Mercurial > repos > artbio > small_rna_maps

changeset 24:e75a10eba0a6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 0293b0f9b07302ba0b71e7877be1ea7a7ed04718
author artbio
date Sun, 31 Mar 2019 20:58:21 -0400
parents 3ca8113cc758
children 07aa8f928d4b
files small_rna_maps.py small_rna_maps.xml test-data/bed1.bed test-data/bed2.bed test-data/bed3.bed test-data/bed4.bed test-data/bed5.bed test-data/clustering.pdf test-data/clustering.tab test-data/clustering_unstranded.pdf test-data/clustering_unstranded.tab
diffstat 11 files changed, 461 insertions(+), 416 deletions(-) [+]
line wrap: on
line diff
--- a/small_rna_maps.py	Tue Dec 25 06:02:08 2018 -0500
+++ b/small_rna_maps.py	Sun Mar 31 20:58:21 2019 -0400
@@ -146,15 +146,33 @@
                 accumulator = []
                 for coor in F_clust_dic[centcoor]:
                     accumulator.extend(map_dic[(chrom, coor, 'F')])
+                '''
+                compute the offset of the cluster due to
+                size of reads
+                '''
+                last = sorted(F_clust_dic[centcoor])[-1]
+                try:
+                    margin = max(map_dic[(chrom, last, 'F')]) - 1
+                except ValueError:
+                    margin = 0
                 clustered_dic[(chrom, centcoor, 'F')] = [len(accumulator), [
                     F_clust_dic[centcoor][0],
-                    F_clust_dic[centcoor][-1]]]
+                    F_clust_dic[centcoor][-1] + margin]]
             for centcoor in R_clust_dic:
                 accumulator = []
                 for coor in R_clust_dic[centcoor]:
                     accumulator.extend(map_dic[(chrom, coor, 'R')])
+                '''
+                compute the offset of the cluster due to
+                size of reads
+                '''
+                first = sorted(R_clust_dic[centcoor])[0]
+                try:
+                    margin = max(map_dic[(chrom, first, 'R')]) - 1
+                except ValueError:
+                    margin = 0
                 clustered_dic[(chrom, centcoor, 'R')] = [len(accumulator), [
-                    R_clust_dic[centcoor][0],
+                    R_clust_dic[centcoor][0] - margin,
                     R_clust_dic[centcoor][-1]]]
         return clustered_dic
 
--- a/small_rna_maps.xml	Tue Dec 25 06:02:08 2018 -0500
+++ b/small_rna_maps.xml	Sun Mar 31 20:58:21 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.11.1">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.12.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -19,7 +19,6 @@
               sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
               samtools index '$file.element_identifier' &&
           #end for
-          ls -la ./ &&
           python '$__tool_directory__'/small_rna_maps.py
               --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
