| Next changeset 1:20429f4c1b95 (2020-01-22) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 9bb5f3c8ed8e87ec5652b5bc8bf9c774d5534a1a |
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data/EWSR1_eCLIP_K562_ENCSR887LPK.tar.gz data/FMR1_eCLIP_K562_ENCSR331VNX.tar.gz data/HNRNPC_eCLIP_HepG2_ENCSR550DVK.tar.gz data/HUR_PAR-CLIP_HEK293_Mukherjee.tar.gz data/IGF2BP1-3_PAR-CLIP_HEK293_Hafner.tar.gz data/IGF2BP1-3_PAR-CLIP_HEK293_Hafner_structure.tar.gz data/KHDRBS1_eCLIP_K562_ENCSR628IDK.tar.gz data/KHDRBS1_eCLIP_K562_ENCSR628IDK_structure.tar.gz data/PUM2_PAR-CLIP_HEK293_Hafner.tar.gz data/PUM2_eCLIP_K562_exonized_3utr.tar.gz data/QKI_PAR-CLIP_HEK293_Hafner.tar.gz data/QKI_eCLIP_HepG2_ENCSR570WLM.tar.gz data/QKI_eCLIP_HepG2_ENCSR570WLM_structure.tar.gz graphprot_predict_profile.xml graphprot_predict_profile_wrapper.pl test-data/GraphProt_predict_profile_test_out1.average_profile test-data/GraphProt_predict_profile_test_out1.peak_regions.bed test-data/GraphProt_predict_profile_test_out1.peak_regions_p50.bed test-data/GraphProt_predict_profile_test_out2.average_profile test-data/GraphProt_predict_profile_test_out2.peak_regions.bed test-data/GraphProt_predict_profile_test_out3.average_profile test-data/GraphProt_predict_profile_test_out3.peak_regions.bed test-data/GraphProt_predict_profile_test_out4.average_profile test-data/GraphProt_predict_profile_test_out4.peak_regions.bed test-data/GraphProt_predict_profile_test_out4.peak_regions_p50.bed test-data/structure_test.model test-data/structure_test.params test-data/test.fa test-data/test.model test-data/test.params |
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| diff -r 000000000000 -r 215925e588c4 graphprot_predict_profile.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphprot_predict_profile.xml Fri May 25 12:17:44 2018 -0400 |
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| b'@@ -0,0 +1,227 @@\n+<tool id="graphprot_predict_profile" name="GraphProt predict profile" version="1.1.7">\n+ <description>- Predict RBP binding profiles</description>\n+ <requirements>\n+ <requirement type="package" version="1.1.7">graphprot</requirement>\n+ </requirements>\n+ <command><![CDATA[\n+ #if $select_model.model_selector == \'select_model_from_repo\':\n+ mkdir -p ./model &&\n+ tar -zxvf \'$__tool_directory__/data/${select_model.repo_model}.tar.gz\' -C ./model &&\n+ #end if\n+ perl \'$__tool_directory__/graphprot_predict_profile_wrapper.pl\' \n+ -fasta \'$fasta_file\'\n+ #if $select_model.model_selector == \'select_model_from_history\':\n+ -model \'$select_model.model_file\'\n+ #if $select_model.set_params.set_params_selector == \'supply_params_file\':\n+ -params \'$select_model.set_params.params_file\'\n+ #elif $select_model.set_params.set_params_selector == \'manual_params_setting\':\n+ #if $select_model.set_params.model_type.model_type_selector == \'sequence\':\n+ -onlyseq\n+ #elif $select_model.set_params.model_type.model_type_selector == \'structure\':\n+ -abstraction $select_model.set_params.model_type.gp_abstraction\n+ #end if\n+ -R $select_model.set_params.gp_r\n+ -D $select_model.set_params.gp_d\n+ -bitsize $select_model.set_params.gp_bitsize\n+ -lambda $select_model.set_params.gp_lambda\n+ -epochs $select_model.set_params.gp_epochs\n+ #if $select_model.set_params.gev_options.distr_my\n+ -distr-my $select_model.set_params.gev_options.distr_my\n+ #end if\n+ #if $select_model.set_params.gev_options.distr_sigma\n+ -distr-sigma $select_model.set_params.gev_options.distr_sigma\n+ #end if\n+ #if $select_model.set_params.gev_options.distr_xi\n+ -distr-xi $select_model.set_params.gev_options.distr_xi\n+ #end if\n+ #end if\n+ #elif $select_model.model_selector == \'select_model_from_repo\':\n+ -model \'./model/${select_model.repo_model}.model\'\n+ -params \'./model/${select_model.repo_model}.params\'\n+ #end if\n+ $peak_region_options.p50_output\n+ #if $peak_region_options.merge_dist\n+ -merge-dist $peak_region_options.merge_dist\n+ #end if\n+ #if $peak_region_options.p_val_thr\n+ -thr-p $peak_region_options.p_val_thr\n+ #end if\n+ #if $peak_region_options.score_thr\n+ -thr-sc $peak_region_options.score_thr\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param name="fasta_file" type="data" format="fasta" label="Input FASTA file" argument="-fasta"\n+ help="FASTA file containing sequences to predict binding profiles on"/>\n+\n+ <conditional name="select_model">\n+ <param name="model_selector" type="select" label="Select GraphProt model" \n+ help="Select GraphProt model for binding profile prediction">\n+ <option value="select_model_from_history" selected="true">Select model from history</option>\n+ <option value="select_model_from_repo">Select model from repository</option>\n+ </param>\n+ <when value="select_model_from_history">\n+ <param name="model_file" type="data" format="data" label="GraphProt model file" argument="-model"\n+ help="Predict binding profile for the given GraphProt RBP model"/>\n+ <conditional name="set_params">\n+ <param name="set_params_selector" type="select" label="Set model parameters">\n+ <option value="supply_params_file" selected="true">Select parameter file from history</option>\n+ <option value="manual_params_setting">Manually set mo'..b' <param name="fasta_file" value="test.fa" ftype="fasta"/>\n+ <param name="model_selector" value="select_model_from_history"/>\n+ <param name="model_file" value="structure_test.model"/>\n+ <param name="set_params_selector" value="supply_params_file"/>\n+ <param name="params_file" value="structure_test.params"/>\n+ <param name="model_type_selector" value="structure"/>\n+ <param name="gp_abstraction" value="3"/>\n+ <param name="score_thr" value="2"/>\n+ <output name="average_profile_outfile" file="GraphProt_predict_profile_test_out3.average_profile"/>\n+ <output name="peak_regions_outfile" file="GraphProt_predict_profile_test_out3.peak_regions.bed"/>\n+ </test>\n+ <test>\n+ <param name="fasta_file" value="test.fa" ftype="fasta"/>\n+ <param name="model_selector" value="select_model_from_repo"/>\n+ <param name="repo_model" value="FMR1_eCLIP_K562_ENCSR331VNX"/>\n+ <param name="p50_output" value="True"/>\n+ <output name="average_profile_outfile" file="GraphProt_predict_profile_test_out4.average_profile"/>\n+ <output name="peak_regions_outfile" file="GraphProt_predict_profile_test_out4.peak_regions.bed"/>\n+ <output name="peak_regions_p50_outfile" file="GraphProt_predict_profile_test_out4.peak_regions_p50.bed"/>\n+ </test>\n+\n+ </tests>\n+ <help>\n+\n+Use GraphProt (-action predict_profile) to predict binding profiles for a given RBP model (supplied as .model and .params file) on a given set of FASTA sequences. After predicting position-wise scores, the scores are averaged over small windows (11 nt with averaged score position in center) to smooth out the profiles and peak regions are extracted based on the set thresholds (p-value or score) and merge distance.