| Next changeset 1:90a4a2e7d876 (2017-01-21) |
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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053 |
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added:
NSPDK_candidateClusters.xml NSPDK_sparseVect.xml test-data/1.group.gspan.bz2 test-data/SVECTOR/data.svector test-data/SVECTOR/data.svector.1.fast_cluster test-data/SVECTOR/data.svector.1.fast_cluster_sim test-data/SVECTOR/data.svector.blacklist.1 test-data/data.fasta test-data/data.names test-data/data.svector.1 |
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| diff -r 000000000000 -r 165fe96228be NSPDK_candidateClusters.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NSPDK_candidateClusters.xml Fri Dec 16 07:36:07 2016 -0500 |
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| @@ -0,0 +1,149 @@ +<tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2"> + <requirements> + <requirement type="package" version="0.1">graphclust-wrappers</requirement> + <requirement type="package" version="0.5">perl-array-utils</requirement> + <requirement type="package" version="9.2">nspdk</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + + mkdir -p SVECTOR && + + cp $data_svector SVECTOR/data.svector && + + 'NSPDK_candidateClusters.pl' '$data_fasta' '$data_names' $noCache $ensf $oc $usn $knn $nhf $nspdk_nhf_max $nspdk_nhf_step $GLOBAL_num_clusters $max_rad $max_dist_relations + + #if $iteration_num.iteration_num_selector: + $iteration_num.CI + '$blacklist' + '$final_partition_soft' + '$fast_cluster_last_round' + $iteration_num.GLOBAL_hit_blacklist_overlap + + #else: + 1 + + #end if + +]]> + </command> + <inputs> + <param type="data" name="data_svector" format="zip" /> + <param type="data" name="data_fasta" format="fasta" /> + <param type="data" name="data_names" format="txt" /> + <conditional name="iteration_num"> + <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> + <when value="true"> + <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> + <param type="data" name="blacklist" format="txt" /> + <param type="data" name="final_partition_soft" format="txt" /> + <param type="data" name="fast_cluster_last_round" format="txt" /> + <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" /> + </when> + <when value="false" > + <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param> + </when> + </conditional> + <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/> + <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/> + <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean" + label="Deactivate caching of kernel value computation (-no-cache)" help="to minimize memory usage"/> + <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/> + <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean" + label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/> + <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean" + label=" flag to output clusters (-oc)" help="by default true"/> + <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/> + <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/> + <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " /> + <param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/> + <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " /> + </inputs> + <outputs> + <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" > + <filter> iteration_num['iteration_num_selector'] is False</filter> + </data> + <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" > + <filter> iteration_num['iteration_num_selector'] is False </filter> + </data> + <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" > + <filter> iteration_num['iteration_num_selector'] is False </filter> + </data> + <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" > + <filter> iteration_num['iteration_num_selector'] is True</filter> + </data> + <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" > + <filter> iteration_num['iteration_num_selector'] is True</filter> + </data> + <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" > + <filter> iteration_num['iteration_num_selector'] is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="data_fasta" value="data.fasta"/> + <param name="data_names" value="data.names"/> + <param name="data_svector" value="data.svector.1" ftype="zip" /> + <conditional name="iteration_num"> + <param name="iteration_num_selector" value="false"/> + </conditional> + <param name="noCache" value="-no-cache"/> + <param name="ensf" value="5"/> + <param name="oc" value="-oc"/> + <param name="max_rad" value="3"/> + <param name="max_dist_relations" value="3"/> + <param name="usn" value="-usn"/> + <param name="knn" value="20"/> + <param name="nhf" value="500"/> + <param name="nspdk_nhf_max" value="1000"/> + <param name="nspdk_nhf_step" value="25"/> + <param name="GLOBAL_num_clusters" value="100"/> + <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" /> + <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" /> + <output name="black_list" file="SVECTOR/data.svector.blacklist.1" /> + </test> + </tests> + <help> + <![CDATA[ + +**What it does** + +Copmutes global feature index and returns top dense sets. +The candidate clusters are chosen as the top ranking neighborhoods provided that the size of their overlap +is below a specified threshold. +For more information see *Fast neighborhood subgraph pairwise distance kernel* paper. + + +**Parameters** + ++ **-knn** : <num