               #set $labels = list()
--- a/test-data/bed1.bed	Tue Dec 25 06:02:08 2018 -0500
+++ b/test-data/bed1.bed	Sun Mar 31 20:58:21 2019 -0400
@@ -1,84 +1,84 @@
-FBtr0070001	0	1	cluster_1	1	+	1.0
-FBtr0070001	6	18	cluster_2	14	+	1.16666666667
-FBtr0070001	26	34	cluster_3	42	+	5.25
-FBtr0070533	0	1	cluster_4	1	+	1.0
-FBtr0070533	11	38	cluster_5	23	+	0.851851851852
-FBtr0070603	0	42	cluster_6	68	+	1.61904761905
-FBtr0070603	50	56	cluster_7	2	+	0.333333333333
-FBtr0070604	0	1	cluster_8	1	+	1.0
-FBtr0070604	17	22	cluster_9	2	+	0.4
-FBtr0070604	29	32	cluster_10	36	+	12.0
-FBtr0070604	56	57	cluster_11	1	+	1.0
-FBtr0070911	14	15	cluster_12	1	+	1.0
-FBtr0070911	37	38	cluster_13	1	+	1.0
-FBtr0078490	12	18	cluster_14	4	+	0.666666666667
-FBtr0078490	24	28	cluster_15	3	+	0.75
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-FBtr0078580	51	52	cluster_18	2	+	2.0
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-FBtr0079064	0	3	cluster_24	2	+	0.666666666667
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--- a/test-data/bed2.bed	Tue Dec 25 06:02:08 2018 -0500
+++ b/test-data/bed2.bed	Sun Mar 31 20:58:21 2019 -0400
@@ -1,83 +1,83 @@
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-FBtr0080663	49	51	cluster_80	10	.	5.0
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-FBtr0080664	27	38	cluster_82	9	.	0.818181818182
-FBtr0080664	49	56	cluster_83	11	.	1.57142857143
+FBtr0079064	0	23	cluster_24	2	.	0.0869565217391
+FBtr0079064	32	47	cluster_25	1	.	0.0666666666667
+FBtr0079064	51	68	cluster_26	1	.	0.0588235294118
+FBtr0079090	0	28	cluster_27	2	.	0.0714285714286
+FBtr0079090	25	49	cluster_28	1	.	0.0416666666667
+FBtr0079090	32	48	cluster_29	1	.	0.0625
+FBtr0079090	52	76	cluster_30	2	.	0.0833333333333
+FBtr0079338	11	31	cluster_31	5	.	0.25
+FBtr0079338	24	40	cluster_32	1	.	0.0625
+FBtr0079338	41	63	cluster_33	10	.	0.454545454545
+FBtr0079528	0	38	cluster_34	97	.	2.55263157895
+FBtr0079528	27	43	cluster_35	1	.	0.0625
+FBtr0079528	34	54	cluster_36	3	.	0.15
+FBtr0079528	50	65	cluster_37	5	.	0.333333333333
+FBtr0079596	0	33	cluster_38	148	.	4.48484848485
+FBtr0079596	52	73	cluster_39	4	.	0.190476190476
+FBtr0079677	0	23	cluster_40	2	.	0.0869565217391
+FBtr0079677	51	70	cluster_41	2	.	0.105263157895
+FBtr0079690	0	15	cluster_42	1	.	0.0666666666667
+FBtr0079690	21	51	cluster_43	2	.	0.0666666666667
+FBtr0079690	32	49	cluster_44	2	.	0.117647058824
+FBtr0079692	0	23	cluster_45	3	.	0.130434782609
+FBtr0079692	17	35	cluster_46	1	.	0.0555555555556
+FBtr0079692	24	41	cluster_47	1	.	0.0588235294118
+FBtr0079692	31	51	cluster_48	1	.	0.05
+FBtr0079693	0	24	cluster_49	5	.	0.208333333333
+FBtr0079693	24	47	cluster_50	1	.	0.0434782608696
+FBtr0079694	0	25	cluster_51	5	.	0.2
+FBtr0079694	17	36	cluster_52	1	.	0.0526315789474
+FBtr0079694	51	68	cluster_53	1	.	0.0588235294118
+FBtr0079702	0	15	cluster_54	1	.	0.0666666666667
