| Next changeset 1:b022c6591515 (2023-12-03) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench commit 0e21bd630200c1f199db8ba5d83b81d4214fc59f |
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added:
batch_table_wrapper.py macros.xml rbpbench.xml test-data/SLBP_USER.cm test-data/comparison_stats.rbpbench_compare.test.tsv test-data/contingency_table_results.rbpbench_search.tsv test-data/fasta_indexes.loc test-data/in_sites.filtered.rbpbench_search.bed test-data/in_sites.filtered.rbpbench_search.fa test-data/motif_hit_stats.compare_test.clipper_idr.tsv test-data/motif_hit_stats.compare_test.dewseq.tsv test-data/motif_hit_stats.rbpbench_search.slbp_user.tsv test-data/motif_hit_stats.rbpbench_search.tsv test-data/motif_hit_stats.table_test.tsv test-data/motif_hit_stats.test_batch.tsv test-data/motif_hits.rbpbench_batch.table_test.bed test-data/motif_hits.rbpbench_batch.test_batch.bed test-data/motif_hits.rbpbench_compare.test.bed test-data/motif_hits.rbpbench_compare.test.tsv test-data/motif_hits.rbpbench_search.bed test-data/motif_hits.rbpbench_search.test_all.bed test-data/rbp_hit_stats.compare_test.clipper_idr.tsv test-data/rbp_hit_stats.compare_test.dewseq.tsv test-data/rbp_hit_stats.rbpbench_search.slbp_user.tsv test-data/rbp_hit_stats.rbpbench_search.tsv test-data/rbp_hit_stats.table_test.tsv test-data/rbp_hit_stats.test_batch.tsv test-data/report.rbpbench_compare.test.html test-data/report.rbpbench_search.html test-data/test.bed test-data/test.fa test-data/test.slbp_user.bed test-data/test.slbp_user.fa test-data/test1.bed test-data/test2.bed test-data/test_custom.info.txt test-data/test_custom.motif_hits.rbpbench_search.bed test-data/test_custom.seq_motifs.meme test-data/test_custom.str_motifs.cm test-data/test_search.gtf test-data/test_search_gtf.region_annotations.tsv test-data/test_table.txt tool-data/fasta_indexes.loc.sample tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 7dd2835ce566 batch_table_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/batch_table_wrapper.py Sun Dec 03 12:51:54 2023 +0000 |
| [ |
| b'@@ -0,0 +1,242 @@\n+#!/usr/bin/env python3\n+\n+import argparse\n+import os\n+import re\n+import subprocess\n+\n+\n+###############################################################################\n+\n+def setup_argument_parser():\n+ """Setup argparse parser."""\n+ help_description = """\n+ Python wrapper for RBPBench Galaxy wrapper to work with collections of\n+ input BED files (i.e. to process them with rbpbench batch).\n+ """\n+ # Define argument parser.\n+ p = argparse.ArgumentParser(add_help=False,\n+ prog="batch_table_wrapper.py",\n+ description=help_description,\n+ formatter_class=argparse.MetavarTypeHelpFormatter)\n+\n+ # Required arguments.\n+ p.add_argument("-h", "--help",\n+ action="help",\n+ help="Print help message")\n+ p.add_argument("--table",\n+ dest="in_table",\n+ type=str,\n+ metavar=\'str\',\n+ required=True,\n+ help="Input table file with data ID, method ID, RBP ID and file name (Galaxy element identifier in dataset collection) for each to be processed dataset by rbpbench batch")\n+ p.add_argument("--paths",\n+ dest="in_paths",\n+ type=str,\n+ metavar=\'str\',\n+ nargs=\'+\',\n+ required=True,\n+ help="List of Galaxy BED file paths (--files path1 path2 .. )")\n+ p.add_argument("--ids",\n+ dest="in_ids",\n+ type=str,\n+ metavar=\'str\',\n+ nargs=\'+\',\n+ required=True,\n+ help="List of Galaxy element identifiers, equal to the BED dataset names in the dataset collection (--ids id1 id2 .. )")\n+ p.add_argument("--genome",\n+ dest="in_genome",\n+ type=str,\n+ metavar=\'str\',\n+ required=True,\n+ help="Genomic sequences file (currently supported formats: FASTA)")\n+ p.add_argument("--out",\n+ dest="out_folder",\n+ type=str,\n+ metavar=\'str\',\n+ required=True,\n+ help="Batch results output folder")\n+ # Optional batch arguments.\n+ p.add_argument("--ext",\n+ dest="ext_up_down",\n+ type=str,\n+ metavar=\'str\',\n+ default="0",\n+ help="Up- and downstream extension of --in sites in nucleotides (nt). Set e.g. --ext 30 for 30 nt on both sides, or --ext 20,10 for different up- and downstream extension (default: 0)")\n+ p.add_argument("--motif-db",\n+ dest="motif_db",\n+ type=int,\n+ default=1,\n+ choices=[1, 2, 3],\n+ help="Motif database to use. 1: human RBP motifs full (259 RBPs, 605 motifs, human_v0.1), 2: human RBP motifs full (low frequencies not rounded, human_v0.1_no_round), 3: human RBP motifs eCLIP (107 RBPs, 316 motifs, human_eclip_v0.1) (default: 1)")\n+ p.add_argument("--fimo-nt-freqs",\n+ dest="fimo_nt_freqs",\n+ type=str,\n+ metavar=\'str\',\n+ default=False,\n+ help="Provide FIMO nucleotide frequencies (FIMO option: --bifile) file (default: use internal frequencies file optimized for human transcripts)")\n+ p.add_argument("--fimo-pval",\n+ dest="fimo_pval",\n+ type=float,\n+ metavar=\'float\',\n+ default=0.001,\n+ help="FIMO p-value threshold (FIMO option: --thresh) (default: 0.001)")\n+ p.add_argument("--bed-score-col",\n+ dest="bed_score_col",\n+ type=int,\n+ metavar=\'int\',\n+ default=5,\n+ help="--in'..b'rt os.path.exists(path), "--paths %s file not found" % (path)\n+ if path not in paths_dic:\n+ paths_dic[path] = 1\n+ else:\n+ assert False, "--paths %s given > 1. Please provide unique paths" % (path)\n+ paths_list.append(path)\n+\n+ # IDs\n+ ids_dic = {}\n+ ids_list = []\n+ for id in args.in_ids:\n+ if id not in ids_dic:\n+ ids_dic[id] = 1\n+ else:\n+ assert False, "--ids \\"%s\\" given > 1. Please provide unique element identifiers (dataset names) inside the dataset collection, in order to unambiguously assign element ID to file path" % (id)\n+ ids_list.append(id)\n+\n+ id2path_dic = {}\n+ for idx, id in enumerate(ids_list):\n+ path = paths_list[idx]\n+ id2path_dic[id] = path\n+\n+ """\n+ Read in table.\n+\n+ Column format:\n+ rbp_id method_id data_id dataset_name\n+\n+ """\n+\n+ comb_ids_dic = {}\n+ id_collect_dic = {}\n+ id_collect_dic["rbp_id"] = []\n+ id_collect_dic["method_id"] = []\n+ id_collect_dic["data_id"] = []\n+ id_collect_dic["set_name"] = []\n+ id_collect_dic["path"] = [] # Galaxy file path.\n+\n+ print("Read in --table ... ")\n+\n+ with open(args.in_table) as f:\n+ for line in f:\n+\n+ if re.search("^#", line):\n+ continue\n+\n+ cols = line.strip().split("\\t")\n+\n+ assert len(cols) == 4, "line in --table with # cols != 4 (%i) encountered:%s" % (len(cols), line)\n+\n+ rbp_id = cols[0]\n+ method_id = cols[1]\n+ data_id = cols[2]\n+ set_name = cols[3]\n+\n+ if rbp_id == "rbp_id":\n+ continue\n+\n+ comb_id = "%s,%s,%s,%s" % (rbp_id, method_id, data_id, set_name)\n+\n+ if comb_id not in comb_ids_dic:\n+ comb_ids_dic[comb_id] = 1\n+ else:\n+ assert False, "data combination (\\"%s\\") appears > 1 in --table file. Please provide unique combinations for rbpbench batch calculation" % (comb_id)\n+\n+ assert set_name in ids_dic, "given dataset name \\"%s\\" from --table not part of given --ids. Please provide dataset names present in dataset collection" % (set_name)\n+\n+ id_collect_dic["rbp_id"].append(rbp_id)\n+ id_collect_dic["method_id"].append(method_id)\n+ id_collect_dic["data_id"].append(data_id)\n+ id_collect_dic["set_name"].append(set_name)\n+ id_collect_dic["path"].append(id2path_dic[set_name])\n+\n+ f.closed\n+\n+ assert id_collect_dic["rbp_id"], "nothing read in from --table. Please provide non-empty table in correct format (columns: rbp_id method_id data_id dataset_name)"\n+\n+ """\n+ Construct RBPBench batch call.\n+\n+ """\n+\n+ batch_call = "rbpbench batch"\n+ batch_call += " --out %s" % (args.out_folder)\n+ batch_call += " --genome %s" % (args.in_genome)\n+ batch_call += " --ext %s" % (args.ext_up_down)\n+ batch_call += " --motif-db %i" % (args.motif_db)\n+ if args.fimo_nt_freqs:\n+ batch_call += " --fimo-nt-freqs %s" % (args.fimo_nt_freqs)\n+ batch_call += " --fimo-pval %s" % (str(args.fimo_pval))\n+ batch_call += " --bed-score-col %i" % (args.bed_score_col)\n+ if args.unstranded:\n+ batch_call += " --unstranded"\n+ if args.unstranded_ct:\n+ batch_call += " --unstranded-ct"\n+\n+ rbp_ids = (" ").join(id_collect_dic["rbp_id"])\n+ method_ids = (" ").join(id_collect_dic["method_id"])\n+ data_ids = (" ").join(id_collect_dic["data_id"])\n+ paths = (" ").join(id_collect_dic["path"])\n+\n+ batch_call += " --rbp-list %s" % (rbp_ids)\n+ batch_call += " --method-list %s" % (method_ids)\n+ batch_call += " --data-list %s" % (data_ids)\n+ batch_call += " --bed %s" % (paths)\n+\n+ """\n+ Execute RBPBench batch call.\n+ """\n+\n+ print("")\n+ print("EXECUTING CALL:\\n%s" % (batch_call))\n+ output = subprocess.getoutput(batch_call)\n+ print("")\n+ print("RUN OUTPUT:\\n%s" % (output))\n+ print("")\n+ print("DONE.")\n' |
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| diff -r 000000000000 -r 7dd2835ce566 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Dec 03 12:51:54 2023 +0000 |
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| @@ -0,0 +1,40 @@ +<macros> + <token name="@TOOL_VERSION@">0.7</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@profile@">22.05</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rbpbench</requirement> + <requirement type="package" version="5.5.4">meme</requirement> + </requirements> + </xml> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">rbpbench</xref> + </xrefs> + </xml> + <!--xml name="citations"> + <citations> + <citation type="doi"></citation> + </citations> + </xml--> + <token name="@PREPARE_REF@"><![CDATA[ + ln -s -f + #if str($action_type.reference_genome.reference_genome_selector) == "history" + '$action_type.reference_genome.history_genome' + #else + '$action_type.reference_genome.builtin_genome.fields.path' + #end if + reference.fa && + ]]></token> + <token name="@COMMON_PARAMS@"><![CDATA[ + --ext $action_type.search_options.search_ext + --fimo-pval $action_type.search_options.search_fimo_pval + --bed-score-col $action_type.search_options.search_bed_score_col + $action_type.search_options.search_unstranded + $action_type.search_options.search_unstranded_ct + #if $action_type.search_options.fimo_nt_freqs_file: + --fimo-nt-freqs '$action_type.search_options.fimo_nt_freqs_file' + #end if + ]]></token> +</macros> |