\n+\n+**Output files**\n+\n+The procedure has three output files (third is optional):\n+\n+1) An average_profile file containing averaged position-scores over all supplied sequences\n+\n+2) A peak regions BED file which contains peak-scoring regions above the supplied threshold (p-value default: 0.05, score default: 0)\n+\n+3) A peak regions BED file using the best average score found in at least 50 % of the positive training sites (p50). NOTE that this requires the p50 score to be given in the .params file, otherwise if set an empty file will be output.\n+\n+**Model selection**\n+\n+The GraphProt model used for profile prediction can either be uploaded to history or chosen from an example collection of models (Select model from repository). For the repository models, the corresponding parameter file is selected automatically, providing all model parameters necessary for prediction and p-value calculation. If you choose to upload a model to the history, it is recommended to use the corresponding .params file for automatically setting the model parameters. Otherwise the model parameters have to be entered manually.\n+\n+**p-value calculation**\n+\n+Signifying the GraphProt scores is done by fitting a generalized extreme value (GEV) distribution on a set of scores derived from 10000 transcript sequences for each GraphProt model. The GEV distribution has three parameters: my (location), sigma (scale), and xi (shape). The fitted parameter values usually are read in from the .params file, but can also be entered manually. Parameter fitting was done in R using the minpack.lm_ package, using the probability density function (PDF) described here_. If no GEV parameter values are specified (either in .params file or manually), p-value calculation for the scores will be skipped and the peak regions will be extracted based on the set threshold score.\n+\n+.. _here: https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution\n+.. _minpack.lm: https://cran.r-project.org/web/packages/minpack.lm\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1186/gb-2014-15-1-r17</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 215925e588c4 graphprot_predict_profile_wrapper.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphprot_predict_profile_wrapper.pl Fri May 25 12:17:44 2018 -0400 |
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| b'@@ -0,0 +1,764 @@\n+#!/usr/bin/perl\n+\n+use strict;\n+use warnings;\n+use Getopt::Long;\n+use Pod::Usage;\n+use Cwd qw(getcwd abs_path);\n+use List::Util qw(sum);\n+\n+=head1 NAME\n+\n+=head1 SYNOPSIS\n+\n+Galaxy wrapper script for GraphProt (-action predict_profile) to compute \n+the binding profile for a given model on a given set of sequences provided \n+in FASTA format. After profile prediction, average profiles get computed, \n+scores signified and binding peak regions extracted. The score signification \n+is done using the provided fitted GEV parameters, either from .params file \n+or manually set. If score threshold is set (-thr-sc), p-value assignment \n+will be skipped and set score threshold will be used to extract peak \n+regions. NOTE: Additional lines .params file are used to store and get \n+GEV parameters, as well as type of model (model_type: sequence|structure).\n+Also, this wrapper currently works for classification mode only.