+FBtr0079702	18	36	cluster_55	2	.	0.111111111111
+FBtr0079702	55	70	cluster_56	1	.	0.0666666666667
+FBtr0079728	0	17	cluster_57	2	.	0.117647058824
+FBtr0079728	7	27	cluster_58	1	.	0.05
+FBtr0079728	18	42	cluster_59	1	.	0.0416666666667
+FBtr0079728	32	49	cluster_60	3	.	0.176470588235
+FBtr0079728	55	70	cluster_61	1	.	0.0666666666667
+FBtr0079729	0	15	cluster_62	1	.	0.0666666666667
+FBtr0079729	12	34	cluster_63	1	.	0.0454545454545
+FBtr0079729	51	72	cluster_64	2	.	0.0952380952381
+FBtr0079752	0	24	cluster_65	2	.	0.0833333333333
+FBtr0079752	6	27	cluster_66	2	.	0.0952380952381
+FBtr0079752	32	49	cluster_67	2	.	0.117647058824
+FBtr0079752	51	71	cluster_68	2	.	0.1
+FBtr0079820	44	74	cluster_69	13	.	0.433333333333
+FBtr0080609	0	44	cluster_70	60	.	1.36363636364
+FBtr0080609	41	62	cluster_71	1	.	0.047619047619
+FBtr0080609	50	66	cluster_72	2	.	0.125
+FBtr0080644	0	27	cluster_73	6	.	0.222222222222
+FBtr0080646	0	27	cluster_74	3	.	0.111111111111
+FBtr0080647	0	27	cluster_75	10	.	0.37037037037
+FBtr0080660	0	27	cluster_76	7	.	0.259259259259
+FBtr0080663	0	34	cluster_77	102	.	3.0
+FBtr0080663	25	43	cluster_78	1	.	0.0555555555556
+FBtr0080663	31	47	cluster_79	2	.	0.125
+FBtr0080663	49	70	cluster_80	10	.	0.47619047619
+FBtr0080664	0	35	cluster_81	108	.	3.08571428571
+FBtr0080664	27	52	cluster_82	9	.	0.36
+FBtr0080664	49	71	cluster_83	11	.	0.5
--- a/test-data/bed3.bed	Tue Dec 25 06:02:08 2018 -0500
+++ b/test-data/bed3.bed	Sun Mar 31 20:58:21 2019 -0400
@@ -1,35 +1,84 @@
-FBtr0070001	6	18	cluster_1	14	+	1.16666666667
-FBtr0070001	26	34	cluster_2	42	+	5.25
-FBtr0070533	11	38	cluster_3	23	+	0.851851851852
-FBtr0070603	0	42	cluster_4	68	+	1.61904761905
-FBtr0070603	50	56	cluster_5	2	+	0.333333333333
-FBtr0070604	17	22	cluster_6	2	+	0.4
-FBtr0070604	29	32	cluster_7	36	+	12.0
-FBtr0078490	12	18	cluster_8	4	+	0.666666666667
-FBtr0078490	24	28	cluster_9	3	+	0.75
-FBtr0078580	0	31	cluster_10	1102	+	35.5483870968
-FBtr0078790	41	52	cluster_11	9	+	0.818181818182
-FBtr0079064	0	3	cluster_12	2	+	0.666666666667
-FBtr0079338	11	17	cluster_13	5	+	0.833333333333
-FBtr0079338	41	46	cluster_14	10	+	2.0
-FBtr0079528	0	18	cluster_15	97	+	5.38888888889
-FBtr0079528	34	37	cluster_16	3	+	1.0
-FBtr0079596	0	19	cluster_17	148	+	7.78947368421
-FBtr0079596	52	54	cluster_18	4	+	2.0
-FBtr0079677	0	5	cluster_19	2	+	0.4
-FBtr0079677	51	53	cluster_20	2	+	1.0
-FBtr0079690	21	27	cluster_21	2	+	0.333333333333
-FBtr0079729	51	57	cluster_22	2	+	0.333333333333
-FBtr0079752	6	12	cluster_23	2	+	0.333333333333
-FBtr0079820	44	56	cluster_24	13	+	1.08333333333
-FBtr0080609	0	20	cluster_25	60	+	3.0
-FBtr0080609	50	52	cluster_26	2	+	1.0
-FBtr0080644	0	12	cluster_27	6	+	0.5
-FBtr0080646	0	7	cluster_28	3	+	0.428571428571
-FBtr0080647	0	12	cluster_29	10	+	0.833333333333
-FBtr0080660	0	7	cluster_30	7	+	1.0
-FBtr0080663	0	17	cluster_31	102	+	6.0