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| diff -r 000000000000 -r 7dd2835ce566 rbpbench.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbpbench.xml Sun Dec 03 12:51:54 2023 +0000 |
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| b'@@ -0,0 +1,1003 @@\n+<tool id="rbpbench" name="RBPBench" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">\n+\n+ <description>- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="bio_tools"/>\n+ <expand macro="requirements"/>\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $action_type.action_type_selector == \'search_motifs\':\n+ @PREPARE_REF@\n+ rbpbench search\n+ --in \'$action_type.search_bed_file\'\n+ --out ./\n+ --genome reference.fa\n+ --method-id \'$action_type.search_method_id\'\n+ --data-id \'$action_type.search_data_id\'\n+ --rbps\n+ #if str($action_type.select_db.select_db_selector) == "default_db":\n+ #if str($action_type.select_db.select_rbps.select_rbps_selector) == "list_db_rbps":\n+ #if str($action_type.select_db.select_rbps.database) != "None":\n+ #for $rbp_id in str($action_type.select_db.select_rbps.database).split(\',\'):\n+ $rbp_id\n+ #end for\n+ #end if\n+ #else:\n+ ALL\n+ #end if\n+ #else:\n+ $action_type.select_db.custom_db_rbp_ids_list\n+ #end if\n+\n+ #if str($action_type.user_rbp.user_rbp_selector) == "sequence":\n+ USER\n+ --user-rbp-id $action_type.user_rbp.seq_rbp_id\n+ --user-meme-xml \'$action_type.user_rbp.meme_motifs_xml\'\n+ #elif str($action_type.user_rbp.user_rbp_selector) == "structure":\n+ USER\n+ --user-rbp-id $action_type.user_rbp.str_rbp_id\n+ --user-cm \'$action_type.user_rbp.cm_model_file\'\n+ #end if\n+\n+ #if str($action_type.select_db.select_db_selector) == "custom_db":\n+ --custom-db-id $action_type.select_db.custom_db_id\n+ --custom-db-info $action_type.select_db.custom_db_info_file\n+ #if $action_type.select_db.custom_db_meme_xml_file:\n+ --custom-db-meme-xml \'$action_type.select_db.custom_db_meme_xml_file\'\n+ #end if\n+ #if $action_type.select_db.custom_db_cm_model_file:\n+ --custom-db-cm \'$action_type.select_db.custom_db_cm_model_file\'\n+ #end if\n+ #end if\n+ @COMMON_PARAMS@\n+ #if $action_type.report_plotting_options.set_rbp_id:\n+ --set-rbp-id \'$action_type.report_plotting_options.set_rbp_id\'\n+ #end if\n+ --motif-distance-plot-range $action_type.report_plotting_options.motif_distance_plot_range\n+ --motif-min-pair-count $action_type.report_plotting_options.motif_min_pair_count\n+ --rbp-min-pair-count $action_type.report_plotting_options.rbp_min_pair_count\n+ #if $action_type.report_plotting_options.gtf_file:\n+ --gtf \'$action_type.report_plotting_options.gtf_file\'\n+ #end if\n+ #if $action_type.report_plotting_options.tr_list_file:\n+ --tr-list \'$action_type.report_plotting_options.tr_list_file\'\n+ #end if\n+ #if $action_type.report_plotting_options.list_tr_biotypes:\n+ --tr-types \'$action_type.report_plotting_options.list_tr_biotypes\'\n+ #end if\n+ --upset-plot-min-degree $action_type.report_plotting_options.upset_plot_min_degree\n+ #if $action_type.report_plotting_options.upset_plot_max_degree:\n+ --upset-plot-max-degree \'$action_type'..b'iles to Galaxy and make a dataset collection out of them, \n+the dataset names will correspond to the uploaded file names.\n+In the above table, we would produce search results for three different \n+methods, on three different RBPs. \n+Likewise, if we would want to compare motif search results across cell types, \n+the table could look like this:\n+\n+========== ============ =============== =============================\n+PUM1 method1 K562_eCLIP PUM1.K562_eclip.method1.bed\n+PUM1 method1 HepG2_eCLIP PUM1.HepG2_eclip.method1.bed\n+PUM2 method1 K562_eCLIP PUM2.K562_eclip.method1.bed\n+PUM2 method1 HepG2_eCLIP PUM2.HepG2_eclip.method1.bed\n+SLBP method1 K562_eCLIP SLBP.K562_eclip.method1.bed\n+SLBP method1 HepG2_eCLIP SLBP.HepG2_eclip.method1.bed\n+========== ============ =============== =============================\n+\n+Here we would create motif search results across cell types K562 and HepG2, while keeping the peak calling \n+method ID constant ("method1").\n+As with the two already discussed search modes, \n+the resulting hit statistics output table files (RBP + motif hit statistics) \n+can subsequently serve as inputs to RBPBench\'s comparison mode (*Compare different search results*, section 5).\n+\n+\n+**4. Plot nucleotide distribution at genomic positions**\n+\n+In this mode, a set of genomic regions is input and the nucleotide distribution is plotted \n+around a defined center positions (*Nucleotide distribution plot settings -> Define zero position for plotting*). By default, \n+the upstream end position of each region is used (other choices are center and downstream end).\n+This for example enables us to look at CLIP-seq crosslink positions and potential nucleotide biases at these sites.\n+\n+\n+**5. Compare different search results**\n+\n+This mode is used to compare different motif search results (produced by any of the three motif search modes \n+described above). Inputs are the RBP and motif hit statistics table files output by the motif search modes.\n+As exemplified in the previous sections, the set method IDs and \n+data IDs (together with the selected RBP IDs) define what gets compared in comparison mode.\n+Based on the IDs in the input tables, RBPBench looks for combinations of RBP ID+method ID+data ID, and produces \n+method-ID-centered (with fixed RBP ID + data ID) and / or data-ID-centered (with fixed RBP ID + method ID) comparisons.\n+At least two different IDs are needed for a comparison (e.g. two different method IDs or two different data IDs, with same RBP ID).\n+The comparison results are presented in an HTML report file, containing a hit statistics table and a \n+Venn diagram plot for each found combination. Moreover, the report results are output as table files,\n+and the combined motifs are output in BED format, for a data ID / method ID centered comparison e.g. inside a Genome Viewer.\n+Comparing numbers of unique and shared motif hits between methods also serves as a way of benchmarking different methods.\n+Since no ground truth (i.e., set of true / experimentally verified transcriptome-wide binding sites of an RBP) exists, one obvious way to \n+benchmark peak calling methods is to look at the enrichment of known RBP binding motifs in regions reported by the peak callers.\n+RBPBench makes such evaluations easy, especially by combining modes 2,3, and 5.\n+\n+\n+-----\n+\n+**Tool documentation & repository**\n+\n+For more information (including a webserver tutorial) please visit the RBPBench website:\n+\n+https://backofenlab.github.io/RBPBench\n+\n+\n+The RBPBench repository can be found at:\n+\n+https://github.com/michauhl/RBPBench\n+\n+The GitHub repository hosts the command line version of RBPBench and also includes a \n+comprehensive manual with installation instructions and various usage examples. \n+\n+\n+.. _RBPBench: https://github.com/michauhl/RBPBench\n+.. _documentation: https://github.com/michauhl/RBPBench#hit-statistics-table-files\n+\n+ ]]></help>\n+</tool>\n' |
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| diff -r 000000000000 -r 7dd2835ce566 test-data/SLBP_USER.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SLBP_USER.cm Sun Dec 03 12:51:54 2023 +0000 |
| [ |
| b"@@ -0,0 +1,385 @@\n+INFERNAL1/a [1.1.3 | Nov 2019]\n+NAME Histone3\n+ACC RF00032\n+DESC Histone 3' UTR stem-loop\n+STATES 142\n+NODES 42\n+CLEN 46\n+W 57\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Fri Apr 4 13:03:46 2014\n+COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED\n+COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi CM\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 46\n+EFFN 46.000000\n+CKSUM 471917655\n+NULL 0.000 0.000 0.000 0.000 \n+GA 25.00\n+TC 25.00\n+NC 24.90\n+EFP7GF -8.9961 0.74543\n+ECMLC 0.73248 -4.63583 3.49505 1600000 463131 0.002591\n+ECMGC 0.50982 -9.05666 1.92502 1600000 108029 0.003703\n+ECMLI 0.86412 -1.32523 4.80439 1600000 239617 0.005008\n+ECMGI 0.55516 -6.80684 2.91667 1600000 88393 0.004525\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 4 1 1 57 76 -10.705 -10.912 -0.004 -9.326 \n+ IL 1 1 2 1 4 1 19 64 83 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 3 1 19 63 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 1 ] 1 - c - - -\n+ ML 3 2 3 5 3 1 19 57 76 -11.622 -0.002 -10.276 0.274 0.676 -1.683 -0.183 \n+ D 4 2 3 5 3 0 15 58 76 -6.174 -1.687 -0.566 \n+ IL 5 5 3 5 3 1 18 62 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 2 ] 2 - c - - -\n+ ML 6 5 3 8 3 1 18 56 75 -11.622 -0.002 -10.276 0.562 0.685 -1.974 -0.595 \n+ D 7 5 3 8 3 0 15 57 75 -6.174 -1.687 -0.566 \n+ IL 8 8 3 8 3 1 17 61 79 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 3 ] 3 - A - - -\n+ ML 9 8 3 11 3 1 17 55 74 -11.622 -0.002 -10.276 1.588 -1.105 -4.684 -1.031 \n+ D 10 8 3 11 3 0 14 56 74 -6.174 -1.687 -0.566 \n+ IL 11 11 3 11 3 1 17 60 78 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 4 ] 4 - A - - -\n+ ML 12 11 3 14 3 1 16 54 73 -11.622 -0.002 -10.276 1.035 -0.025 -1.895 -0.517 \n+ D 13 11 3 14 3 0 14 55 73 -6.174 -1.687 -0.566 \n+ IL 14 14 3 14 3 1 16 59 77 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 5 ] 5 - a - - -\n+ ML 15 14 3 17 3 1 15 53 72 -11.923 -0.687 -1.402 0.970 0.662 -4.530 -1.266 \n+ D 16 14 3 17 3 0 14 52 71 -5.620 -0.734 -1.403 \n+ IL 17 17 3 17 3 1 15 55 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 6 ] - 47 - U - -\n+ MR 18 17 3 20 3 1 14 52 71 -11.239 -0.003 -9.556 -1.280 -3.255 -0.399 1.446 \n"..b'0.01098 4.51736 1.09861 0.40547\n+ 25 0.90589 0.99871 2.78941 1.79574 26 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 26 0.37936 2.45545 2.76975 1.78857 27 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03553 6.17794 3.41622 1.46634 0.26236 1.09861 0.40547\n+ 27 2.00288 0.98595 2.07379 1.00440 28 c - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00429 6.14670 6.14670 1.46634 0.26236 0.11900 2.18757\n+ 28 0.58277 2.57844 2.26067 1.34141 29 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 29 2.04103 1.64155 1.24300 0.94698 30 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04224 6.17794 3.23682 1.46634 0.26236 1.09861 0.40547\n+ 30 0.90025 2.40010 