\n+\n+PARAMETERS:\n+\n+ -help|h display help page\n+ -fasta Input FASTA file (option -fasta)\n+ -model Input .model file (option -model)\n+ -params Input .params file\n+ NOTE: uses .params file with additional\n+ parameters\n+ Manually set parameters (below) will override \n+ found settings in .params file\n+ -data-id Data ID (option -prefix)\n+\n+GraphProt model parameters (by default get from .params file):\n+\n+ -onlyseq Set if model is a sequence model\n+ -R GraphProt model R parameter\n+ -D GraphProt model D parameter\n+ -epochs GraphProt model epochs parameter\n+ -lambda GraphProt model lambda parameter\n+ -bitsize GraphProt model bitsize parameter\n+ -abstraction GraphProt model RNAshapes abstraction level \n+ parameter (set for structure models)\n+\n+Peak region extraction parameters:\n+\n+ -thr-sc Score threshold for extracting peak regions\n+ By default p-value of 0.05 is used. If no p-value \n+ calculation possible, -thr-sc is used with default: 0\n+ -thr-p p-value threshold for extracting peak regions\n+ By default, peak regions with p = 0.05 are extracted,\n+ as well as p50 score peak regions (if info given)\n+ Default: 0.05\n+ -merge-dist Maximum merge distance for nearby peak regions\n+ Default: report all non-overlapping regions\n+ -p50-out Output p50 score filtered peak regions BED file\n+ default: false\n+\n+GEV distribution parameters:\n+\n+ -distr-my GEV distribution my parameter for calculating p-values\n+ from scores\n+ -distr-sigma GEV distrubution sigma parameter for calculating \n+ p-values from scores\n+ -distr-xi GEV distribution xi parameter for calculating p-values\n+ from scores\n+ -ap-extlr Used average profile left right extension for \n+ averaging scores, which were used for distribution \n+ fitting. NOTE: usually a value of 5 was used for \n+ for getting GEV distribution and parameters. If you \n+ choose a different value here, calculated p-values \n+ will be wrong!\n+ default : 5\n+\n+\n+=head1 DISCRIPTION\n+\n+5) Write manual\n+6) add output p50 file with NOTE\n+\n+6) put GP into rna_tools\n+\n+NOTE:\n+Additional lines .params file used to store and get gev parameters, as well \n+as type of model (model_type: sequence|structure).\n+\n+Example .params content:\n+epochs: 20\n+lambda: 0.001\n+R: 1\n+D: 4\n+bitsize: 14\n+model_type: sequence\n+#ADDITIONAL MODEL PARAMETERS\n+ap_extlr: 5\n+gev_my: -2.5408\n+gev_sigma: 1.6444\n+gev_xi: -0.1383\n+p50_score: 6.51534 \n+p50_p_val: 0.0009059744 \n+\n+=cut\n+\n+############################\n+# COMMAND LINE CHECKING.\n+####'..b'f, $s, $sc) = (split /\\t/)[0,1,2];\n+ # If file has zero-based positions.\n+ if ($s == 0) {\n+ $zero_pos = 1;\n+ }\n+ # If positions are one-based, make them zero-based.\n+ unless ($zero_pos) {\n+ $s -= 1;\n+ }\n+ # At transcript ends, if in positive region, write and reset.\n+ if ($old_ref ne $ref) {\n+ if ($in eq "Y") {\n+ print OUT "$ref_id\\t$region_s\\t$region_e\\t$end;$best_sc\\t0\\t+\\n";\n+ $in = "N";\n+ }\n+ }\n+ $old_ref = $ref;\n+ # Deal with positive regions.\n+ if ($sc > $min_sc) {\n+ # Start of a positive cluster.\n+ if ($in eq "N") {\n+ $start = $s;\n+ $region_s = $s;\n+ $region_e = $s + 1;\n+ $end = $s + 1;\n+ $best_sc = $sc;\n+ $ref_id = $ref;\n+ $in = "Y";\n+ next;\n+ # Inside a positive cluster.\n+ } elsif ($in eq "Y") {\n+ if ($sc > $best_sc) {\n+ $start = $s;\n+ $end = $s + 1;\n+ $best_sc = $sc;\n+ $ref_id = $ref;\n+ }\n+ $region_e++;\n+ next;\n+ }\n+ } else {\n+ # If we were in positive cluster before.\n+ if ($in eq "Y") {\n+ print OUT "$ref_id\\t$region_s\\t$region_e\\t$end;$best_sc\\t0\\t+\\n";\n+ $in = "N";\n+ }\n+ }\n+ }\n+ # After last line processed.\n+ if ($in eq "Y") {\n+ print OUT "$ref_id\\t$region_s\\t$region_e\\t$end;$best_sc\\t0\\t+\\n";\n+ $in = "N";\n+ }\n+ close IN;\n+ close OUT;\n+ # If merge distance zero (i.e. end of one block is -1 from start of next block).