-FBtr0080663	49	51	cluster_32	10	+	5.0
-FBtr0080664	0	21	cluster_33	108	+	5.14285714286
-FBtr0080664	27	38	cluster_34	9	+	0.818181818182
-FBtr0080664	49	56	cluster_35	11	+	1.57142857143
+FBtr0070001	0	17	cluster_1	1	+	0.0588235294118
+FBtr0070001	6	33	cluster_2	14	+	0.518518518519
+FBtr0070001	26	53	cluster_3	42	+	1.55555555556
+FBtr0070533	0	15	cluster_4	1	+	0.0666666666667
+FBtr0070533	11	55	cluster_5	23	+	0.522727272727
+FBtr0070603	0	62	cluster_6	68	+	1.09677419355
+FBtr0070603	50	71	cluster_7	2	+	0.0952380952381
+FBtr0070604	0	15	cluster_8	1	+	0.0666666666667
+FBtr0070604	17	40	cluster_9	2	+	0.0869565217391
+FBtr0070604	29	53	cluster_10	36	+	1.5
+FBtr0070604	56	71	cluster_11	1	+	0.0666666666667
+FBtr0070911	14	35	cluster_12	1	+	0.047619047619
+FBtr0070911	37	52	cluster_13	1	+	0.0666666666667
+FBtr0078490	12	32	cluster_14	4	+	0.2
+FBtr0078490	24	50	cluster_15	3	+	0.115384615385
+FBtr0078490	37	55	cluster_16	1	+	0.0555555555556
+FBtr0078580	0	47	cluster_17	1102	+	23.4468085106
+FBtr0078580	51	68	cluster_18	2	+	0.117647058824
+FBtr0078790	0	19	cluster_19	1	+	0.0526315789474
+FBtr0078790	16	32	cluster_20	2	+	0.125
+FBtr0078790	32	55	cluster_21	1	+	0.0434782608696
+FBtr0078790	41	71	cluster_22	9	+	0.3
+FBtr0078790	54	69	cluster_23	1	-	0.0666666666667
+FBtr0079064	0	23	cluster_24	2	+	0.0869565217391
+FBtr0079064	32	47	cluster_25	1	+	0.0666666666667
+FBtr0079064	51	68	cluster_26	1	+	0.0588235294118
+FBtr0079090	0	28	cluster_27	2	+	0.0714285714286
+FBtr0079090	25	49	cluster_28	1	+	0.0416666666667
+FBtr0079090	32	48	cluster_29	1	+	0.0625
+FBtr0079090	52	70	cluster_30	1	+	0.0555555555556
+FBtr0079090	35	56	cluster_31	1	-	0.047619047619
+FBtr0079338	11	31	cluster_32	5	+	0.25
+FBtr0079338	24	40	cluster_33	1	+	0.0625
+FBtr0079338	41	63	cluster_34	10	+	0.454545454545
+FBtr0079528	0	38	cluster_35	97	+	2.55263157895
+FBtr0079528	27	43	cluster_36	1	+	0.0625
+FBtr0079528	34	54	cluster_37	3	+	0.15
+FBtr0079528	50	65	cluster_38	5	+	0.333333333333
+FBtr0079596	0	33	cluster_39	148	+	4.48484848485
+FBtr0079596	52	73	cluster_40	4	+	0.190476190476
+FBtr0079677	0	23	cluster_41	2	+	0.0869565217391
+FBtr0079677	51	70	cluster_42	2	+	0.105263157895
+FBtr0079690	0	15	cluster_43	1	+	0.0666666666667
+FBtr0079690	21	51	cluster_44	2	+	0.0666666666667
+FBtr0079690	32	49	cluster_45	2	+	0.117647058824
+FBtr0079692	0	23	cluster_46	3	+	0.130434782609
+FBtr0079692	17	35	cluster_47	1	+	0.0555555555556
+FBtr0079692	24	41	cluster_48	1	+	0.0588235294118
+FBtr0079692	31	51	cluster_49	1	+	0.05
+FBtr0079693	0	24	cluster_50	5	+	0.208333333333
+FBtr0079693	24	47	cluster_51	1	+	0.0434782608696
+FBtr0079694	0	25	cluster_52	5	+	0.2
+FBtr0079694	17	36	cluster_53	1	+	0.0526315789474
+FBtr0079694	51	68	cluster_54	1	+	0.0588235294118
+FBtr0079702	0	15	cluster_55	1	+	0.0666666666667
+FBtr0079702	18	36	cluster_56	2	+	0.111111111111