2.48509 0.86868 31 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00432 6.14002 6.14002 1.46634 0.26236 0.10040 2.34838\n+ 31 1.14658 1.52988 1.97258 1.11897 32 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 32 0.99477 1.56394 2.34075 1.12508 33 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 33 1.30260 0.91111 1.74486 1.88763 34 c - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 34 0.81644 1.95418 2.55798 1.08218 35 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 35 0.88707 2.68494 1.54697 1.18084 36 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02155 6.17794 3.95035 1.46634 0.26236 1.09861 0.40547\n+ 36 0.88692 1.97884 1.71659 1.30871 37 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00423 6.16062 6.16062 1.46634 0.26236 0.19522 1.72966\n+ 37 0.78649 1.68131 1.71782 1.72051 38 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 38 0.59588 2.08432 1.60986 2.08251 39 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 39 0.76886 1.58017 1.51684 2.19720 40 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02859 6.17794 3.64554 1.46634 0.26236 1.09861 0.40547\n+ 40 0.91147 2.90974 1.18115 1.44117 41 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00426 6.15362 6.15362 1.46634 0.26236 0.14750 1.98676\n+ 41 1.19023 1.82584 1.84655 0.97555 42 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 42 1.35396 2.21010 1.23260 1.07716 43 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 43 1.25472 1.71330 1.50591 1.16232 44 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 44 1.37043 1.66018 2.98397 0.68259 45 U - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 45 1.15612 1.70216 1.15511 1.67140 46 g - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.47997 6.17794 0.96989 1.46634 0.26236 1.09861 0.40547\n+ 46 2.25321 3.55314 1.66807 0.38906 47 U - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00335 5.70132 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/comparison_stats.rbpbench_compare.test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/comparison_stats.rbpbench_compare.test.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +combined_id method_id data_id motif_db rbp_id c_regions c_uniq_motif_hits perc_reg_with_hits perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt +k562_eclip,human_v0.1,PUM1 dewseq_w100_s5 k562_eclip human_v0.1 PUM1 23 24 43.47826086956522 3.2 4.859283255719781 +k562_eclip,human_v0.1,PUM1 clipper_idr k562_eclip human_v0.1 PUM1 32 8 18.75 2.691013935607881 3.8443056222969725 +k562_eclip,human_v0.1,PUM2 dewseq_w100_s5 k562_eclip human_v0.1 PUM2 70 448 92.85714285714286 14.084164436876673 31.46288362946836 +k562_eclip,human_v0.1,PUM2 clipper_idr k562_eclip human_v0.1 PUM2 77 219 76.62337662337663 17.64076214943267 46.88503532434168 |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/contingency_table_results.rbpbench_search.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contingency_table_results.rbpbench_search.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +#rbp_id PUM1 PUM2 +PUM1 1.0 1.0 +PUM2 1.0 1.0 |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa +testid testdbkey testdisplay ${__HERE__}/test.fa \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/in_sites.filtered.rbpbench_search.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_sites.filtered.rbpbench_search.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +chr1 10 80 chr1:10-80(+) 0.0 + |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/in_sites.filtered.rbpbench_search.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_sites.filtered.rbpbench_search.fa Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>chr1:10-80(+) +ACTGGTTGTGATTTGTAGATACTGGCTCTTCTCAGATGAAGTTCCAGGATTATTCATTGAAAAAGGCTGG |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hit_stats.compare_test.clipper_idr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.compare_test.clipper_idr.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| b'@@ -0,0 +1,228 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|
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hit_stats.compare_test.dewseq.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.compare_test.dewseq.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| b'@@ -0,0 +1,584 @@\n+data_id\tmethod_id\trun_id\tmotif_db\tregion_id\trbp_id\tmotif_id\tchr_id\tgen_s\tgen_e\tstrand\tregion_s\tregion_e\tregion_len\tuniq_count\tfimo_score\tfimo_pval\tcms_score\tcms_eval\tinternal_id\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8214212-8214407(+)\tPUM1\tPUM1_1\tchr21\t8214298\t8214304\t+\t86\t92\t195\t1\t8.83838\t0.000473\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8214212-8214407(+)\tPUM1\tPUM1_1\tchr21\t8214324\t8214330\t+\t112\t118\t195\t1\t12.1616\t5.85e-05\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8218652-8218957(+)\tPUM1\tPUM1_1\tchr21\t8218698\t8218704\t+\t46\t52\t305\t1\t11.3232\t0.00018\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8213907-8214127(+)\tPUM1\tPUM1_1\tchr21\t8214075\t8214081\t+\t168\t174\t220\t1\t6.9798\t0.000768\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8217782-8218632(+)\tPUM1\tPUM1_1\tchr21\t8217841\t8217847\t+\t59\t65\t850\t1\t6.9798\t0.000768\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8217782-8218632(+)\tPUM1\tPUM1_1\tchr21\t8217884\t8217890\t+\t102\t108\t850\t1\t11.1515\t0.000238\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8217782-8218632(+)\tPUM1\tPUM1_1\tchr21\t8217961\t8217967\t+\t179\t185\t850\t1\t11.3232\t0.00018\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8217782-8218632(+)\tPUM1\tPUM1_1\tchr21\t8217962\t8217968\t+\t180\t186\t850\t1\t6.9798\t0.000768\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8401688-8401913(+)\tPUM1\tPUM1_1\tchr21\t8401737\t8401743\t+\t49\t55\t225\t1\t11.3232\t0.00018\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397514\t8397520\t+\t11\t17\t220\t1\t11.1515\t0.000238\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397534\t8397540\t+\t31\t37\t220\t1\t9.0101\t0.000415\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397536\t8397542\t+\t33\t39\t220\t1\t12.1616\t5.85e-05\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397540\t8397546\t+\t37\t43\t220\t1\t11.1515\t0.000238\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397544\t8397550\t+\t41\t47\t220\t1\t11.1515\t0.000238\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397554\t8397560\t+\t51\t57\t220\t1\t9.0101\t0.000415\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397556\t8397562\t+\t53\t59\t220\t1\t12.1616\t5.85e-05\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397503-8397723(+)\tPUM1\tPUM1_1\tchr21\t8397680\t8397686\t+\t177\t183\t220\t1\t6.9798\t0.000768\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397243-8397453(+)\tPUM1\tPUM1_1\tchr21\t8397336\t8397342\t+\t93\t99\t210\t1\t8.83838\t0.000473\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:8397243-8397453(+)\tPUM1\tPUM1_1\tchr21\t8397362\t8397368\t+\t119\t125\t210\t1\t12.1616\t5.85e-05\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:43687515-43687745(+)\tPUM1\tPUM1_1\tchr21\t43687623\t43687629\t+\t108\t114\t230\t1\t9.0101\t0.000415\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:32764357-32764462(-)\tPUM1\tPUM1_2\tchr21\t32764358\t32764366\t-\t97\t105\t105\t1\t6.31313\t0.000191\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:36375527-36375647(+)\tPUM1\tPUM1_2\tchr21\t36375632\t36375640\t+\t105\t113\t120\t1\t-2.35354\t0.000906\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:36375527-36375647(+)\tPUM1\tPUM1_3\tchr21\t36375534\t36375541\t+\t7\t14\t120\t1\t12.5354\t6.6e-05\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:36375527-36375647(+)\tPUM1\tPUM1_3\tchr21\t36375556\t36375563\t+\t29\t36\t120\t1\t4.61616\t0.000739\t-\t-\tMVuT5ext\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:5240799-5240909(-)\tPUM2\tPUM2_1\tchr21\t5240861\t5240868\t-\t42\t49\t110\t1\t14.2121\t3.34e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:14371114-14371439(-)\tPU'..b'0\t1\t12.9394\t1.5e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:38823273-38823463(+)\tPUM2\tPUM2_5\tchr21\t38823411\t38823420\t+\t138\t147\t190\t1\t8.33333\t0.00049\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:39175448-39175648(-)\tPUM2\tPUM2_5\tchr21\t39175591\t39175600\t-\t49\t58\t200\t1\t8.66667\t0.000419\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:39175448-39175648(-)\tPUM2\tPUM2_5\tchr21\t39175562\t39175571\t-\t78\t87\t200\t1\t11.3434\t7.4e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:39175448-39175648(-)\tPUM2\tPUM2_5\tchr21\t39175515\t39175524\t-\t125\t134\t200\t1\t10.1616\t0.000175\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:39175448-39175648(-)\tPUM2\tPUM2_5\tchr21\t39175463\t39175472\t-\t177\t186\t200\t1\t10.1111\t0.000186\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:41988240-41988435(-)\tPUM2\tPUM2_5\tchr21\t41988361\t41988370\t-\t66\t75\t195\t1\t11.1515\t8.53e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:41988240-41988435(-)\tPUM2\tPUM2_5\tchr21\t41988342\t41988351\t-\t85\t94\t195\t1\t9.05051\t0.000345\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:41988240-41988435(-)\tPUM2\tPUM2_5\tchr21\t41988257\t41988266\t-\t170\t179\t195\t1\t8.60606\t0.000427\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:43693279-43693514(+)\tPUM2\tPUM2_5\tchr21\t43693399\t43693408\t+\t120\t129\t235\t1\t7.35354\t0.00076\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:43693279-43693514(+)\tPUM2\tPUM2_5\tchr21\t43693415\t43693424\t+\t136\t145\t235\t1\t12.2929\t3.08e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:43760950-43761125(+)\tPUM2\tPUM2_5\tchr21\t43761042\t43761051\t+\t92\t101\t175\t1\t12.1515\t3.69e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:43982948-43983178(+)\tPUM2\tPUM2_5\tchr21\t43983057\t43983066\t+\t109\t118\t230\t1\t12.1717\t3.39e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:44805616-44805856(-)\tPUM2\tPUM2_5\tchr21\t44805799\t44805808\t-\t49\t58\t240\t1\t6.82828\t0.000958\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:44805616-44805856(-)\tPUM2\tPUM2_5\tchr21\t44805668\t44805677\t-\t180\t189\t240\t1\t13.6061