nearest neighbors> (default: 10) + ++ **-otknn** : flag to output true (i.e. implies full kernel matrix evaluation) k-nearest neighburs (default: 0) + ++ **-oc** : flag to output clusters (default: 0) + ++ **-nhf** : <num hash functions> for the Locality Sensitive Hashing function (default: 250) + ++ **-ensf** : <eccess neighbour size factor> (default: 10) (0 to avoid trimming) + ++ **-usn** : use shared neighbourhood to weight center density (default: 0) + + + ]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts224</citation> + <citation type="bibtex">@inproceedings{costa2010fast, + title={Fast neighborhood subgraph pairwise distance kernel}, + author={Costa, Fabrizio and De Grave, Kurt}, + booktitle={Proceedings of the 26th International Conference on Machine Learning}, + pages={255--262}, + year={2010}, + organization={Omnipress} + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 165fe96228be NSPDK_sparseVect.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NSPDK_sparseVect.xml Fri Dec 16 07:36:07 2016 -0500 |
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| @@ -0,0 +1,66 @@ +<tool id="nspdk_sparse" name="NSPDK_sparseVect" version="9.2"> + <requirements> + <requirement type="package" version="0.1">graphclust-wrappers</requirement> + <requirement type="package" version="9.2">nspdk</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + + + 'NSPDK_sparseVect.pl' '$data_fasta' '$gspan_file' $max_rad $max_dist_relations + +]]> + </command> + <inputs> + <param type="data" name="gspan_file" format="searchgui_archive" /> + <param type="data" name="data_fasta" format="fasta" /> + <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/> + <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/> + </inputs> + <outputs> + <data name="data_svector" format="zip" from_work_dir="SVECTOR/data.svector" label="data_svector"/> + </outputs> + <tests> + <test> + <param name="data_fasta" value="data.fasta"/> + <param name="gspan_file" value="1.group.gspan.bz2" ftype="searchgui_archive"/> + <param name="max_rad" value="3"/> + <param name="max_dist_relations" value="3"/> + <output name="data_svector" file="SVECTOR/data.svector" ftype="zip" /> + </test> + </tests> + <help> + <![CDATA[ + +**What it does** + +Produces an explicit sparse feature encoding. +Integer code for the invariant graph encoding is used as a feature indicator. In this way, +the integer associated to each feature (i.e. each pair or neighborhood subgraphs of radius r whose +roots are at distance d) can be interpreted as the feature key and the (normalized) count of occurrences as its value. +This allows to obtain an explicit feature encoding for a given graph G as a sparse vector in ℝ^m (with a very high dimension m). + +**Parameters** + ++ **-R** <max radius> (default: 1) ++ **-D** <max distance relations> (default: 4) + + + ]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts224</citation> + <citation type="bibtex">@inproceedings{costa2010fast, + title={Fast neighborhood subgraph pairwise distance kernel}, + author={Costa, Fabrizio and De Grave, Kurt}, + booktitle={Proceedings of the 26th International Conference on Machine Learning}, + pages={255--262}, + year={2010}, + organization={Omnipress} + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 165fe96228be test-data/SVECTOR/data.svector.1.fast_cluster --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SVECTOR/data.svector.1.fast_cluster Fri Dec 16 07:36:07 2016 -0500 |
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| diff -r 000000000000 -r 165fe96228be test-data/SVECTOR/data.svector.1.fast_cluster_sim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SVECTOR/data.svector.1.fast_cluster_sim Fri Dec 16 07:36:07 2016 -0500 |
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| b |
| b'@@ -0,0 +1,184 @@\n+>1 SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0\n+GUCUAUGGCCAUACCACCCUGAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGGAAUAUAAGCUGCUGUUGGCU\n+>2 SEQ2#1#118#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001_rep.1\n+CUUUACGGCCACACCACCCUGAACGCACCGGAUCUCGACUGACCUUGAAAGCUAAGCAGGAUCGGGCCUGGUUAGUAUUGGGAUGGCAGACCCCCUGGAAAUACAGGGUGCUGAAGGU\n+>3 SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2\n+GUCUACAGCCAUACCAUCCUGAACAUGCCAGAUCUUGUCUGACCUCUGAAGCUAAGCAGGGUCAAGCCUGGUUAGUACUUGGGAGAAGCUGGUGUGGCUAGACC\n+>4 SEQ4#1#73#+ ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0\n+GGCUCCAUAGCUCAGGGGUUAGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCUU\n+>5 SEQ5#1#72#+ ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10\n+GGUCCCAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGGACCU\n+>6 SEQ6#1#66#+ ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11\n+GUCCUUGUAGUAUAAACUAAUACACCAGUCUUGUAAACCGGAGAUGAAAACCUUUUUCCAAGGACA\n+>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12\n+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA\n+>8 SEQ8#1#70#+ ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13\n+CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAGAACCAACACCUCUUUACAGUGA\n+>9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14\n+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA\n+>10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15\n+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG\n+>11 SEQ11#1#82#+ ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16\n+GCAGCGAUGGCCGAGUGGUUAAGGCGUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG\n+>12 