolFactory autogenerated tool
+name: absval
+owner: fubar2
+synopsis: Returns a file of absolute values from differences
+type: unrestricted
diff -r 551c076a635c -r aff6409d16d1 absval/absval.python.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/absval/absval.python.txt Fri Dec 08 08:47:36 2023 +0000
@@ -0,0 +1,11 @@
+#raw
+import sys
+inp = []
+for line in sys.stdin:
+ if line.strip() > '':
+ x = line.split()[0]
+ inp.append(str(abs(float(x))))
+ else:
+ break
+sys.stdout.write('\n'.join(inp))
+#end raw
diff -r 551c076a635c -r aff6409d16d1 absval/absval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/absval/absval.xml Fri Dec 08 08:47:36 2023 +0000
@@ -0,0 +1,56 @@
+
+
+
+ Returns a file of absolute values from differences
+
+ python
+
+
+
+$absout]]>
+
+ '':
+ ls = line.split()
+ if len(ls) > 2:
+ x = abs(int(ls[2]) - int(ls[1]))
+ ls.append((str(x)))
+ inp.append('\t'.join(ls))
+ else:
+ break
+sys.stdout.write('\n'.join(inp))
+#end raw]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1093/bioinformatics/bts573
+
+
+
diff -r 551c076a635c -r aff6409d16d1 absval/test-data/absin_sample
diff -r 551c076a635c -r aff6409d16d1 absval/test-data/absout_sample