\t6.92e-06\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:44861162-44861271(-)\tPUM2\tPUM2_5\tchr21\t44861192\t44861201\t-\t71\t80\t109\t1\t13.0505\t1.29e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:45512427-45512547(+)\tPUM2\tPUM2_5\tchr21\t45512511\t45512520\t+\t84\t93\t120\t1\t8.51515\t0.000442\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:45602615-45602770(+)\tPUM2\tPUM2_5\tchr21\t45602619\t45602628\t+\t4\t13\t155\t1\t7.25253\t0.000803\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:45602615-45602770(+)\tPUM2\tPUM2_5\tchr21\t45602697\t45602706\t+\t82\t91\t155\t1\t12.1515\t3.69e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:45602615-45602770(+)\tPUM2\tPUM2_5\tchr21\t45602706\t45602715\t+\t91\t100\t155\t1\t7.77778\t0.00064\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:45602615-45602770(+)\tPUM2\tPUM2_5\tchr21\t45602731\t45602740\t+\t116\t125\t155\t1\t10.1717\t0.000174\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:46324121-46324226(+)\tPUM2\tPUM2_5\tchr21\t46324156\t46324165\t+\t35\t44\t105\t1\t11.1212\t8.74e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:46569284-46569479(+)\tPUM2\tPUM2_5\tchr21\t46569299\t46569308\t+\t15\t24\t195\t1\t6.81818\t0.00096\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:46569284-46569479(+)\tPUM2\tPUM2_5\tchr21\t46569388\t46569397\t+\t104\t113\t195\t1\t11.5051\t6.62e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:46569554-46569659(+)\tPUM2\tPUM2_5\tchr21\t46569555\t46569564\t+\t1\t10\t105\t1\t9.0101\t0.000356\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:46569554-46569659(+)\tPUM2\tPUM2_5\tchr21\t46569592\t46569601\t+\t38\t47\t105\t1\t11.2222\t8.1e-05\t-\t-\t-sbAn7Po\n+k562_eclip\tdewseq_w100_s5\trun_id\thuman_v0.1\tchr21:46569554-46569659(+)\tPUM2\tPUM2_5\tchr21\t46569649\t46569658\t+\t95\t104\t105\t1\t10.1919\t0.000172\t-\t-\t-sbAn7Po\n' |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hit_stats.rbpbench_search.slbp_user.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.rbpbench_search.slbp_user.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +data_id method_id run_id user chr1:50-113(+) SLBP_USER RF00032 chr1 89 113 + 39 63 63 1 - - 27.8 1.5e-08 RuDIjV1k |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hit_stats.rbpbench_search.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.rbpbench_search.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM1 PUM1_3 chr1 24 31 + 14 21 70 1 12.8182 4.87e-05 - - h2FelLqa +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_1 chr1 24 31 + 14 21 70 1 10.404 0.000113 - - HcD7_nJz +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_3 chr1 24 31 + 14 21 70 1 6.20202 0.000212 - - HcD7_nJz +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_4 chr1 24 31 + 14 21 70 1 15.8485 1.64e-05 - - HcD7_nJz +data_id method_id run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_5 chr1 22 31 + 12 21 70 1 10.8788 0.000113 - - HcD7_nJz |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hit_stats.table_test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.table_test.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +did1 mid1 run_id human_v0.1 chr1:10-80(+) PUM1 PUM1_3 chr1 24 31 + 14 21 70 1 12.8182 4.87e-05 - - NInGOqIN +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_1 chr1 24 31 + 14 21 70 1 10.404 0.000113 - - u7eY1SoG +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_3 chr1 24 31 + 14 21 70 1 6.20202 0.000212 - - u7eY1SoG +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_4 chr1 24 31 + 14 21 70 1 15.8485 1.64e-05 - - u7eY1SoG +did2 mid2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_5 chr1 22 31 + 12 21 70 1 10.8788 0.000113 - - u7eY1SoG |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hit_stats.test_batch.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hit_stats.test_batch.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +data_id method_id run_id motif_db region_id rbp_id motif_id chr_id gen_s gen_e strand region_s region_e region_len uniq_count fimo_score fimo_pval cms_score cms_eval internal_id +data-id1 method-id1 run_id human_v0.1 chr1:10-80(+) PUM1 PUM1_3 chr1 24 31 + 14 21 70 1 12.8182 4.87e-05 - - TT41sPJM +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_1 chr1 24 31 + 14 21 70 1 10.404 0.000113 - - -dJ6C0OI +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_3 chr1 24 31 + 14 21 70 1 6.20202 0.000212 - - -dJ6C0OI +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_4 chr1 24 31 + 14 21 70 1 15.8485 1.64e-05 - - -dJ6C0OI +data-id2 method-id2 run_id human_v0.1 chr1:10-80(+) PUM2 PUM2_5 chr1 22 31 + 12 21 70 1 10.8788 0.000113 - - -dJ6C0OI |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hits.rbpbench_batch.table_test.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_batch.table_test.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +chr1 23 31 PUM1,PUM1_3;1;mid1,did1 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;mid2,did2 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;mid2,did2 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;mid2,did2 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;mid2,did2 0 + 10.8788 0.000113 -1.0 -1.0 |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hits.rbpbench_batch.test_batch.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_batch.test_batch.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +chr1 23 31 PUM1,PUM1_3;1;method-id1,data-id1 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method-id2,data-id2 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method-id2,data-id2 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method-id2,data-id2 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method-id2,data-id2 0 + 10.8788 0.000113 -1.0 -1.0 |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hits.rbpbench_compare.test.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_compare.test.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| b'@@ -0,0 +1,479 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UM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t33560581\t33560590\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t33560583\t33560592\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t33560585\t33560594\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t33560587\t33560596\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t34105653\t34105662\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t34098703\t34098712\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t34100072\t34100081\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t34100074\t34100083\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t34100082\t34100091\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t34788319\t34788328\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t34887755\t34887764\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t36375372\t36375381\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t36375532\t36375541\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t36375742\t36375751\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t36375810\t36375819\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t36375812\t36375821\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t36375929\t36375938\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t36376469\t36376478\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t37223447\t37223456\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t37223420\t37223429\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t37515006\t37515015\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t37514620\t37514629\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t37514672\t37514681\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823550\t38823559\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823557\t38823566\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823760\t38823769\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823339\t38823348\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823341\t38823350\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823388\t38823397\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823404\t38823413\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t38823411\t38823420\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t39175591\t39175600\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t39175463\t39175472\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t41988361\t41988370\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t41988342\t41988351\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t41988257\t41988266\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t44805799\t44805808\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t-\n+chr21\t45602619\t45602628\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t46569299\t46569308\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t46569555\t46569564\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t46569592\t46569601\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n+chr21\t46569649\t46569658\tPUM2_5;k562_eclip,human_v0.1,PUM2;dewseq_w100_s5\t0\t+\n' |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hits.rbpbench_compare.test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_compare.test.