changeset 2:ae537f4d4b93 draft

planemo upload for repository https://github.com/open2c/pairtools commit 01e7e0814f8bb4253a92ee4541b555e9af74fb0a
author iuc
date Fri, 05 Apr 2024 10:33:39 +0000
parents ccc7a8e707fb
children 5412142130ad
files test-data/pairs_output.stats test-data/pairs_output2.stats test-data/pairs_output_merged.stats test-data/pairs_output_with_chromsize.stats test-data/pairs_output_yaml.stats
diffstat 5 files changed, 935 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pairs_output.stats	Fri Apr 05 10:33:39 2024 +0000
@@ -0,0 +1,185 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pairs_output2.stats	Fri Apr 05 10:33:39 2024 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pairs_output_merged.stats	Fri Apr 05 10:33:39 2024 +0000
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+dist_freq/5623413-10000000/++	0
+dist_freq/10000000-17782794/+-	0
+dist_freq/10000000-17782794/-+	0
+dist_freq/10000000-17782794/--	0
+dist_freq/10000000-17782794/++	0
+dist_freq/17782794-31622777/+-	0
+dist_freq/17782794-31622777/-+	0
+dist_freq/17782794-31622777/--	0
+dist_freq/17782794-31622777/++	0
+dist_freq/31622777-56234133/+-	0
+dist_freq/31622777-56234133/-+	0
+dist_freq/31622777-56234133/--	0
+dist_freq/31622777-56234133/++	0
+dist_freq/56234133-100000000/+-	0
+dist_freq/56234133-100000000/-+	0
+dist_freq/56234133-100000000/--	0
+dist_freq/56234133-100000000/++	0
+dist_freq/100000000-177827941/+-	0
+dist_freq/100000000-177827941/-+	0
+dist_freq/100000000-177827941/--	0
+dist_freq/100000000-177827941/++	0
+dist_freq/177827941-316227766/+-	0
+dist_freq/177827941-316227766/-+	0
+dist_freq/177827941-316227766/--	0
+dist_freq/177827941-316227766/++	0
+dist_freq/316227766-562341325/+-	0
+dist_freq/316227766-562341325/-+	0
+dist_freq/316227766-562341325/--	0
+dist_freq/316227766-562341325/++	0
+dist_freq/562341325-1000000000/+-	0
+dist_freq/562341325-1000000000/-+	0
+dist_freq/562341325-1000000000/--	0
+dist_freq/562341325-1000000000/++	0
+dist_freq/562341325+/+-	0
+dist_freq/562341325+/-+	0
+dist_freq/562341325+/--	0
+dist_freq/562341325+/++	0
+chromsizes/Test_seq	450060
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pairs_output_with_chromsize.stats	Fri Apr 05 10:33:39 2024 +0000
@@ -0,0 +1,185 @@
+total	592
+total_unmapped	4
+total_single_sided_mapped	147
+total_mapped	441
+total_dups	0
+total_nodups	441
+cis	441
+trans	0
+pair_types/UU	405
+pair_types/NR	119
+pair_types/MU	21
+pair_types/UR	19
+pair_types/RU	17
+pair_types/MR	6
+pair_types/MM	4
+pair_types/NU	1
+cis_1kb+	75
+cis_2kb+	72
+cis_4kb+	70
+cis_10kb+	67
+cis_20kb+	61
+cis_40kb+	61
+summary/frac_cis	1.0
+summary/frac_cis_1kb+	0.17006802721088435
+summary/frac_cis_2kb+	0.16326530612244897
+summary/frac_cis_4kb+	0.15873015873015872
+summary/frac_cis_10kb+	0.15192743764172337
+summary/frac_cis_20kb+	0.1383219954648526
+summary/frac_cis_40kb+	0.1383219954648526
+summary/frac_dups	0.0
+summary/complexity_naive	nan
+chrom_freq/Test_seq/Test_seq	441
+dist_freq/0-1/+-	0
+dist_freq/0-1/-+	0
+dist_freq/0-1/--	0
+dist_freq/0-1/++	0
+dist_freq/1-2/+-	0
+dist_freq/1-2/-+	0
+dist_freq/1-2/--	0
+dist_freq/1-2/++	0
+dist_freq/2-3/+-	0
+dist_freq/2-3/-+	0
+dist_freq/2-3/--	0
+dist_freq/2-3/++	0
+dist_freq/3-6/+-	0
+dist_freq/3-6/-+	0
+dist_freq/3-6/--	0
+dist_freq/3-6/++	0
+dist_freq/6-10/+-	0
+dist_freq/6-10/-+	0
+dist_freq/6-10/--	0
+dist_freq/6-10/++	0
+dist_freq/10-18/+-	0
+dist_freq/10-18/-+	0
+dist_freq/10-18/--	0
+dist_freq/10-18/++	0
+dist_freq/18-32/+-	0
+dist_freq/18-32/-+	0
