| Previous changeset 0:b797e13169a0 (2016-12-16) Next changeset 2:b8e32e577597 (2016-12-24) |
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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9 |
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modified:
evaluation.py test-data/RESULTS/1.cluster.all test-data/RESULTS/2.cluster.all test-data/RESULTS/partitions/final_partition.used_cmsearch |
| b |
| diff -r b797e13169a0 -r ed8c7191b322 evaluation.py --- a/evaluation.py Fri Dec 16 07:34:49 2016 -0500 +++ b/evaluation.py Thu Dec 22 09:06:48 2016 -0500 |
| [ |
| @@ -2,12 +2,11 @@ from os import system import re - def sh(script): system("bash -c '%s'" % script) +dataNames = "FASTA/data.names" -dataNames = "FASTA/data.names" listOfClusters = [] listOfClasses = [] cluster_seqs_stats_path = "RESULTS/*.cluster.all" @@ -19,7 +18,7 @@ numberOfClusters += 1 with open(singleFile, "r") as f: for line in f.readlines(): - uniqueId = line.split()[6] + uniqueId = line.split()[7] clustNum = line.split()[1] rnaClass, sep, tail = uniqueId.partition("_") listOfClasses.append(rnaClass) @@ -28,8 +27,7 @@ for line in names.readlines(): fullUniqeId = line.split()[3] rnaClass, sep, tail = fullUniqeId.partition("_") - short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0] - if short_unique == uniqueId: + if fullUniqeId == uniqueId: blackList.append(uniqueId) numberOfClusters += 1 # 1 cluster for all unassigned seqs @@ -37,9 +35,8 @@ for line in names.readlines(): fullUniqeId = line.split()[3] rnaClass, sep, tail = fullUniqeId.partition("_") - short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0] rnaClass, sep, tail = fullUniqeId.partition("_") - if short_unique not in blackList: + if fullUniqeId not in blackList: listOfClasses.append(rnaClass) listOfClusters.append(str(numberOfClusters)) numberOfClusters += 1 # separate cluster for all unassigned seqs |
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| diff -r b797e13169a0 -r ed8c7191b322 test-data/RESULTS/1.cluster.all --- a/test-data/RESULTS/1.cluster.all Fri Dec 16 07:34:49 2016 -0500 +++ b/test-data/RESULTS/1.cluster.all Thu Dec 22 09:06:48 2016 -0500 |
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| @@ -1,33 +1,33 @@ -CLUSTER 1 CM_SCORE 84.9 MODEL 1.1 RF00005_rep.34 -CLUSTER 1 CM_SCORE 84.9 MODEL 1.1 RF00005_rep.3 -CLUSTER 1 CM_SCORE 83.8 MODEL 1.1 RF00005_rep.14 -CLUSTER 1 CM_SCORE 82.5 MODEL 1.1 RF00005_rep.35 -CLUSTER 1 CM_SCORE 82.4 MODEL 1.1 RF00005_rep.31 -CLUSTER 1 CM_SCORE 81.0 MODEL 1.1 RF00005_rep.12 -CLUSTER 1 CM_SCORE 80.9 MODEL 1.1 RF00005_rep.5 -CLUSTER 1 CM_SCORE 78.9 MODEL 1.1 RF00005_rep.21 -CLUSTER 1 CM_SCORE 76.6 MODEL 1.1 RF00005_rep.1 -CLUSTER 1 CM_SCORE 76.3 MODEL 1.1 RF00005_rep.27 -CLUSTER 1 CM_SCORE 74.7 MODEL 1.1 RF00005_rep.20 -CLUSTER 1 CM_SCORE 73.6 MODEL 1.1 RF00005_rep.22 -CLUSTER 1 CM_SCORE 73.3 MODEL 1.1 RF00005_rep.15 -CLUSTER 1 CM_SCORE 72.3 MODEL 1.1 RF00005_rep.33 -CLUSTER 1 CM_SCORE 71.7 MODEL 1.1 RF00005_rep.38 -CLUSTER 1 CM_SCORE 69.3 MODEL 1.1 RF00005_rep.36 -CLUSTER 1 CM_SCORE 21.4 MODEL 1.1 RF00005_rep.41 -CLUSTER 1 CM_SCORE 88.8 CMSEARCH 1.1 RF00005_rep.16 -CLUSTER 1 CM_SCORE 87.5 CMSEARCH 1.1 RF00005_rep.18 -CLUSTER 