SEQ12#1#82#+ ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17\n+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG\n+>13 SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18\n+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG\n+>14 SEQ14#1#73#+ ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19\n+UAGAUUGAAGCCAGUUGAUUAGGGUGCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUUGGUCUAG\n+>15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1\n+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA\n+>16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20\n+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA\n+>17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21\n+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA\n+>18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22\n+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA\n+>19 SEQ19#1#82#+ ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23\n+GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCA\n+>20 SEQ20#1#72#+ ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24\n+GGGGGUAUAGCUCAGGGGUAGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU\n+>21 SEQ21#1#74#+ ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25\n+GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACG\n+>22 SEQ22#1#72#+ ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26\n+UAGGAUGGGGUGUGAUAGGUGGCACGGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUAGUCCUAG\n+>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27\n+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA\n+>24 SEQ24#1#73#+ ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28\n+CCUUCGAU'..b'7587.1/1-68_70 ORIGHEAD RF00049_rep.1\n+UUGCCAAUGAUGGUUAAGAAUUUCUUCACCGUAAUAAACCAUGUGGUCAGCAUUGCAUCUGAGGCAAA\n+>71 SEQ71#1#76#+ ORIGID RF00049_rep.2_X61923.1/2094-2169_71 ORIGHEAD RF00049_rep.2\n+UAGCAGUCGAUGUCAAAAUUUCUUGGCUCGAAAUUACUGUGAAGAGUAAAAUCGAGCUUUUUAAGAGUGAGUCAGC\n+>72 SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0\n+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA\n+>73 SEQ73#1#126#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618_rep.1\n+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAAGAGCAUGUAGUGAGGGCAGUACUGCUAACGUCUACACAACACACCCACCUCAACUAGAGCUUUGCUUUAGCUUGGUGUAAUUUUUGGAAAA\n+>74 SEQ74#1#127#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618_rep.2\n+ACCAUCCUUUUCUUGGGGUUGCGCUACUGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUGCUUUAUUUUGGUGCAAUUUUUGGAAAA\n+>75 SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3\n+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA\n+>76 SEQ76#1#79#+ ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0\n+GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC\n+>77 SEQ77#1#77#+ ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10\n+GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC\n+>78 SEQ78#1#80#+ ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11\n+GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC\n+>79 SEQ79#1#79#+ ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12\n+GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC\n+>80 SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13\n+GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC\n+>81 SEQ81#1#77#+ ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1\n+GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC\n+>82 SEQ82#1#81#+ ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2\n+GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC\n+>83 SEQ83#1#79#+ ORIGID RF00641_rep.3_AADD01141098.1/2614-2692_83 ORIGHEAD RF00641_rep.3\n+GCUACUUGAAGAGAGGUAAUCCUUCAUGCAUUUGCUUUACUUGCAAUGAUUAUACAAGGGCAGACUCUCUCUGGGGAGC\n+>84 SEQ84#1#79#+ ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4\n+GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU\n+>85 SEQ85#1#79#+ ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5\n+GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC\n+>86 SEQ86#1#79#+ ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6\n+GGUACUUAAGGGGGAGGUGGGCUUUGAAUAAUAAGUUUAUUGACGUGGAAUAUACAAGGGCAAGCUCUCUGUGAGUAUC\n+>87 SEQ87#1#78#+ ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7\n+GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC\n+>88 SEQ88#1#81#+ ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8\n+GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU\n+>89 SEQ89#1#80#+ ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9\n+GGUACUUGGAGAGAUAGUAGACCGUAUAGCGUACGCUUUAUCUGUGACGUAUGUAACACGGUCCACUAACCCUCAGUAUC\n+>90 SEQ90#1#66#+ ORIGID RF00693_rep.0_AADD01093451.1/1636-1571_90 ORIGHEAD RF00693_rep.0\n+AAUCUUAUGGAAACAUUUCUGCACACAAUAAAGAAACUAGUGUACAGAAAUGUUUACUUGUCUAUG\n+>91 SEQ91#1#69#+ ORIGID RF00693_rep.1_AL031669.28/23303-23371_91 ORIGHEAD RF00693_rep.1\n+GGUCUAGUGGAAACAUUUCUGCACAACCAGAAUACUCAAACUAGCAUGAGGAAAGGCUUCUGUAACAGU\n+>92 SEQ92#1#69#+ ORIGID RF00693_rep.2_ABBA01075050.1/41249-41181_92 ORIGHEAD RF00693_rep.2\n+UAUUUCGUGGAUGAUUUCUACACAGACUAGGCCAUAGAAACCAGUGCGUAGAAAUGCUUCUGUUACAUG\n' |
| b |
| diff -r 000000000000 -r 165fe96228be test-data/data.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.names Fri Dec 16 07:36:07 2016 -0500 |
| b |