\n+ if ($max_merge_dist == 0) {\n+ qx/cat $temp_bed_file > $peak_regions_bed_file/;\n+ } else {\n+ # Merge nearby regions.\n+ open(IN, $temp_bed_file) or die "Cannot open $temp_bed_file: $!";\n+ open(OUT, \'>\', $peak_regions_bed_file) or die "Cannot open $peak_regions_bed_file: $!";\n+ # For storing current block stats.\n+ my $block_chr = 0;\n+ my ($block_s, $block_e, $block_best_pos, $block_best_sc);\n+ while (<IN>) {\n+ chomp;\n+ my ($chr, $s, $e, $id) = (split /\\t/)[0,1,2,3];\n+ my ($best_pos, $best_sc) = (split /;/, $id);\n+ if ($chr eq $block_chr) {\n+ # If $block_e, $s within merge merge.\n+ if ( ($s - $block_e) <= $max_merge_dist ) {\n+ # Update block stats.\n+ $block_e = $e;\n+ if ($block_best_sc < $best_sc) {\n+ $block_best_sc = $best_sc;\n+ $block_best_pos = $best_pos;\n+ }\n+ } else {\n+ # If $e outside merge range, print block.\n+ print OUT "$block_chr\\t$block_s\\t$block_e\\t$block_best_pos;$block_best_sc\\t0\\t+\\n";\n+ # Store new block.\n+ ($block_chr, $block_s, $block_e, $block_best_pos, $block_best_sc) = ($chr, $s, $e, $best_pos, $best_sc);\n+ }\n+\n+ } else {\n+ # If new chromosome, print last block, otherwise it is the first block.\n+ if ($block_chr) {\n+ print OUT "$block_chr\\t$block_s\\t$block_e\\t$block_best_pos;$block_best_sc\\t0\\t+\\n";\n+ }\n+ ($block_chr, $block_s, $block_e, $block_best_pos, $block_best_sc) = ($chr, $s, $e, $best_pos, $best_sc);\n+ }\n+ \n+ }\n+ # Print last block.\n+ if ($block_chr) {\n+ print OUT "$block_chr\\t$block_s\\t$block_e\\t$block_best_pos;$block_best_sc\\t0\\t+\\n";\n+ }\n+ close OUT;\n+ close IN;\n+ }\n+ qx/rm -f $temp_bed_file/;\n+}\n+\n+\n+################################################################################\n+\n+\n+\n' |
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| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out1.average_profile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out1.average_profile Fri May 25 12:17:44 2018 -0400 |
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| b'@@ -0,0 +1,4532 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|
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out1.peak_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out1.peak_regions.bed Fri May 25 12:17:44 2018 -0400 |
| b |
| @@ -0,0 +1,41 @@ +ENST00000620398 40 55 48;5.28355;0.00042667 0 + +ENST00000620398 345 350 348;1.96970;0.03127996 0 + +ENST00000620398 366 374 371;2.99552;0.01071062 0 + +ENST00000620398 399 409 406;3.74594;0.00433045 0 + +ENST00000620398 500 502 502;1.84967;0.03508185 0 + +ENST00000620398 565 574 570;4.55760;0.00139889 0 + +ENST00000620398 634 642 637;3.61150;0.00513819 0 + +ENST00000620398 771 777 776;2.10449;0.02743062 0 + +ENST00000550775 28 47 39;5.51074;0.00028155 0 + +ENST00000550775 164 168 166;1.87947;0.03410347 0 + +ENST00000550775 193 201 198;3.51905;0.00576589 0 + +ENST00000550775 295 301 298;2.24890;0.02375878 0 + +ENST00000550775 348 354 352;2.37461;0.02091027 0 + +ENST00000550775 466 478 475;2.84867;0.01262256 0 + +ENST00000550775 698 706 700;3.10360;0.00946697 0 + +ENST00000550775 717 724 720;2.52530;0.01788293 0 + +ENST00000550775 751 759 754;3.37203;0.00689960 0 + +ENST00000550775 764 775 771;5.09839;0.00058872 0 + +ENST00000550775 824 828 825;2.06144;0.02861391 0 + +ENST00000550775 861 872 868;4.04621;0.00290997 0 + +ENST00000550775 1032 1053 1045;5.84555;0.00014555 0 + +ENST00000550775 1119 1124 1122;2.51525;0.01807250 0 + +ENST00000550775 1202 1208 