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| b'@@ -0,0 +1,480 @@\n+combined_id\tmotif_hit_id\tmethod_data_ids_with_hit\n+k562_eclip,human_v0.1,PUM1\tchr21:43687623-43687629(+),PUM1_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397362-8397368(+),PUM1_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8215042-8215048(+),PUM1_1\tclipper_idr\n+k562_eclip,human_v0.1,PUM1\tchr21:8215045-8215051(+),PUM1_1\tclipper_idr\n+k562_eclip,human_v0.1,PUM1\tchr21:8215075-8215081(+),PUM1_1\tclipper_idr\n+k562_eclip,human_v0.1,PUM1\tchr21:8214324-8214330(+),PUM1_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:36375632-36375640(+),PUM1_2\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:32764358-32764366(-),PUM1_2\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8214298-8214304(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8218698-8218704(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8214075-8214081(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8217841-8217847(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8217884-8217890(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8217961-8217967(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8217962-8217968(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8401737-8401743(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397514-8397520(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397534-8397540(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397536-8397542(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397540-8397546(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397544-8397550(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397554-8397560(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397556-8397562(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397680-8397686(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:8397336-8397342(+),PUM1_1\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:36375534-36375541(+),PUM1_3\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM1\tchr21:36375556-36375563(+),PUM1_3\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:14371170-14371177(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:14371168-14371175(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:14371143-14371150(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:32734896-32734903(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:32734887-32734894(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:32734055-32734062(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:32734041-32734048(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:14961325-14961332(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:28945911-28945918(-),PUM2_1\tclipper_idr\n+k562_eclip,human_v0.1,PUM2\tchr21:33576754-33576761(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33576671-33576678(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33576685-33576692(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33576643-33576650(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36376310-36376317(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36376312-36376319(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:37223459-37223466(-),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:37203027-37203034(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:46569382-46569389(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36375544-36375551(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560605-33560612(+),PUM2_1\tclipper_idr,dewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:14485730-14485737(-),PUM2_1\tclipper_idr,dewse'..b'_eclip,human_v0.1,PUM2\tchr21:33450622-33450631(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33524156-33524165(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33524135-33524144(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33576725-33576734(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33558869-33558878(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33558892-33558901(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560565-33560574(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560567-33560576(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560569-33560578(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560575-33560584(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560581-33560590(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560583-33560592(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560585-33560594(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:33560587-33560596(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:34105653-34105662(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:34098703-34098712(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:34100072-34100081(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:34100074-34100083(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:34100082-34100091(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:34788319-34788328(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:34887755-34887764(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36375372-36375381(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36375532-36375541(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36375742-36375751(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36375810-36375819(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36375812-36375821(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36375929-36375938(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:36376469-36376478(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:37223447-37223456(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:37223420-37223429(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:37515006-37515015(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:37514620-37514629(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:37514672-37514681(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823550-38823559(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823557-38823566(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823760-38823769(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823339-38823348(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823341-38823350(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823388-38823397(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823404-38823413(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:38823411-38823420(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:39175591-39175600(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:39175463-39175472(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:41988361-41988370(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:41988342-41988351(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:41988257-41988266(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:44805799-44805808(-),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:45602619-45602628(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:46569299-46569308(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:46569555-46569564(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:46569592-46569601(+),PUM2_5\tdewseq_w100_s5\n+k562_eclip,human_v0.1,PUM2\tchr21:46569649-46569658(+),PUM2_5\tdewseq_w100_s5\n' |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hits.rbpbench_search.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_search.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +chr1 23 31 PUM1,PUM1_3;1;method_id,data_id 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method_id,data_id 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method_id,data_id 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method_id,data_id 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method_id,data_id 0 + 10.8788 0.000113 -1.0 -1.0 |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/motif_hits.rbpbench_search.test_all.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_hits.rbpbench_search.test_all.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,56 @@ +chr1 66 76 ACIN1,ACIN1_2;1;method_id,data_id 0 + 7.83168 0.000976 -1.0 -1.0 +chr1 35 42 ADAR,ADAR_2;1;method_id,data_id 0 + 7.76761 0.000162 -1.0 -1.0 +chr1 21 28 BUD13,BUD13_4;1;method_id,data_id 0 + 8.50505 0.000528 -1.0 -1.0 +chr1 16 23 CELF6,CELF6_1;1;method_id,data_id 0 + 7.54545 0.000859 -1.0 -1.0 +chr1 20 32 DDX6,DDX6_1;1;method_id,data_id 0 + 11.1616 5.8e-05 -1.0 -1.0 +chr1 47 53 DDX54,DDX54_2;1;method_id,data_id 0 + 10.0101 0.000506 -1.0 -1.0 +chr1 20 31 DGCR8,DGCR8_1;1;method_id,data_id 0 + 10.4646 0.000102 -1.0 -1.0 +chr1 57 64 ELAVL4,ELAVL4_1;1;method_id,data_id 0 + 8.90909 0.000307 -1.0 -1.0 +chr1 31 39 EWSR1,EWSR1_2;1;method_id,data_id 0 + 7.39394 0.000281 -1.0 -1.0 +chr1 25 35 FMR1,FMR1_1;1;method_id,data_id 0 + -1.28283 0.000939 -1.0 -1.0 +chr1 55 62 G3BP2,G3BP2_1;1;method_id,data_id 0 + 10.2323 0.00027 -1.0 -1.0 +chr1 20 29 GPKOW,GPKOW_1;1;method_id,data_id 0 + 7.56566 0.000629 -1.0 -1.0 +chr1 42 49 GPKOW,GPKOW_2;1;method_id,data_id 0 + 7.66337 0.000616 -1.0 -1.0 +chr1 13 20 HNRNPM,HNRNPM_2;1;method_id,data_id 0 + 9.36 0.000225 -1.0 -1.0 +chr1 65 74 LSM11,LSM11_4;1;method_id,data_id 0 + 7.32323 0.000681 -1.0 -1.0 +chr1 43 53 MTPAP,MTPAP_1;1;method_id,data_id 0 + 7.51485 0.000853 -1.0 -1.0 +chr1 65 75 NUP42,NUP42_1;1;method_id,data_id 0 + 7.56566 0.000678 -1.0 -1.0 +chr1 67 74 PABPC1,PABPC1_2;1;method_id,data_id 0 + 8.22 0.000763 -1.0 -1.0 +chr1 69 76 PABPC4,PABPC4_1;1;method_id,data_id 0 + 7.46 0.000936 -1.0 -1.0 +chr1 48 56 PCBP1,PCBP1_3;1;method_id,data_id 0 + 4.08081 0.00076 -1.0 -1.0 +chr1 35 41 PTBP1,PTBP1_5;1;method_id,data_id 0 + 9.37374 0.000653 -1.0 -1.0 +chr1 23 31 PUM1,PUM1_3;1;method_id,data_id 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method_id,data_id 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method_id,data_id 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method_id,data_id 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method_id,data_id 0 + 10.8788 0.000113 -1.0 -1.0 +chr1 35 47 QKI,QKI_4;1;method_id,data_id 0 + -5.90909 0.000181 -1.0 -1.0 +chr1 35 44 RBM5,RBM5_1;1;method_id,data_id 0 + 7.52525 5.21e-05 -1.0 -1.0 +chr1 60 67 RC3H1,RC3H1_2;1;method_id,data_id 0 + 7.76768 0.000997 -1.0 -1.0 +chr1 13 27 TROVE2,TROVE2_2;1;method_id,data_id 0 + -20.1313 0.00042 -1.0 -1.0 +chr1 27 41 TROVE2,TROVE2_2;1;method_id,data_id 0 + -20.1919 0.000704 -1.0 -1.0 +chr1 32 40 TROVE2,TROVE2_5;1;method_id,data_id 0 + 8.83 0.000368 -1.0 -1.0 +chr1 59 72 TROVE2,TROVE2_7;1;method_id,data_id 0 + -12.6061 0.000794 -1.0 -1.0 +chr1 65 76 SAFB2,SAFB2_1;1;method_id,data_id 0 + 6.32 0.00098 -1.0 -1.0 +chr1 67 74 SART3,SART3_1;1;method_id,data_id 0 + 8.22 0.000763 -1.0 -1.0 +chr1 18 29 SF3A3,SF3A3_1;1;method_id,data_id 0 + 7.58416 0.000793 -1.0 -1.0 +chr1 35 46 SF3A3,SF3A3_1;1;method_id,data_id 0 + 10.3168 0.000128 -1.0 -1.0 +chr1 32 40 SF3A3,SF3A3_4;1;method_id,data_id 0 + 9.57 0.000254 -1.0 -1.0 +chr1 22 30 SF3B4,SF3B4_1;1;method_id,data_id 0 + 7.34 0.000985 -1.0 -1.0 +chr1 43 51 SRSF1,SRSF1_4;1;method_id,data_id 0 + 7.93939 0.000678 -1.0 -1.0 +chr1 50 59 SRSF2,SRSF2_8;1;method_id,data_id 0 + 11.4646 5.89e-05 -1.0 -1.0 +chr1 44 53 SRSF4,SRSF4_1;1;method_id,data_id 0 + 8.28283 0.000231 -1.0 -1.0 +chr1 44 52 SRSF5,SRSF5_1;1;method_id,data_id 0 + 3.93939 0.000409 -1.0 -1.0 +chr1 68 76 SRSF5,SRSF5_1;1;method_id,data_id 0 + 10.8081 0.0002 -1.0 -1.0 +chr1 67 78 SRSF7,SRSF7_2;1;method_id,data_id 0 + 7.27723 0.000652 -1.0 -1.0 +chr1 12 21 TAF15,TAF15_3;1;method_id,data_id 0 + 7.19 0.000808 -1.0 -1.0 +chr1 42 51 TRA2A,TRA2A_5;1;method_id,data_id 0 + 7.68317 0.000727 -1.0 -1.0 +chr1 26 33 TUT1,TUT1_1;1;method_id,data_id 0 + 9.56566 0.000191 -1.0 -1.0 +chr1 26 33 TUT1,TUT1_2;1;method_id,data_id 0 + 9.56566 0.000191 -1.0 -1.0 +chr1 36 45 U2AF1,U2AF1_1;1;method_id,data_id 0 + 10.03 0.000165 -1.0 -1.0 +chr1 36 45 U2AF2,U2AF2_1;1;method_id,data_id 0 + 9.9697 0.000192 -1.0 -1.0 +chr1 25 32 UNK,UNK_2;1;method_id,data_id 0 + 7.78 0.000861 -1.0 -1.0 +chr1 60 68 ZFP36,ZFP36_1;1;method_id,data_id 0 + 9.28 0.000317 -1.0 -1.0 +chr1 59 68 ZFP36L2,ZFP36L2_1;1;method_id,data_id 0 + 8.33333 0.000104 -1.0 -1.0 +chr1 59 68 ZFP36L2,ZFP36L2_2;1;method_id,data_id 0 + 8.33333 0.000104 -1.0 -1.0 +chr1 28 46 SLBP,RF00032;1;method_id,data_id 0 + 13.8 4.2e-05 -1.0 -1.0 |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/rbp_hit_stats.compare_test.clipper_idr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.compare_test.clipper_idr.