+dist_freq/18-32/--	0
+dist_freq/18-32/++	0
+dist_freq/32-56/+-	7
+dist_freq/32-56/-+	0
+dist_freq/32-56/--	0
+dist_freq/32-56/++	0
+dist_freq/56-100/+-	9
+dist_freq/56-100/-+	0
+dist_freq/56-100/--	0
+dist_freq/56-100/++	0
+dist_freq/100-178/+-	5
+dist_freq/100-178/-+	0
+dist_freq/100-178/--	0
+dist_freq/100-178/++	0
+dist_freq/178-316/+-	60
+dist_freq/178-316/-+	0
+dist_freq/178-316/--	0
+dist_freq/178-316/++	0
+dist_freq/316-562/+-	284
+dist_freq/316-562/-+	0
+dist_freq/316-562/--	0
+dist_freq/316-562/++	0
+dist_freq/562-1000/+-	1
+dist_freq/562-1000/-+	0
+dist_freq/562-1000/--	0
+dist_freq/562-1000/++	0
+dist_freq/1000-1778/+-	1
+dist_freq/1000-1778/-+	0
+dist_freq/1000-1778/--	1
+dist_freq/1000-1778/++	0
+dist_freq/1778-3162/+-	1
+dist_freq/1778-3162/-+	0
+dist_freq/1778-3162/--	1
+dist_freq/1778-3162/++	1
+dist_freq/3162-5623/+-	0
+dist_freq/3162-5623/-+	0
+dist_freq/3162-5623/--	0
+dist_freq/3162-5623/++	0
+dist_freq/5623-10000/+-	2
+dist_freq/5623-10000/-+	0
+dist_freq/5623-10000/--	0
+dist_freq/5623-10000/++	1
+dist_freq/10000-17783/+-	2
+dist_freq/10000-17783/-+	2
+dist_freq/10000-17783/--	0
+dist_freq/10000-17783/++	1
+dist_freq/17783-31623/+-	1
+dist_freq/17783-31623/-+	0
+dist_freq/17783-31623/--	0
+dist_freq/17783-31623/++	0
+dist_freq/31623-56234/+-	0
+dist_freq/31623-56234/-+	1
+dist_freq/31623-56234/--	21
+dist_freq/31623-56234/++	10
+dist_freq/56234-100000/+-	3
+dist_freq/56234-100000/-+	0
+dist_freq/56234-100000/--	1
+dist_freq/56234-100000/++	3
+dist_freq/100000-177828/+-	3
+dist_freq/100000-177828/-+	3
+dist_freq/100000-177828/--	2
+dist_freq/100000-177828/++	7
+dist_freq/177828-316228/+-	4
+dist_freq/177828-316228/-+	0
+dist_freq/177828-316228/--	0
+dist_freq/177828-316228/++	2
+dist_freq/316228-562341/+-	0
+dist_freq/316228-562341/-+	1
+dist_freq/316228-562341/--	0
+dist_freq/316228-562341/++	0
+dist_freq/562341-1000000/+-	0
+dist_freq/562341-1000000/-+	0
+dist_freq/562341-1000000/--	0
+dist_freq/562341-1000000/++	0
+dist_freq/1000000-1778279/+-	0
+dist_freq/1000000-1778279/-+	0
+dist_freq/1000000-1778279/--	0
+dist_freq/1000000-1778279/++	0
+dist_freq/1778279-3162278/+-	0
+dist_freq/1778279-3162278/-+	0
+dist_freq/1778279-3162278/--	0
+dist_freq/1778279-3162278/++	0
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+dist_freq/3162278-5623413/++	0
+dist_freq/5623413-10000000/+-	0
+dist_freq/5623413-10000000/-+	0
+dist_freq/5623413-10000000/--	0
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+dist_freq/10000000-17782794/+-	0
+dist_freq/10000000-17782794/-+	0
+dist_freq/10000000-17782794/--	0
+dist_freq/10000000-17782794/++	0
+dist_freq/17782794-31622777/+-	0
+dist_freq/17782794-31622777/-+	0
+dist_freq/17782794-31622777/--	0
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+dist_freq/56234133-100000000/+-	0
+dist_freq/56234133-100000000/-+	0
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+dist_freq/56234133-100000000/++	0
+dist_freq/100000000-177827941/+-	0
+dist_freq/100000000-177827941/-+	0
+dist_freq/100000000-177827941/--	0
+dist_freq/100000000-177827941/++	0
+dist_freq/177827941-316227766/+-	0
+dist_freq/177827941-316227766/-+	0
+dist_freq/177827941-316227766/--	0
+dist_freq/177827941-316227766/++	0
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+dist_freq/316227766-562341325/-+	0
+dist_freq/316227766-562341325/--	0
+dist_freq/316227766-562341325/++	0
+dist_freq/562341325-1000000000/+-	0
+dist_freq/562341325-1000000000/-+	0
+dist_freq/562341325-1000000000/--	0
+dist_freq/562341325-1000000000/++	0