1207;2.70965;0.01469401 0 + +ENST00000550775 1273 1281 1280;2.26778;0.02331108 0 + +ENST00000550775 1351 1358 1355;3.29173;0.00759587 0 + +ENST00000550775 1377 1378 1378;1.89003;0.03376233 0 + +ENST00000550775 1396 1400 1398;2.26149;0.02345943 0 + +ENST00000622300 6 14 10;3.01318;0.01049835 0 + +ENST00000622300 15 16 16;2.09397;0.02771589 0 + +ENST00000622300 68 79 76;4.32748;0.00196318 0 + +ENST00000622300 113 127 119;6.64918;0.00002212 0 + +ENST00000622300 157 162 161;2.39282;0.02052276 0 + +ENST00000622300 195 209 202;5.46547;0.00030646 0 + +ENST00000622300 218 228 223;3.51626;0.00578582 0 + +ENST00000622300 311 314 313;1.82067;0.03605652 0 + +ENST00000622300 522 528 527;2.46351;0.01907576 0 + +ENST00000622300 1035 1038 1036;1.95475;0.03173367 0 + +ENST00000622300 1177 1188 1183;3.26978;0.00779636 0 + +ENST00000622300 1949 1950 1950;1.55761;0.04598351 0 + +ENST00000622300 2111 2119 2117;3.39975;0.00667232 0 + +ENST00000622300 2120 2121 2121;1.98523;0.03081446 0 + |
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out1.peak_regions_p50.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out1.peak_regions_p50.bed Fri May 25 12:17:44 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +ENST00000620398 45 48 48;5.28355;0.00042667 0 + +ENST00000550775 37 41 39;5.51074;0.00028155 0 + +ENST00000550775 769 771 771;5.09839;0.00058872 0 + +ENST00000550775 1039 1049 1045;5.84555;0.00014555 0 + +ENST00000622300 116 124 119;6.64918;0.00002212 0 + +ENST00000622300 199 203 202;5.46547;0.00030646 0 + |
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out2.average_profile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out2.average_profile Fri May 25 12:17:44 2018 -0400 |
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|
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out2.peak_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out2.peak_regions.bed Fri May 25 12:17:44 2018 -0400 |
| b |
| @@ -0,0 +1,46 @@ +ENST00000620398 39 55 48;5.28355 0 + +ENST00000620398 199 201 200;1.16279 0 + +ENST00000620398 343 351 348;1.96970 0 + +ENST00000620398 365 375 371;2.99552 0 + +ENST00000620398 399 410 406;3.74594 0 + +ENST00000620398 497 503 502;1.84967 0 + +ENST00000620398 565 575 570;4.55760 0 + +ENST00000620398 633 643 637;3.61150 0 + +ENST00000620398 713 714 714;1.06658 0 + +ENST00000620398 770 778 776;2.10449 0 + +ENST00000550775 27 49 39;5.51074 0 + +ENST00000550775 163 169 166;1.87947 0 + +ENST00000550775 192 201 198;3.51905 0 + +ENST00000550775 294 301 298;2.24890 0 + +ENST00000550775 347 354 352;2.37461 0 + +ENST00000550775 449 452 451;1.36497 0 + +ENST00000550775 466 478 475;2.84867 0 + +ENST00000550775 697 706 700;3.10360 0 + +ENST00000550775 716 725 720;2.52530 0 + +ENST00000550775 751 776 771;5.09839 0 + +ENST00000550775 823 828 825;2.06144 0 + +ENST00000550775 860 873 868;4.04621 0 + +ENST00000550775 972 977 975;1.45895 0 + +ENST00000550775 1030 1053 1045;5.84555 0 + +ENST00000550775 1118 1125 1122;2.51525 0 + +ENST00000550775 1190 1191 1191;1.07250 0 + +ENST00000550775 1201 1209 1207;2.70965 0 + +ENST00000550775 1251 1252 1252;1.00154 0 + +ENST00000550775 1273 1281 1280;2.26778 0 + +ENST00000550775 1351 1358 1355;3.29173 0 + +ENST00000550775 1376 1379 1378;1.89003 0 + +ENST00000550775 1395 1401 1398;2.26149 0 + +ENST00000550775 1422 1423 1423;1.15116 0 + +ENST00000622300 3 24 10;3.01318 0 + +ENST00000622300 68 80 76;4.32748 0 + +ENST00000622300 112 128 119;6.64918 0 + +ENST00000622300 155 163 161;2.39282 0 + +ENST00000622300 194 210 202;5.46547 0 + +ENST00000622300 217 229 223;3.51626 0 + +ENST00000622300 310 314 313;1.82067 0 + +ENST00000622300 521 528 527;2.46351 0 + +ENST00000622300 1032 1038 1036;1.95475 0 + +ENST00000622300 1176 1189 1183;3.26978 0 + +ENST00000622300 1948 1951 1950;1.55761 0 + +ENST00000622300 1953 1954 1954;1.14118 0 + +ENST00000622300 2111 2122 2117;3.39975 0 + |