1 CM_SCORE 84.8 CMSEARCH 1.1 RF00005_rep.17 -CLUSTER 1 CM_SCORE 80.0 CMSEARCH 1.1 RF00005_rep.2 -CLUSTER 1 CM_SCORE 79.6 CMSEARCH 1.1 RF00005_rep.10 -CLUSTER 1 CM_SCORE 79.0 CMSEARCH 1.1 RF00005_rep.28 -CLUSTER 1 CM_SCORE 78.5 CMSEARCH 1.1 RF00005_rep.39 -CLUSTER 1 CM_SCORE 78.4 CMSEARCH 1.1 RF00005_rep.9 -CLUSTER 1 CM_SCORE 76.3 CMSEARCH 1.1 RF00005_rep.25 -CLUSTER 1 CM_SCORE 75.1 CMSEARCH 1.1 RF00005_rep.0 -CLUSTER 1 CM_SCORE 73.3 CMSEARCH 1.1 RF00005_rep.24 -CLUSTER 1 CM_SCORE 69.4 CMSEARCH 1.1 RF00005_rep.23 -CLUSTER 1 CM_SCORE 69.3 CMSEARCH 1.1 RF00005_rep.4 -CLUSTER 1 CM_SCORE 47.8 CMSEARCH 1.1 RF00005_rep.26 -CLUSTER 1 CM_SCORE 45.6 CMSEARCH 1.1 RF00005_rep.19 -CLUSTER 1 CM_SCORE 34.4 CMSEARCH 1.1 RF00005_rep.32 +CLUSTER 1 CM_SCORE 84.9 MODEL 1.1 ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3 +CLUSTER 1 CM_SCORE 84.9 MODEL 1.1 ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34 +CLUSTER 1 CM_SCORE 83.8 MODEL 1.1 ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +CLUSTER 1 CM_SCORE 82.5 MODEL 1.1 ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35 +CLUSTER 1 CM_SCORE 82.4 MODEL 1.1 ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31 +CLUSTER 1 CM_SCORE 81.0 MODEL 1.1 ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +CLUSTER 1 CM_SCORE 80.9 MODEL 1.1 ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5 +CLUSTER 1 CM_SCORE 78.9 MODEL 1.1 ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +CLUSTER 1 CM_SCORE 76.6 MODEL 1.1 ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +CLUSTER 1 CM_SCORE 76.3 MODEL 1.1 ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27 +CLUSTER 1 CM_SCORE 74.7 MODEL 1.1 ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +CLUSTER 1 CM_SCORE 73.6 MODEL 1.1 ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22 +CLUSTER 1 CM_SCORE 73.3 MODEL 1.1 ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +CLUSTER 1 CM_SCORE 72.3 MODEL 1.1 ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33 +CLUSTER 1 CM_SCORE 71.7 MODEL 1.1 ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38 +CLUSTER 1 CM_SCORE 69.3 MODEL 1.1 ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36 +CLUSTER 1 CM_SCORE 21.4 MODEL 1.1 ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41 +CLUSTER 1 CM_SCORE 88.8 CMSEARCH 1.1 ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16 +CLUSTER 1 CM_SCORE 87.5 CMSEARCH 1.1 ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18 +CLUSTER 1 CM_SCORE 84.8 CMSEARCH 1.1 ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17 +CLUSTER 1 CM_SCORE 80.0 CMSEARCH 1.1 ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2 +CLUSTER 1 CM_SCORE 79.6 CMSEARCH 1.1 ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10 +CLUSTER 1 CM_SCORE 79.0 CMSEARCH 1.1 ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28 +CLUSTER 1 CM_SCORE 78.5 CMSEARCH 1.1 ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39 +CLUSTER 1 CM_SCORE 78.4 CMSEARCH 1.1 ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9 +CLUSTER 1 CM_SCORE 76.3 CMSEARCH 1.1 ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25 +CLUSTER 1 CM_SCORE 75.1 CMSEARCH 1.1 ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0 +CLUSTER 1 CM_SCORE 73.3 CMSEARCH 1.1 ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24 +CLUSTER 1 CM_SCORE 69.4 CMSEARCH 1.1 ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23 +CLUSTER 1 CM_SCORE 69.3 CMSEARCH 1.1 ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4 +CLUSTER 1 CM_SCORE 47.8 CMSEARCH 1.1 ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26 +CLUSTER 1 CM_SCORE 45.6 CMSEARCH 1.1 ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19 +CLUSTER 1 CM_SCORE 34.4 CMSEARCH 1.1 ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32 |
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| diff -r b797e13169a0 -r ed8c7191b322 test-data/RESULTS/2.cluster.all --- a/test-data/RESULTS/2.cluster.all Fri Dec 16 07:34:49 2016 -0500 +++ b/test-data/RESULTS/2.cluster.all Thu Dec 22 09:06:48 2016 -0500 |
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| @@ -1,13 +1,13 @@ -CLUSTER 2 CM_SCORE 86.6 MODEL 1.2 RF00641_rep.2 -CLUSTER 2 CM_SCORE 79.8 MODEL 1.2 RF00641_rep.4 -CLUSTER 2 CM_SCORE 76.7 MODEL 1.2 RF00641_rep.12 -CLUSTER 2 CM_SCORE 75.4 MODEL 1.2 RF00641_rep.9 -CLUSTER 2 CM_SCORE 74.4 MODEL 1.2 RF00641_rep.11 -CLUSTER 2 CM_SCORE 73.2 MODEL 1.2 RF00641_rep.5 -CLUSTER 2 CM_SCORE 72.1 MODEL 1.2 RF00641_rep.7 -CLUSTER 2 CM_SCORE 70.3 MODEL 1.2 RF00641_rep.1 -CLUSTER 2 CM_SCORE 69.6 MODEL 1.2 RF00641_rep.6 -CLUSTER 2 CM_SCORE 62.3 MODEL 1.2 RF00641_rep.8 -CLUSTER 2 CM_SCORE 57.6 MODEL 1.2 RF00641_rep.13 -CLUSTER 2 CM_SCORE 81.8 CMSEARCH 1.2 RF00641_rep.0 -CLUSTER 2 CM_SCORE 56.6 CMSEARCH 1.2 RF00641_rep.10 +CLUSTER 2 CM_SCORE 86.6 MODEL 1.2 ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2 +CLUSTER 2 CM_SCORE 79.8 MODEL 1.2 ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4 +CLUSTER 2 CM_SCORE 76.7 MODEL 1.2 ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12 +CLUSTER 2 CM_SCORE 75.4 MODEL 1.2 ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9 +CLUSTER 2 CM_SCORE 74.4 MODEL 1.2 ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11 +CLUSTER 2 CM_SCORE 73.2 MODEL 1.2 ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5 +CLUSTER 2 CM_SCORE 72.1 MODEL 1.2 ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7 +CLUSTER 2 CM_SCORE 70.3 MODEL 1.2 ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1 +CLUSTER 2 CM_SCORE 69.6 MODEL 1.2 ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6 +CLUSTER 2 CM_SCORE 62.3 MODEL 1.2 ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8 +CLUSTER 2 CM_SCORE 57.6 MODEL 1.2 ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13 +CLUSTER 2 CM_SCORE 81.8 CMSEARCH 1.2 ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0 +CLUSTER 2 CM_SCORE 56.6 CMSEARCH 1.2 ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10 |
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| diff -r b797e13169a0 -r ed8c7191b322 test-data/RESULTS/partitions/final_partition.used_cmsearch --- a/test-data/RESULTS/partitions/final_partition.used_cmsearch Fri Dec 16 07:34:49 2016 -0500 +++ b/test-data/RESULTS/partitions/final_partition.used_cmsearch Thu Dec 22 09:06:48 2016 -0500 |
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| @@ -1,2 +1,2 @@ +1.2 1.1 -1.2 |