+FBtr0079702	55	70	cluster_57	1	+	0.0666666666667
+FBtr0079728	0	17	cluster_58	2	+	0.117647058824
+FBtr0079728	7	27	cluster_59	1	+	0.05
+FBtr0079728	18	42	cluster_60	1	+	0.0416666666667
+FBtr0079728	32	49	cluster_61	3	+	0.176470588235
+FBtr0079728	55	70	cluster_62	1	+	0.0666666666667
+FBtr0079729	0	15	cluster_63	1	+	0.0666666666667
+FBtr0079729	12	34	cluster_64	1	+	0.0454545454545
+FBtr0079729	51	72	cluster_65	2	+	0.0952380952381
+FBtr0079752	0	24	cluster_66	2	+	0.0833333333333
+FBtr0079752	6	27	cluster_67	2	+	0.0952380952381
+FBtr0079752	32	49	cluster_68	2	+	0.117647058824
+FBtr0079752	51	71	cluster_69	2	+	0.1
+FBtr0079820	44	74	cluster_70	13	+	0.433333333333
+FBtr0080609	0	44	cluster_71	60	+	1.36363636364
+FBtr0080609	41	62	cluster_72	1	+	0.047619047619
+FBtr0080609	50	66	cluster_73	2	+	0.125
+FBtr0080644	0	27	cluster_74	6	+	0.222222222222
+FBtr0080646	0	27	cluster_75	3	+	0.111111111111
+FBtr0080647	0	27	cluster_76	10	+	0.37037037037
+FBtr0080660	0	27	cluster_77	7	+	0.259259259259
+FBtr0080663	0	34	cluster_78	102	+	3.0
+FBtr0080663	25	43	cluster_79	1	+	0.0555555555556
+FBtr0080663	31	47	cluster_80	2	+	0.125
+FBtr0080663	49	70	cluster_81	10	+	0.47619047619
+FBtr0080664	0	35	cluster_82	108	+	3.08571428571
+FBtr0080664	27	52	cluster_83	9	+	0.36
+FBtr0080664	49	71	cluster_84	11	+	0.5
--- a/test-data/bed4.bed	Tue Dec 25 06:02:08 2018 -0500
+++ b/test-data/bed4.bed	Sun Mar 31 20:58:21 2019 -0400
@@ -1,15 +1,9 @@
-FBtr0070001	6	18	cluster_1	14	+	1.16666666667
-FBtr0070001	26	34	cluster_2	42	+	5.25
-FBtr0070603	0	42	cluster_3	68	+	1.61904761905
-FBtr0070604	29	32	cluster_4	36	+	12.0
-FBtr0078580	0	31	cluster_5	1102	+	35.5483870968
-FBtr0079338	41	46	cluster_6	10	+	2.0
-FBtr0079528	0	18	cluster_7	97	+	5.38888888889
-FBtr0079596	0	19	cluster_8	148	+	7.78947368421
-FBtr0079596	52	54	cluster_9	4	+	2.0
-FBtr0079820	44	56	cluster_10	13	+	1.08333333333
-FBtr0080609	0	20	cluster_11	60	+	3.0
-FBtr0080663	0	17	cluster_12	102	+	6.0
-FBtr0080663	49	51	cluster_13	10	+	5.0
-FBtr0080664	0	21	cluster_14	108	+	5.14285714286
-FBtr0080664	49	56	cluster_15	11	+	1.57142857143
+FBtr0070001	26	53	cluster_1	42	+	1.55555555556
+FBtr0070603	0	62	cluster_2	68	+	1.09677419355
+FBtr0070604	29	53	cluster_3	36	+	1.5
+FBtr0078580	0	47	cluster_4	1102	+	23.4468085106
+FBtr0079528	0	38	cluster_5	97	+	2.55263157895
+FBtr0079596	0	33	cluster_6	148	+	4.48484848485
+FBtr0080609	0	44	cluster_7	60	+	1.36363636364
+FBtr0080663	0	34	cluster_8	102	+	3.0
+FBtr0080664	0	35	cluster_9	108	+	3.08571428571
--- a/test-data/bed5.bed	Tue Dec 25 06:02:08 2018 -0500
+++ b/test-data/bed5.bed	Sun Mar 31 20:58:21 2019 -0400
@@ -1,30 +1,15 @@
-FBtr0070001	6	18	cluster_1	14	.	1.16666666667
-FBtr0070001	26	34	cluster_2	42	.	5.25
-FBtr0070533	11	38	cluster_3	23	.	0.851851851852
-FBtr0070603	0	42	cluster_4	68	.	1.61904761905
-FBtr0070604	29	32	cluster_5	36	.	12.0
-FBtr0078490	12	18	cluster_6	4	.	0.666666666667