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +k562_eclip clipper_idr run_id human_v0.1 PUM1 32 65.03 61 10 202 2081 2081 6 18.75 8 8 56 2.691013935607881 2.691013935607881 3.8443056222969725 3.8443056222969725 0.12193332097392165 PUM1_1,PUM1_2,PUM1_3 6,2,0 - - pZFAGsHH +k562_eclip clipper_idr run_id human_v0.1 PUM2 77 60.66 55 3 172 4671 4671 59 76.62337662337663 219 219 824 17.64076214943267 17.64076214943267 46.88503532434168 46.88503532434168 0.4736101622265477 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 68,16,39,24,72 - - AJ40lTA6 |
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| diff -r 000000000000 -r 7dd2835ce566 test-data/rbp_hit_stats.compare_test.dewseq.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.compare_test.dewseq.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +k562_eclip dewseq_w100_s5 run_id human_v0.1 PUM1 23 214.74 195 68 850 4939 4750 10 43.47826086956522 24 24 152 3.0775460619558612 3.2 4.859283255719781 5.052631578947368 0.0071490418994820636 PUM1_1,PUM1_2,PUM1_3 20,2,2 - - MVuT5ext +k562_eclip dewseq_w100_s5 run_id human_v0.1 PUM2 70 203.41 187 100 745 14239 12333 65 92.85714285714286 559 448 1737 12.198890371514853 14.084164436876673 31.46288362946836 36.32530608935377 0.9472904311972452 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 138,27,69,48,166 - - -sbAn7Po |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/rbp_hit_stats.rbpbench_search.slbp_user.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.rbpbench_search.slbp_user.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +data_id method_id run_id user SLBP_USER 1 63 63 63 63 63 63 1 100.0 1 1 25 39.682539682539684 39.682539682539684 15.873015873015873 15.873015873015873 1.0 - - RF00032 1 RuDIjV1k |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/rbp_hit_stats.rbpbench_search.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.rbpbench_search.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +data_id method_id run_id human_v0.1 PUM1 1 70 70 70 70 70 70 1 100.0 1 1 8 11.428571428571429 11.428571428571429 14.285714285714285 14.285714285714285 1.0 PUM1_1,PUM1_2,PUM1_3 0,0,1 - - h2FelLqa +data_id method_id run_id human_v0.1 PUM2 1 70 70 70 70 70 70 1 100.0 4 4 10 14.285714285714285 14.285714285714285 57.14285714285714 57.14285714285714 1.0 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 1,0,1,1,1 - - HcD7_nJz |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/rbp_hit_stats.table_test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.table_test.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +did1 mid1 run_id human_v0.1 PUM1 1 70 70 70 70 70 70 1 100.0 1 1 8 11.428571428571429 11.428571428571429 14.285714285714285 14.285714285714285 1.0 PUM1_1,PUM1_2,PUM1_3 0,0,1 - - NInGOqIN +did2 mid2 run_id human_v0.1 PUM2 1 70 70 70 70 70 70 1 100.0 4 4 10 14.285714285714285 14.285714285714285 57.14285714285714 57.14285714285714 1.0 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 1,0,1,1,1 - - u7eY1SoG |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/rbp_hit_stats.test_batch.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rbp_hit_stats.test_batch.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +data_id method_id run_id motif_db rbp_id c_regions mean_reg_len median_reg_len min_reg_len max_reg_len called_reg_size effective_reg_size c_reg_with_hits perc_reg_with_hits c_motif_hits c_uniq_motif_hits c_uniq_motif_nts perc_uniq_motif_nts_cal_reg perc_uniq_motif_nts_eff_reg uniq_motif_hits_cal_1000nt uniq_motif_hits_eff_1000nt wc_pval seq_motif_ids seq_motif_hits str_motif_ids str_motif_hits internal_id +data-id1 method-id1 run_id human_v0.1 PUM1 1 70 70 70 70 70 70 1 100.0 1 1 8 11.428571428571429 11.428571428571429 14.285714285714285 14.285714285714285 1.0 PUM1_1,PUM1_2,PUM1_3 0,0,1 - - TT41sPJM +data-id2 method-id2 run_id human_v0.1 PUM2 1 70 70 70 70 70 70 1 100.0 4 4 10 14.285714285714285 14.285714285714285 57.14285714285714 57.14285714285714 1.0 PUM2_1,PUM2_2,PUM2_3,PUM2_4,PUM2_5 1,0,1,1,1 - - -dJ6C0OI |
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| diff -r 000000000000 -r 7dd2835ce566 test-data/report.rbpbench_compare.test.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.rbpbench_compare.test.html Sun Dec 03 12:51:54 2023 +0000 |
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| @@ -0,0 +1,98 @@ +<p><head> +<title>RBPBench - Motif Search Comparison Report</title></p> +<script src="/home/malong/miniconda3/envs/rbpbench/lib/python3.9/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script> +<p></head></p> +<h1>Comparison Report</h1> +<p>List of available comparison statistics generated +by RBPBench (rbpbench compare):</p> +<ul> +<li><a href="#method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison table</a></li> +<li><a href="#method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison table</a></li> +<li><a href="#method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</a></li> +<li><a href="#method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</a></li> +</ul> +<p> </p> +<h2 id="method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison statistics</h2> +<p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">Method ID</th> +<th style="text-align: center;"># regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">% regions with motifs</th> +<th style="text-align: center;">% motif nucleotides</th> +<th style="text-align: center;"># motif hits per 1000 nt</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">dewseq_w100_s5</td> +<td style="text-align: center;">23</td> +<td style="text-align: center;">24</td> +<td style="text-align: center;">43.48</td> +<td style="text-align: center;">3.20</td> +<td style="text-align: center;">4.86</td> +</tr> +<tr> +<td style="text-align: center;">clipper_idr</td> +<td style="text-align: center;">32</td> +<td style="text-align: center;">8</td> +<td style="text-align: center;">18.75</td> +<td style="text-align: center;">2.69</td> +<td style="text-align: center;">3.84</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>Method ID</strong> -> method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -> number of peak regions used for motif search, <strong># motif hits</strong> -> number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -> percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -> percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -> number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p> +<h2 id="method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison statistics</h2> +<p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">Method ID</th> +<th style="text-align: center;"># regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">% regions with motifs</th> +<th style="text-align: center;">% motif nucleotides</th> +<th style="text-align: center;"># motif hits per 1000 nt</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">dewseq_w100_s5</td> +<td style="text-align: center;">70</td> +<td style="text-align: center;">448</td> +<td style="text-align: center;">92.86</td> +<td style="text-align: center;">14.08</td> +<td style="text-align: center;">31.46</td> +</tr> +<tr> +<td style="text-align: center;">clipper_idr</td> +<td style="text-align: center;">77</td> +<td style="text-align: center;">219</td> +<td style="text-align: center;">76.62</td> +<td style="text-align: center;">17.64</td> +<td style="text-align: center;">46.89</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>Method ID</strong> -> method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -> number of peak regions used for motif search, <strong># motif hits</strong> -> number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -> percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -> percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -> number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p> +<h2 id="method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</h2> +<p>Based on the same combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram. +Any given motif hit can either be found only by one method, or be identified by any set (>=2) of methods (intersection areas).</p> +<p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM1.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM1 +title="dataset comparison plot k562_eclip,human_v0.1,PUM1" width="700" /></p> +<p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM1) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p> +<p> </p> +<h2 id="method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</h2> +<p>Based on the same combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram. +Any given motif hit can either be found only by one method, or be identified by any set (>=2) of methods (intersection areas).</p> +<p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM2.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM2 +title="dataset comparison plot k562_eclip,human_v0.1,PUM2" width="700" /></p> +<p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM2) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p> +<p> </p> |