+dist_freq/562341325+/+-	0
+dist_freq/562341325+/-+	0
+dist_freq/562341325+/--	0
+dist_freq/562341325+/++	0
+chromsizes/Test_seq	450060
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pairs_output_yaml.stats	Fri Apr 05 10:33:39 2024 +0000
@@ -0,0 +1,195 @@
+no_filter:
+  total: 592
+  total_unmapped: 4
+  total_single_sided_mapped: 147
+  total_mapped: 441
+  total_dups: 0
+  total_nodups: 441
+  cis: 441
+  trans: 0
+  pair_types:
+    UU: 405
+    NR: 119
+    MU: 21
+    UR: 19
+    RU: 17
+    MR: 6
+    MM: 4
+    NU: 1
+  cis_1kb+: 75
+  cis_2kb+: 72
+  cis_4kb+: 70
+  cis_10kb+: 67
+  cis_20kb+: 61
+  cis_40kb+: 61
+  summary:
+    frac_cis: 1.0
+    frac_cis_1kb+: 0.17006802721088435
+    frac_cis_2kb+: 0.16326530612244897
+    frac_cis_4kb+: 0.15873015873015872
+    frac_cis_10kb+: 0.15192743764172337
+    frac_cis_20kb+: 0.1383219954648526
+    frac_cis_40kb+: 0.1383219954648526
+    frac_dups: 0.0
+    complexity_naive: .nan
+  chrom_freq:
+    Test_seq/Test_seq: 441
+  dist_freq:
+    +-:
+      0: 0
+      1: 0
+      2: 0
+      3: 0
+      6: 0
+      10: 0
+      18: 0
+      32: 7
+      56: 9
+      100: 5
+      178: 60
+      316: 284
+      562: 1
+      1000: 1
+      1778: 1
+      3162: 0
+      5623: 2
+      10000: 2
+      17783: 1
+      31623: 0
+      56234: 3
+      100000: 3
+      177828: 4
+      316228: 0
+      562341: 0
+      1000000: 0
+      1778279: 0
+      3162278: 0
+      5623413: 0
+      10000000: 0
+      17782794: 0
+      31622777: 0
+      56234133: 0
+      100000000: 0
+      177827941: 0
+      316227766: 0
+      562341325: 0
+      1000000000: 0
+    -+:
+      0: 0
+      1: 0
+      2: 0
+      3: 0
+      6: 0
+      10: 0
+      18: 0
+      32: 0
+      56: 0
+      100: 0
+      178: 0
+      316: 0
+      562: 0
+      1000: 0
+      1778: 0
+      3162: 0
+      5623: 0
+      10000: 2
+      17783: 0
+      31623: 1
+      56234: 0
+      100000: 3
+      177828: 0
+      316228: 1
+      562341: 0
+      1000000: 0
+      1778279: 0
+      3162278: 0
+      5623413: 0
+      10000000: 0
+      17782794: 0
+      31622777: 0
+      56234133: 0
+      100000000: 0
+      177827941: 0
+      316227766: 0
+      562341325: 0
+      1000000000: 0
+    --:
+      0: 0
+      1: 0
+      2: 0
+      3: 0
+      6: 0
+      10: 0
+      18: 0
+      32: 0
+      56: 0
+      100: 0
+      178: 0
+      316: 0
+      562: 0
+      1000: 1
+      1778: 1
+      3162: 0
+      5623: 0
+      10000: 0
+      17783: 0
+      31623: 21
+      56234: 1
+      100000: 2
+      177828: 0
+      316228: 0
+      562341: 0
+      1000000: 0
+      1778279: 0
+      3162278: 0
+      5623413: 0
+      10000000: 0
+      17782794: 0
+      31622777: 0
+      56234133: 0
+      100000000: 0
+      177827941: 0
+      316227766: 0
+      562341325: 0
+      1000000000: 0
+    ++:
+      0: 0
+      1: 0
+      2: 0
+      3: 0
+      6: 0
+      10: 0
+      18: 0
+      32: 0
+      56: 0
+      100: 0
+      178: 0
+      316: 0
+      562: 0
+      1000: 0
+      1778: 1
+      3162: 0
+      5623: 1
+      10000: 1
+      17783: 0
+      31623: 10
+      56234: 3
+      100000: 7
+      177828: 2
+      316228: 0
+      562341: 0
+      1000000: 0
+      1778279: 0
+      3162278: 0
+      5623413: 0
+      10000000: 0
+      17782794: 0
+      31622777: 0
+      56234133: 0
+      100000000: 0
+      177827941: 0
+      316227766: 0
+      562341325: 0
+      1000000000: 0
+  chromsizes:
+    Test_seq: 450060