-FBtr0078490	24	28	cluster_7	3	.	0.75
-FBtr0078580	0	31	cluster_8	1102	.	35.5483870968
-FBtr0078790	41	52	cluster_9	9	.	0.818181818182
-FBtr0079064	0	3	cluster_10	2	.	0.666666666667
-FBtr0079090	52	56	cluster_11	2	.	0.5
-FBtr0079338	11	17	cluster_12	5	.	0.833333333333
-FBtr0079338	41	46	cluster_13	10	.	2.0
-FBtr0079528	0	18	cluster_14	97	.	5.38888888889
-FBtr0079528	34	37	cluster_15	3	.	1.0
-FBtr0079596	0	19	cluster_16	148	.	7.78947368421
-FBtr0079596	52	54	cluster_17	4	.	2.0
-FBtr0079677	51	53	cluster_18	2	.	1.0
-FBtr0079820	44	56	cluster_19	13	.	1.08333333333
-FBtr0080609	0	20	cluster_20	60	.	3.0
-FBtr0080609	50	52	cluster_21	2	.	1.0
-FBtr0080644	0	12	cluster_22	6	.	0.5
-FBtr0080646	0	7	cluster_23	3	.	0.428571428571
-FBtr0080647	0	12	cluster_24	10	.	0.833333333333
-FBtr0080660	0	7	cluster_25	7	.	1.0
-FBtr0080663	0	17	cluster_26	102	.	6.0
-FBtr0080663	49	51	cluster_27	10	.	5.0
-FBtr0080664	0	21	cluster_28	108	.	5.14285714286
-FBtr0080664	27	38	cluster_29	9	.	0.818181818182
-FBtr0080664	49	56	cluster_30	11	.	1.57142857143
+FBtr0070001	6	33	cluster_1	14	.	0.518518518519
+FBtr0070001	26	53	cluster_2	42	.	1.55555555556
+FBtr0070533	11	55	cluster_3	23	.	0.522727272727
+FBtr0070603	0	62	cluster_4	68	.	1.09677419355
+FBtr0070604	29	53	cluster_5	36	.	1.5
+FBtr0078580	0	47	cluster_6	1102	.	23.4468085106
+FBtr0079338	41	63	cluster_7	10	.	0.454545454545
+FBtr0079528	0	38	cluster_8	97	.	2.55263157895
+FBtr0079596	0	33	cluster_9	148	.	4.48484848485
+FBtr0079820	44	74	cluster_10	13	.	0.433333333333
+FBtr0080609	0	44	cluster_11	60	.	1.36363636364
+FBtr0080663	0	34	cluster_12	102	.	3.0
+FBtr0080663	49	70	cluster_13	10	.	0.47619047619
+FBtr0080664	0	35	cluster_14	108	.	3.08571428571
+FBtr0080664	49	71	cluster_15	11	.	0.5
Binary file test-data/clustering.pdf has changed
--- a/test-data/clustering.tab	Tue Dec 25 06:02:08 2018 -0500
+++ b/test-data/clustering.tab	Sun Mar 31 20:58:21 2019 -0400
@@ -1,119 +1,119 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
-input1.bam	FBtr0070001	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070001	72	12	F	14	7-18	12	1.16666666667
-input1.bam	FBtr0070001	72	30	F	42	27-34	8	5.25
+input1.bam	FBtr0070001	72	1	F	1	1-17	17	0.0588235294118
+input1.bam	FBtr0070001	72	12	F	14	7-33	27	0.518518518519
+input1.bam	FBtr0070001	72	30	F	42	27-53	27	1.55555555556
 input1.bam	FBtr0070001	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070533	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070533	72	25	F	23	12-38	27	0.851851851852
+input1.bam	FBtr0070533	72	1	F	1	1-15	15	0.0666666666667
+input1.bam	FBtr0070533	72	25	F	23	12-55	44	0.522727272727
 input1.bam	FBtr0070533	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070603	72	21	F	68	1-42	42	1.61904761905
-input1.bam	FBtr0070603	72	53	F	2	51-56	6	0.333333333333
+input1.bam	FBtr0070603	72	21	F	68	1-62	62	1.09677419355