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out3.average_profile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out3.average_profile Fri May 25 12:17:44 2018 -0400 |
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|
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out3.peak_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out3.peak_regions.bed Fri May 25 12:17:44 2018 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out4.average_profile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out4.average_profile Fri May 25 12:17:44 2018 -0400 |
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|
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out4.peak_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out4.peak_regions.bed Fri May 25 12:17:44 2018 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 215925e588c4 test-data/GraphProt_predict_profile_test_out4.peak_regions_p50.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GraphProt_predict_profile_test_out4.peak_regions_p50.bed Fri May 25 12:17:44 2018 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 215925e588c4 test-data/structure_test.model --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/structure_test.model Fri May 25 12:17:44 2018 -0400 |
| b |
| b'@@ -0,0 +1,3 @@\n+bias -0.553788\n+wscale 0.00116856\n+w 0:-4.0135382e+02 1:1.9925323e+02 2:5.0541817e+01 3:1.8746223e+01 4:4.7938229e+01 5:-1.3184420e+00 6:1.7999487e+02 7:2.6940073e+02 8:1.6889235e+01 9:6.0267132e+01 10:-1.1699441e+02 11:-1.5380527e+02 12:1.0863457e+02 13:2.2859363e+02 14:-1.1410797e+02 15:-2.8184515e+01 16:-4.8148053e+02 17:-2.0947812e+02 18:-1.8556664e+02 19:1.1845671e+02 20:-1.1883872e+02 21:-2.1624365e+03 22:-2.0481577e+01 23:1.2171440e+01 24:1.7009158e+02 25:-1.4347870e+02 26:-7.0251373e+02 27:1.6310406e+02 28:-5.2023670e+01 29:7.8187976e+02 30:-1.2321568e+02 31:-2.3541357e+01 32:3.9875206e+01 33:-2.2114096e+02 34:2.2337152e+02 35:1.5582236e+01 36:-1.0316161e+02 37:-1.9433070e+02 38:2.5308902e+00 39:-6.3811334e+02 40:2.2934598e+02 41:-2.3333070e+02 42:2.4731702e+02 43:-7.7959183e+01 44:-1.0662012e+02 45:-8.0184425e+01 46:4.3575726e+02 47:7.8634888e+02 48:-1.2234956e+02 49:4.4087677e+02 50:3.7999119e+01 51:2.4422890e+01 52:1.3852211e+02 53:7.2109711e+01 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218:-1.1375249e+02 219:'..b' 16189:-3.8923160e+02 16190:1.9454342e-01 16191:2.2205391e+02 16192:-3.0325488e+02 16193:2.0289177e+01 16194:1.3297751e+02 16195:-5.0635857e+01 16196:-1.5914134e+02 16197:7.6227020e+02 16198:-1.8649309e+02 16199:-1.0087193e+02 16200:2.7067329e+01 16201:5.6069350e+00 16202:7.1741508e+01 16203:1.0398770e+02 16204:1.5457289e+02 16205:1.4142047e+02 16206:4.3580337e+00 16207:8.2620613e+01 16208:2.2853886e+02 16209:-6.7359276e+01 16210:3.1518135e+01 16211:1.0528749e+02 16212:-1.3292932e+02 16213:-3.6427322e+02 16214:2.0843103e+02 16215:1.2301257e+02 16216:4.6732077e+02 16217:-1.5728828e+02 16218:-3.8228699e+01 16219:-6.2153629e+01 16220:9.3722038e+01 16221:1.0082492e+02 16222:-1.9527151e+02 16223:-1.0604891e+02 16224:1.4530508e+02 16225:1.9284476e+02 16226:-1.8522855e+00 16227:-3.5758786e+02 16228:1.3658163e+02 16229:-3.8850092e+02 16230:1.5093387e+02 16231:2.1205777e+02 16232:-6.3815804e+01 16233:7.6644470e+01 16234:1.1010138e+02 16235:-2.1285620e+02 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16380:-4.6628574e+01 16381:2.9751631e+01 16382:4.3969955e+00 16383:-4.1308667e+02\n' |