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| diff -r 000000000000 -r 7dd2835ce566 test-data/report.rbpbench_search.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.rbpbench_search.html Sun Dec 03 12:51:54 2023 +0000 |
| [ |
| @@ -0,0 +1,83 @@ +<p><head> +<title>RBPBench - Search Report</title></p> +<script src="/home/uhlm/Programme/miniconda3/envs/rbpbench/lib/python3.11/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script> +<p></head></p> +<h1>Search report</h1> +<p>List of available statistics and plots generated +by RBPBench (rbpbench search --report):</p> +<ul> +<li><a href="#rbp-enrich-stats">RBP motif enrichment statistics</a></li> +<li><a href="#cooc-heat-map">RBP co-occurrences heat map</a></li> +<li><a href="#corr-heat-map">RBP correlations heat map</a> + </li> +</ul> +<h2 id="rbp-enrich-stats">RBP motif enrichment statistics</h2> +<p><strong>Table:</strong> RBP motif enrichment statistics. Given a score for each genomic region (# input regions = 1), +RBPbench checks whether motifs are enriched +in higher-scoring regions (using Wilcoxon rank-sum test). A low Wilcoxon rank-sum test p-value for a given RBP thus indicates +that higher-scoring regions are more likely to contain motif hits of the respective RBP. NOTE that if scores associated to +input genomic regions are all the same, p-values become meaningless (i.e., they result in p-values of 1.0).</p> +<table class="sortable"> +<thead> +<tr> +<th style="text-align: center;">RBP ID</th> +<th style="text-align: center;"># hit regions</th> +<th style="text-align: center;">% hit regions</th> +<th style="text-align: center;"># motif hits</th> +<th style="text-align: center;">p-value</th> +</tr> +</thead> +<tbody> +<tr> +<td style="text-align: center;">PUM1</td> +<td style="text-align: center;">1</td> +<td style="text-align: center;">100.00</td> +<td style="text-align: center;">1</td> +<td style="text-align: center;">1.0</td> +</tr> +<tr> +<td style="text-align: center;">PUM2</td> +<td style="text-align: center;">1</td> +<td style="text-align: center;">100.00</td> +<td style="text-align: center;">4</td> +<td style="text-align: center;">1.0</td> +</tr> +</tbody> +</table> +<p> + </p> +<p>Column IDs have the following meanings: <strong>RBP ID</strong> -> RBP ID from database or user-defined (typically RBP name), <strong># hit regions</strong> -> number of input genomic regions with motif hits (after filtering and optional extension), <strong>% hit regions</strong> -> percentage of hit regions over all regions (i.e. how many input regions contain >= 1 RBP binding motif), <strong># motif hits</strong> -> number of unique motif hits in input regions (removed double counts), <strong>p-value</strong> -> Wilcoxon rank-sum test p-value.</p> +<h2 id="cooc-heat-map">RBP co-occurrences heat map</h2> +<p>RBP co-occurrences heat map.</p> +<div class=class="container-fluid" style="margin-top:40px"> +<iframe src="html_report_plots/co-occurrence_plot.plotly.html" width="1200" height="1200"></iframe> +</div> + +<p><strong>Figure:</strong> Heat map of co-occurrences (Fisher's exact test p-values) between RBPs. +Legend color: negative logarithm (base 10) of Fisher's exact test p-value. +Hover box: 1) RBP1. 2) RBP2. 3) p-value: Fisher's exact test p-value (calculated based on contingency table between RBP1 and RBP2). +4) RBPs compaired. 5) Counts[]: Contingency table of co-occurrence counts (i.e., number of genomic regions with/without shared motif hits) between compaired RBPs, +with format [[A, B], [C, D]], where +A: RBP1 AND RBP2, +B: NOT RBP1 AND RBP2 +C: RBP1 AND NOT RBP2 +D: NOT RBP1 AND NOT RBP2. </p> +<p> </p> +<h2 id="corr-heat-map">RBP correlations heat map</h2> +<p>RBP correlations heat map.</p> +<div class=class="container-fluid" style="margin-top:40px"> +<iframe src="html_report_plots/correlation_plot.plotly.html" width="1200" height="1200"></iframe> +</div> + +<p><strong>Figure:</strong> Heat map of correlations (Pearson correlation coefficients) between RBPs. +Genomic regions are labelled 1 or 0 (RBP motif present or not), resulting in a vector of 1s and 0s for each RBP. +Correlations are then calculated by comparing vectors for every pair of RBPs. +Legend color: Pearson correlation coefficient. +Hover box: 1) RBP1. 2) RBP2. +3) RBPs compaired. 5) Counts[]: Contingency table of co-occurrence counts (i.e., number of genomic regions with/without shared motif hits) between compaired RBPs, +with format [[A, B], [C, D]], where +A: RBP1 AND RBP2, +B: NOT RBP1 AND RBP2 +C: RBP1 AND NOT RBP2 +D: NOT RBP1 AND NOT RBP2. </p> +<p> </p> |
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| diff -r 000000000000 -r 7dd2835ce566 test-data/test.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +chr1 10 80 PUM1_K562_IDR 0 + |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fa Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>chr1 +TCTTATTAATACTGGTTGTGATTTGTAGATACTGGCTCTTCTCAGATGAAGTTCCAGGATTATTCATTGAAAAAGGCTGGGTACATGAC |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test.slbp_user.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.slbp_user.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +chr1 50 113 SLBP_K562_IDR 0 + |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test.slbp_user.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.slbp_user.fa Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>chr1 +AACATCCAGGCTGTGCTACTGCCCAAGAAGACCGAGAGTCACCACAAGGCCAAAGGCAAATAATGTCTCCATAGAATCACTTTCCAATACAACGGCTCTTTTCAGAGCCACCT |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +chr1 10 80 PUM1_K562_IDR 0 + |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +chr1 10 80 PUM1_K562_IDR 0 + |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test_custom.info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.info.txt Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,10 @@ +RBP_motif_id RBP_name Motif_type Organism +PUM1_1 PUM1 meme_xml human +PUM1_2 PUM1 meme_xml human +PUM1_3 PUM1 meme_xml human +PUM2_1 PUM2 meme_xml human +PUM2_2 PUM2 meme_xml human +PUM2_3 PUM2 meme_xml human +PUM2_4 PUM2 meme_xml human +PUM2_5 PUM2 meme_xml human +RF00032 SLBP cm human |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test_custom.motif_hits.rbpbench_search.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.motif_hits.rbpbench_search.bed Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +chr1 23 31 PUM1,PUM1_3;1;method_id,data_id 0 + 12.8182 4.87e-05 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_1;1;method_id,data_id 0 + 10.404 0.000113 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_3;1;method_id,data_id 0 + 6.20202 0.000212 -1.0 -1.0 +chr1 23 31 PUM2,PUM2_4;1;method_id,data_id 0 + 15.8485 1.64e-05 -1.0 -1.0 +chr1 21 31 PUM2,PUM2_5;1;method_id,data_id 0 + 10.8788 0.000113 -1.0 -1.0 +chr1 28 46 SLBP,RF00032;1;method_id,data_id 0 + 13.8 4.2e-05 -1.0 -1.0 |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test_custom.seq_motifs.meme --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.seq_motifs.meme Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,99 @@ +MEME version 5 + +ALPHABET= ACGT + +strands: + + +Background letter frequencies +A 0.250000 C 0.250000 G 0.250000 T 0.250000 + +MOTIF PUM1_1 +letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 0 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.223900 0.184800 0.212700 0.378600 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.835718 0.164282 + 0.041300 0.041200 0.876300 0.041200 + +MOTIF PUM1_2 +letter-probability matrix: alength= 4 w= 9 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 0.500000 0.500000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.500000 0.000000 0.500000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 0.000000 1.000000 + +MOTIF PUM1_3 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.919505 0.080495 0.000000 0.000000 + 0.145800 0.458500 0.168500 0.227200 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.100031 0.899969 + 0.867950 0.132050 0.000000 0.000000 + +MOTIF PUM2_1 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.397900 0.158200 0.026000 0.417900 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.843493 0.000000 0.000000 0.156507 + +MOTIF PUM2_2 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 1.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 1.000000 0.000000 0.000000 + +MOTIF PUM2_3 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + +MOTIF PUM2_4 +letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 0 + 0.000000 0.000000 0.000000 1.000000 + 0.000000 0.000000 1.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 1.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 1.000000 + 1.000000 0.000000 0.000000 0.000000 + +MOTIF PUM2_5 +letter-probability matrix: alength= 4 w= 10 nsites= 20 E= 0 + 0.253775 0.137486 0.112989 0.495750 + 0.270800 0.141400 0.146600 0.441200 + 0.000000 0.000000 0.000000 1.000000 + 0.072132 0.000000 0.896223 0.031646 + 0.000000 0.000000 0.000000 1.000000 + 0.968974 0.000000 0.031026 0.000000 + 0.232400 0.319800 0.028700 0.419100 + 0.932355 0.000000 0.000000 0.067645 + 0.121986 0.000000 0.173847 0.704167 + 0.517200 0.063500 0.123600 0.295700 + |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test_custom.str_motifs.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_custom.str_motifs.cm Sun Dec 03 12:51:54 2023 +0000 |
| [ |