| @@ -0,0 +1,92 @@ +1 SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0 +2 SEQ2#1#118#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001_rep.1 +3 SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2 +4 SEQ4#1#73#+ ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0 +5 SEQ5#1#72#+ ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10 +6 SEQ6#1#66#+ ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11 +7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +8 SEQ8#1#70#+ ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13 +9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +11 SEQ11#1#82#+ ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16 +12 SEQ12#1#82#+ ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17 +13 SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18 +14 SEQ14#1#73#+ ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19 +15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22 +19 SEQ19#1#82#+ ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23 +20 SEQ20#1#72#+ ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24 +21 SEQ21#1#74#+ ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25 +22 SEQ22#1#72#+ ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26 +23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27 +24 SEQ24#1#73#+ ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28 +25 SEQ25#1#69#+ ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005_rep.29 +26 SEQ26#1#72#+ ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2 +27 SEQ27#1#69#+ ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005_rep.30 +28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31 +29 SEQ29#1#66#+ ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32 +30 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33 +31 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34 +32 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35 +33 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36 +34 SEQ34#1#68#+ ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37 +35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38 +36 SEQ36#1#73#+ ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39 +37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3 +38 SEQ38#1#65#+ ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40 +39 SEQ39#1#69#+ ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41 +40 SEQ40#1#66#+ ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005_rep.42 +41 SEQ41#1#68#+ ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43 +42 SEQ42#1#69#+ ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44 +43 SEQ43#1#71#+ ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45 +44 SEQ44#1#69#+ ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46 +45 SEQ45#1#72#+ ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4 +46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5 +47 SEQ47#1#68#+ ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6 +48 SEQ48#1#71#+ ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7 +49 SEQ49#1#68#+ ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005_rep.8 +50 SEQ50#1#73#+ ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9 +51 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0 +52 SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1 +53 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2 +54 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3 +55 SEQ55#1#113#+ ORIGID RF00019_rep.0_V00584.1/39-151_55 ORIGHEAD RF00019_rep.0 +56 SEQ56#1#95#+ ORIGID RF00019_rep.1_L32608.1/283-377_56 ORIGHEAD RF00019_rep.1 +57 SEQ57#1#102#+ ORIGID RF00019_rep.2_ABBA01033605.1/1707-1808_57 ORIGHEAD RF00019_rep.2 +58 SEQ58#1#84#+ ORIGID RF00019_rep.3_AADD01087475.1/2469-2552_58 ORIGHEAD RF00019_rep.3 +59 SEQ59#1#79#+ ORIGID RF00027_rep.0_AF480570.1/1-79_59 ORIGHEAD RF00027_rep.0 +60 SEQ60#1#87#+ ORIGID RF00027_rep.1_AC048341.22/3536-3622_60 ORIGHEAD RF00027_rep.1 +61 SEQ61#1#76#+ ORIGID RF00027_rep.2_AC018755.3/119936-120011_61 ORIGHEAD RF00027_rep.2 +62 SEQ62#1#62#+ ORIGID RF00031_rep.0_X71973.1/730-791_62 ORIGHEAD RF00031_rep.0 +63 SEQ63#1#68#+ ORIGID RF00031_rep.1_U67171.1/375-442_63 ORIGHEAD RF00031_rep.1 +64 SEQ64#1#62#+ ORIGID RF00031_rep.2_S79854.1/1605-1666_64 ORIGHEAD RF00031_rep.2 +65 SEQ65#1#57#+ ORIGID RF00031_rep.3_X53463.1/847-903_65 ORIGHEAD RF00031_rep.3 +66 SEQ66#1#71#+ ORIGID RF00031_rep.4_AF195141.1/689-759_66 ORIGHEAD RF00031_rep.4 +67 SEQ67#1#66#+ ORIGID RF00031_rep.5_AF093774.1/5851-5916_67 ORIGHEAD RF00031_rep.5 +68 SEQ68#1#64#+ ORIGID RF00031_rep.6_BC003127.1/865-928_68 ORIGHEAD RF00031_rep.6 +69 SEQ69#1#82#+ ORIGID RF00049_rep.0_X52138.1/3930-4011_69 ORIGHEAD RF00049_rep.0 +70 SEQ70#1#68#+ ORIGID RF00049_rep.1_X97587.1/1-68_70 ORIGHEAD RF00049_rep.1 +71 SEQ71#1#76#+ ORIGID RF00049_rep.2_X61923.1/2094-2169_71 ORIGHEAD RF00049_rep.2 +72 SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0 +73 SEQ73#1#126#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618_rep.1 +74 SEQ74#1#127#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618_rep.2 +75 SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3 +76 SEQ76#1#79#+ ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0 +77 SEQ77#1#77#+ ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10 +78 SEQ78#1#80#+ ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11 +79 SEQ79#1#79#+ ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12 +80 SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD 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| b |
| diff -r 000000000000 -r 165fe96228be test-data/data.svector.1 |
| b |
| Binary file test-data/data.svector.1 has changed |