+input1.bam	FBtr0070603	72	53	F	2	51-71	21	0.0952380952381
 input1.bam	FBtr0070603	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070604	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070604	72	20	F	2	18-22	5	0.4
-input1.bam	FBtr0070604	72	31	F	36	30-32	3	12.0
-input1.bam	FBtr0070604	72	57	F	1	57-57	1	1.0
+input1.bam	FBtr0070604	72	1	F	1	1-15	15	0.0666666666667
+input1.bam	FBtr0070604	72	20	F	2	18-40	23	0.0869565217391
+input1.bam	FBtr0070604	72	31	F	36	30-53	24	1.5
+input1.bam	FBtr0070604	72	57	F	1	57-71	15	0.0666666666667
 input1.bam	FBtr0070604	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0070911	73	1	F	0	1-1	1	0.0
-input1.bam	FBtr0070911	73	15	F	1	15-15	1	1.0
-input1.bam	FBtr0070911	73	38	F	1	38-38	1	1.0
+input1.bam	FBtr0070911	73	15	F	1	15-35	21	0.047619047619
+input1.bam	FBtr0070911	73	38	F	1	38-52	15	0.0666666666667
 input1.bam	FBtr0070911	73	73	F	0	73-73	1	0.0
 input1.bam	FBtr0078490	72	1	F	0	1-1	1	0.0
-input1.bam	FBtr0078490	72	15	F	4	13-18	6	0.666666666667
-input1.bam	FBtr0078490	72	26	F	3	25-28	4	0.75
-input1.bam	FBtr0078490	72	38	F	1	38-38	1	1.0
+input1.bam	FBtr0078490	72	15	F	4	13-32	20	0.2
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-input1.bam	FBtr0078580	72	52	F	2	52-52	1	2.0
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-input1.bam	FBtr0079728	72	8	F	1	8-8	1	1.0
-input1.bam	FBtr0079728	72	19	F	1	19-19	1	1.0
-input1.bam	FBtr0079728	72	33	F	3	33-33	1	3.0
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-input1.bam	FBtr0079729	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0079729	72	13	F	1	13-13	1	1.0
-input1.bam	FBtr0079729	72	54	F	2	52-57	6	0.333333333333
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-input1.bam	FBtr0079752	72	1	F	2	1-1	1	2.0
-input1.bam	FBtr0079752	72	9	F	2	7-12	6	0.333333333333
-input1.bam	FBtr0079752	72	33	F	2	33-33	1	2.0
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 input1.bam	FBtr0079820	74	1	F	0	1-1	1	0.0
-input1.bam	FBtr0079820	74	50	F	13	45-56	12	1.08333333333
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-input1.bam	FBtr0080609	72	10	F	60	1-20	20	3.0
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-input1.bam	FBtr0080609	72	51	F	2	51-52	2	1.0
+input1.bam	FBtr0080609	72	10	F	60	1-44	44	1.36363636364
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-input1.bam	FBtr0080644	72	6	F	6	1-12	12	0.5
+input1.bam	FBtr0080644	72	6	F	6	1-27	27	0.222222222222
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-input1.bam	FBtr0080646	72	4	F	3	1-7	7	0.428571428571
+input1.bam	FBtr0080646	72	4	F	3	1-27	27	0.111111111111
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-input1.bam	FBtr0080647	72	6	F	10	1-12	12	0.833333333333
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-input1.bam	FBtr0080660	72	4	F	7	1-7	7	1.0
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-input1.bam	FBtr0080663	71	9	F	102	1-17	17	6.0