| b"@@ -0,0 +1,385 @@\n+INFERNAL1/a [1.1.3 | Nov 2019]\n+NAME Histone3\n+ACC RF00032\n+DESC Histone 3' UTR stem-loop\n+STATES 142\n+NODES 42\n+CLEN 46\n+W 57\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Fri Apr 4 13:03:46 2014\n+COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED\n+COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi CM\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 46\n+EFFN 46.000000\n+CKSUM 471917655\n+NULL 0.000 0.000 0.000 0.000 \n+GA 25.00\n+TC 25.00\n+NC 24.90\n+EFP7GF -8.9961 0.74543\n+ECMLC 0.73248 -4.63583 3.49505 1600000 463131 0.002591\n+ECMGC 0.50982 -9.05666 1.92502 1600000 108029 0.003703\n+ECMLI 0.86412 -1.32523 4.80439 1600000 239617 0.005008\n+ECMGI 0.55516 -6.80684 2.91667 1600000 88393 0.004525\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 4 1 1 57 76 -10.705 -10.912 -0.004 -9.326 \n+ IL 1 1 2 1 4 1 19 64 83 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 3 1 19 63 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 1 ] 1 - c - - -\n+ ML 3 2 3 5 3 1 19 57 76 -11.622 -0.002 -10.276 0.274 0.676 -1.683 -0.183 \n+ D 4 2 3 5 3 0 15 58 76 -6.174 -1.687 -0.566 \n+ IL 5 5 3 5 3 1 18 62 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 2 ] 2 - c - - -\n+ ML 6 5 3 8 3 1 18 56 75 -11.622 -0.002 -10.276 0.562 0.685 -1.974 -0.595 \n+ D 7 5 3 8 3 0 15 57 75 -6.174 -1.687 -0.566 \n+ IL 8 8 3 8 3 1 17 61 79 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 3 ] 3 - A - - -\n+ ML 9 8 3 11 3 1 17 55 74 -11.622 -0.002 -10.276 1.588 -1.105 -4.684 -1.031 \n+ D 10 8 3 11 3 0 14 56 74 -6.174 -1.687 -0.566 \n+ IL 11 11 3 11 3 1 17 60 78 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 4 ] 4 - A - - -\n+ ML 12 11 3 14 3 1 16 54 73 -11.622 -0.002 -10.276 1.035 -0.025 -1.895 -0.517 \n+ D 13 11 3 14 3 0 14 55 73 -6.174 -1.687 -0.566 \n+ IL 14 14 3 14 3 1 16 59 77 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 5 ] 5 - a - - -\n+ ML 15 14 3 17 3 1 15 53 72 -11.923 -0.687 -1.402 0.970 0.662 -4.530 -1.266 \n+ D 16 14 3 17 3 0 14 52 71 -5.620 -0.734 -1.403 \n+ IL 17 17 3 17 3 1 15 55 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 6 ] - 47 - U - -\n+ MR 18 17 3 20 3 1 14 52 71 -11.239 -0.003 -9.556 -1.280 -3.255 -0.399 1.446 \n"..b'0.01098 4.51736 1.09861 0.40547\n+ 25 0.90589 0.99871 2.78941 1.79574 26 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 26 0.37936 2.45545 2.76975 1.78857 27 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03553 6.17794 3.41622 1.46634 0.26236 1.09861 0.40547\n+ 27 2.00288 0.98595 2.07379 1.00440 28 c - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00429 6.14670 6.14670 1.46634 0.26236 0.11900 2.18757\n+ 28 0.58277 2.57844 2.26067 1.34141 29 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 29 2.04103 1.64155 1.24300 0.94698 30 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04224 6.17794 3.23682 1.46634 0.26236 1.09861 0.40547\n+ 30 0.90025 2.40010 2.48509 0.86868 31 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00432 6.14002 6.14002 1.46634 0.26236 0.10040 2.34838\n+ 31 1.14658 1.52988 1.97258 1.11897 32 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 32 0.99477 1.56394 2.34075 1.12508 33 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 33 1.30260 0.91111 1.74486 1.88763 34 c - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 34 0.81644 1.95418 2.55798 1.08218 35 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 35 0.88707 2.68494 1.54697 1.18084 36 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02155 6.17794 3.95035 1.46634 0.26236 1.09861 0.40547\n+ 36 0.88692 1.97884 1.71659 1.30871 37 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00423 6.16062 6.16062 1.46634 0.26236 0.19522 1.72966\n+ 37 0.78649 1.68131 1.71782 1.72051 38 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 38 0.59588 2.08432 1.60986 2.08251 39 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 39 0.76886 1.58017 1.51684 2.19720 40 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02859 6.17794 3.64554 1.46634 0.26236 1.09861 0.40547\n+ 40 0.91147 2.90974 1.18115 1.44117 41 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00426 6.15362 6.15362 1.46634 0.26236 0.14750 1.98676\n+ 41 1.19023 1.82584 1.84655 0.97555 42 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 42 1.35396 2.21010 1.23260 1.07716 43 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 43 1.25472 1.71330 1.50591 1.16232 44 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 44 1.37043 1.66018 2.98397 0.68259 45 U - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00416 6.17794 6.17794 1.46634 0.26236 1.09861 0.40547\n+ 45 1.15612 1.70216 1.15511 1.67140 46 g - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.47997 6.17794 0.96989 1.46634 0.26236 1.09861 0.40547\n+ 46 2.25321 3.55314 1.66807 0.38906 47 U - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00335 5.70132 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test_search.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_search.gtf Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,11 @@ +chr1 HAVANA gene 21 60 . + . gene_id "g1"; gene_type "protein_coding"; gene_name "GENE1"; +chr1 HAVANA transcript 21 60 . + . gene_id "g1"; transcript_id "g1_t1"; transcript_type "protein_coding"; gene_type "protein_coding"; transcript_name "g1_t1"; level 1; transcript_support_level "2"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 21 60 . + . gene_id "g1"; transcript_id "g1_t1"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t1-202"; exon_number 1; exon_id "g1_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA CDS 31 44 . + . gene_id "g1"; transcript_id "g1_t1"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t1-202"; exon_number 1; exon_id "g1_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA transcript 21 60 . + . gene_id "g1"; transcript_id "g1_t2"; transcript_type "protein_coding"; gene_type "protein_coding"; transcript_name "g1_t2"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 21 60 . + . gene_id "g1"; transcript_id "g1_t2"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t2-202"; exon_number 1; exon_id "g1_t2_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA CDS 31 44 . + . gene_id "g1"; transcript_id "g1_t2"; gene_type "protein_coding"; gene_name "GENE1"; transcript_type "protein_coding"; transcript_name "g1_t2-202"; exon_number 1; exon_id "g1_t2_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA gene 21 60 . - . gene_id "g2"; gene_type "lncRNA"; gene_name "GENE2"; +chr1 HAVANA transcript 20 60 . - . gene_id "g2"; transcript_id "g2_t1"; transcript_type "lncRNA"; gene_type "lncRNA"; transcript_name "g2_t1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 51 60 . - . gene_id "g2"; transcript_id "g2_t1"; gene_type "lncRNA"; gene_name "GENE1"; transcript_type "lncRNA"; transcript_name "g2_t1-202"; exon_number 1; exon_id "g2_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; +chr1 HAVANA exon 21 40 . - . gene_id "g2"; transcript_id "g2_t1"; gene_type "lncRNA"; gene_name "GENE1"; transcript_type "lncRNA"; transcript_name "g2_t1-202"; exon_number 2; exon_id "g2_t1_e1"; level 1; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test_search_gtf.region_annotations.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_search_gtf.region_annotations.tsv Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +region_id gene_id gene_name transcript_id region_annotation transcript_biotype +chr1:10-80(+) g1 GENE1 g1_t2 3'UTR protein_coding |
| b |
| diff -r 000000000000 -r 7dd2835ce566 test-data/test_table.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_table.txt Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +PUM1 mid1 did1 test1.bed +PUM2 mid2 did2 test2.bed |
| b |
| diff -r 000000000000 -r 7dd2835ce566 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
| b |
| diff -r 000000000000 -r 7dd2835ce566 tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,259 @@ +A1CF +ACIN1 +ACO1 +ADAR +AGGF1 +AGO1 +AGO2 +AKAP1 +AKAP8 +ANKHD1 +AUH +BCCIP +BOLL +BUD13 +CAPRIN1 +CBX7 +CDC40 +CELF1 +CELF2 +CELF4 +CELF5 +CELF6 +CNBP +CNOT4 +CPEB1 +CPEB2 +CPEB4 +CPSF6 +CPSF7 +CSTF2 +CSTF2T +DAZ3 +DAZAP1 +DDX3X +DDX6 +DDX19B +DDX24 +DDX54 +DDX55 +DDX58 +DDX59 +DGCR8 +DKC1 +EFTUD2 +EIF3D +EIF4A3 +EIF4B +EIF4G2 +ELAVL1 +ELAVL2 +ELAVL3 +ELAVL4 +ENOX1 +ERI1 +ESRP1 +ESRP2 +EWSR1 +FAM120A +FASTKD2 +FBL +FIP1L1 +FMR1 +FTO +FUBP1 +FUBP3 +FUS +FXR1 +FXR2 +G3BP1 +G3BP2 +GNL3 +GPKOW +GRSF1 +GRWD1 +GTF2F1 +HLTF +HNRNPA0 +HNRNPA1 +HNRNPA1L2 +HNRNPA2B1 +HNRNPA3 +HNRNPAB +HNRNPC +HNRNPCL1 +HNRNPD +HNRNPDL +HNRNPF +HNRNPH1 +HNRNPH2 +HNRNPK +HNRNPL +HNRNPLL +HNRNPM +HNRNPU +HNRNPUL1 +IFIH1 +IGF2BP1 +IGF2BP2 +IGF2BP3 +IGHMBP2 +ILF2 +ILF3 +KHDRBS1 +KHDRBS2 +KHDRBS3 +KHSRP +LARP4 +LARP4B +LIN28A +LIN28B +LSM11 +MATR3 +MBNL1 +METAP2 +MSI1 +MSI2 +MTPAP +NCBP2 +NELFE +NKRF +NOL12 +NONO +NOP56 +NOP58 +NOVA1 +NOVA2 +NPM1 +NSUN2 +NUMA1 +NUP42 +NXF1 +OAS1 +OBI1 +PABPC1 +PABPC3 +PABPC4 +PABPC5 +PABPN1 +PABPN1L +PARP1 +PCBP1 +PCBP2 +PCBP4 +PPIE +PPIG +PPIL4 +PPRC1 +PRPF8 +PRR3 +PTBP1 +PTBP2 +PTBP3 +PUF60 +PUM1 +PUM2 +QKI +RALY +RALYL +RANGAP1 +RBFOX1 +RBFOX2 +RBFOX3 +RBM3 +RBM4 +RBM4B +RBM5 +RBM6 +RBM8A +RBM10 +RBM14 +RBM15 +RBM15B +RBM22 +RBM23 +RBM24 +RBM25 +RBM28 +RBM39 +RBM41 +RBM42 +RBM45 +RBM46 +RBM47 +RBMS1 +RBMS2 +RBMS3 +RBMX +RBMY1A1 +RC3H1 +TROVE2 +RPS5 +SAFB2 +SAMD4A +SART3 +SF1 +SF3A3 +SF3B4 +SFPQ +SLTM +SMNDC1 +SND1 +SNRNP70 +SNRPA +SNRPB2 +SOX2 +SRP14 +SRP68 +SRRM4 +SRSF1 +SRSF2 +SRSF3 +SRSF4 +SRSF5 +SRSF6 +SRSF7 +SRSF8 +SRSF9 +SRSF10 +SRSF11 +SSB +SUB1 +SUGP2 +SUPV3L1 +SYNCRIP +TAF15 +TARBP2 +TARDBP +TBRG4 +TIA1 +TIAL1 +TNRC6A +TRA2A +TRA2B +TRNAU1AP +TUT1 +U2AF1 +U2AF2 +UCHL5 +UNK +UPF1 +WDR33 +XPO5 +XRCC6 +XRN2 +YBX1 +YBX2 +YBX3 +YTHDC1 +YWHAG +ZC3H10 +ZCRB1 +ZFP36 +ZFP36L2 +ZNF184 +ZNF326 +ZNF622 +ZNF638 +ZRANB2 +SLBP |
| b |
| diff -r 000000000000 -r 7dd2835ce566 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of built-in genome --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> + <!-- IDs table file --> + <table name="rbp_ids_table" comment_char="#"> + <columns>value</columns> + <file path="${__HERE__}/tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7dd2835ce566 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Dec 03 12:51:54 2023 +0000 |
| b |
| @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of built-in genome --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> + <!-- IDs table file --> + <table name="rbp_ids_table" comment_char="#"> + <columns>value</columns> + <file path="${__HERE__}/tool-data/rbp_ids.catrapid.omics.v2.1.human.6plus.txt" /> + </table> +</tables> \ No newline at end of file |