-input1.bam	FBtr0080663	71	26	F	1	26-26	1	1.0
-input1.bam	FBtr0080663	71	32	F	2	32-32	1	2.0
-input1.bam	FBtr0080663	71	50	F	10	50-51	2	5.0
+input1.bam	FBtr0080663	71	9	F	102	1-34	34	3.0
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+input1.bam	FBtr0080663	71	32	F	2	32-47	16	0.125
+input1.bam	FBtr0080663	71	50	F	10	50-70	21	0.47619047619
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-input1.bam	FBtr0080664	71	11	F	108	1-21	21	5.14285714286
-input1.bam	FBtr0080664	71	33	F	9	28-38	11	0.818181818182
-input1.bam	FBtr0080664	71	53	F	11	50-56	7	1.57142857143
+input1.bam	FBtr0080664	71	11	F	108	1-35	35	3.08571428571
+input1.bam	FBtr0080664	71	33	F	9	28-52	25	0.36
+input1.bam	FBtr0080664	71	53	F	11	50-71	22	0.5
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Binary file test-data/clustering_unstranded.pdf has changed
--- a/test-data/clustering_unstranded.tab	Tue Dec 25 06:02:08 2018 -0500
+++ b/test-data/clustering_unstranded.tab	Sun Mar 31 20:58:21 2019 -0400
@@ -1,117 +1,117 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
-input1.bam	FBtr0070001	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070001	72	12	F	14	7-18	12	1.16666666667
-input1.bam	FBtr0070001	72	30	F	42	27-34	8	5.25
+input1.bam	FBtr0070001	72	1	F	1	1-17	17	0.0588235294118
+input1.bam	FBtr0070001	72	12	F	14	7-33	27	0.518518518519
+input1.bam	FBtr0070001	72	30	F	42	27-53	27	1.55555555556
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-input1.bam	FBtr0070533	72	1	F	1	1-1	1	1.0
-input1.bam	FBtr0070533	72	25	F	23	12-38	27	0.851851851852
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-input1.bam	FBtr0070603	72	21	F	68	1-42	42	1.61904761905
-input1.bam	FBtr0070603	72	53	F	2	51-56	6	0.333333333333
+input1.bam	FBtr0070603	72	21	F	68	1-62	62	1.09677419355
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-input1.bam	FBtr0070604	72	20	F	2	18-22	5	0.4
-input1.bam	FBtr0070604	72	31	F	36	30-32	3	12.0
-input1.bam	FBtr0070604	72	57	F	1	57-57	1	1.0
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+input1.bam	FBtr0070604	72	31	F	36	30-53	24	1.5
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-input1.bam	FBtr0070911	73	38	F	1	38-38	1	1.0
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-input1.bam	FBtr0078490	72	26	F	3	25-28	4	0.75
-input1.bam	FBtr0078490	72	38	F	1	38-38	1	1.0
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-input1.bam	FBtr0078580	72	16	F	1102	1-31	31	35.5483870968
-input1.bam	FBtr0078580	72	52	F	2	52-52	1	2.0
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-input1.bam	FBtr0078790	73	1	F	1	1-1	1	1.0
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-input1.bam	FBtr0079338	73	14	F	5	12-17	6	0.833333333333
-input1.bam	FBtr0079338	73	25	F	1	25-25	1	1.0
-input1.bam	FBtr0079338	73	44	F	10	42-46	5	2.0
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