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/structure_test.params --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/structure_test.params Fri May 25 12:17:44 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +epochs: 50 +lambda: 0.0001 +R: 4 +D: 0 +bitsize: 14 +abstraction: 3 |
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/test.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fa Fri May 25 12:17:44 2018 -0400 |
| b |
| @@ -0,0 +1,80 @@ +>ENST00000620398 +ACTCTGGGAGGGCTAAGGAGCCATCATGATCCCTAAGCTGCTTTCCCTCCTCTGTTTCAG +ACTGTGCGTGGGCCAAGGAGACACAAGGGGAGATGGGTCACTGCCCAAGCCGTCCCTCAG +TGCCTGGCCCAGCTCGGTGGTCCCTGCCAACAGCAATGTGACGCTGCGATGTTGGACTCC +TGCCAGAGGTGTGAGCTTTGTTCTCAGGAAGGGAGGAATTATTCTGGAGTCCCCGAAGCC +CCTTGATTCTACAGAGGGCGCGGCCGAATTTCACCTCAATAATCTAAAAGTCAGAAATGC +TGGAGAGTACACCTGTGAATACTACAGAAAAGCATCCCCCCACATCCTTTCACAGCGCAG +TGACGTCCTTCTACTGTTGGTGACAGGACATTTATCTAAACCTTTCCTCCGAACCTACCA +AAGGGGTACAGTGACCGCAGGTGGAAGGGTGACTCTGCAGTGCCAGAAGCGAGACCAATT +GTTTGTGCCTATCATGTTCGCTCTACTGAAGGCAGGGACGCCATCACCCATCCAGCTGCA +GAGTCCAGCGGGGAAGGAGATAGACTTCTCTCTGGTGGACGTGACAGCCGGCGATGCTGG +GAACTACAGCTGCATGTACTACCAGACAAAGTCTCCCTTCTGGGCCTCAGAACCCAGTGA +TCAGCTTGAGATATTGGTGACAGTTCCCCCAGGTACCACATCGAGCAACTACTCCCTGGG +TAACTTCGTACGACTGGGTCTGGCTGCCGTAATTGTGGTTATCATGGGAGCTTTCCTGGT +GGAGGCCTGGTACAGCCGGAATGTGTCTCCAGGTGAATCAGAGGCCTTCAAACCAGAGTG +ACTCCATCTTGAACCGGGGCTGGGTAAACTGAGGCTGCAACCTGCTGGACTGCATTC +>ENST00000550775 +TCATGACTACACAGTTAAGGGTCGTCCATCTGCTTCCCCTTCTCCTAGCCTGCTTTGTGC +AAACAAGTCCCAAGCAGGAGAAGATGAAGATGGATTGCCACAAAGACGAGAAAGGCACCA +TCTATGACTATGAGGCCATCGCACTTAATAAGAATGAATATGTTTCCTTCAAGCAGTATG +TGGGCAAGCACATCCTCTTCGTCAACGTGGCCACCTACTGTGGTCTGACAGCGCAATATC +CTGAACTAAATGCACTCCAGGAGGAGCTGAAGCCCTATGGTCTAGTTGTGTTGGGCTTTC +CCTGCAACCAATTTGGAAAGCAAGAACCAGGAGATAACAAAGAGATTCTTCCTGGGCTCA +AGTATGTCCGTCCAGGGGGAGGATTTGTACCTAGTTTCCAGCTTTTTGAGAAAGGGGATG +TGAATGGTGAAAAAGAACAGAAAGTCTTCAGTTTCTTGAAGCACTCCTGTCCTCATCCCT +CTGAGATTTTGGGCACATTCAAATCTATATCCTGGGACCCTGTAAAGGTCCATGACATCC +GTTGGAACTTTGAAAAGTTCCTGGTGGGGCCTGATGGAATCCCTGTCATGCGCTGGTCCC +ACCGGGCTACGGTCAGCTCAGTCAAGACAGACATCCTGGCGTACTTGAAGCAATTCAAAA +CCAAATAGGAAGGTGGAGTTAAGGGCAGGAGCAACCCTACTTCTCACCTAATGACTTGCT +CTCCCCACCCCTCCAAAAAAAAGGAATACCCATCTTCTCACCACACTCTCTTCCTGCATG +GGCTCCACCTGAGTAAATCACCGCCACATACTGCCAGAATTCCCACTCTCCACAAACTAG +ATTTATATTTGGAAGGCTACTGCTCTTTTGCCTCTCAAGAGTATGTGGGTGAAGACTGAA +ACAAATGGAAACCTAAAATCCCCAGACCTCTGTTACAGGTTGAATCATTCATATCCACCA +GAGGGAAATCATCCTTCCACGACAATGGTTCAGTCGGCCATCACATCCTGAAGAACATTC +CTAGACATTCTGACTCTTCCATCTCTCTCTACCCTGGAGGTGTAGAAATAGCAATGGGGT +CACAGTCACACAATTTAGGTTCCACTTCATAACATTTTTTGTCTCCTAGGACAAACGTGT +ATCATCAGTTTCCAACTGTTTTGGCTCAGTTTTCATCCATGACACCTCCCCCTACCAGCC +ATTCTCCTGTGGGAGCAAGAACATTGCTTCAAAAGAAGAGAGGGCATCTCCATGCTTGTG +GGACCCAAAACCTATCTCTGGCCCTACAAAAGTTTTCCTAATTGTCTGATCTTTAGTGCA +TTCAGGTTATGGCACCTGGAGAGGAATGCCCTTTATCTTTTGAAGGATGGGATTTCCCAT +CTCAACCCTGGATTCCTCACCTTCAGAACGAGCCCTGCCACTGTCTCCAATAAAATGTTT +TCTGCAGCATCG +>ENST00000622300 +TAGTTTCCTGTTTCCGGCTTCGCTTCGGCCCACCCCCACGTCCACCCCGAATCCCTGCTT +AAAGGCCTTGCTTTCTTGTCTAACGCCGCAACCAGTCCTCTGAGTTGCCAACGTCTTTCT +TCTTGTCTCGACGCCCCGTCGTCCGGCCACAGCGATTCTCTGCTTAGCAGGATCGGTCCA +CAGCGGGACGTGAGTCCCTTTCCTCCTCGCGGCTTACCGCCTCTCTCCGCCTAGTGCCAG +GTGCTAATAAAGTTGTTGTTTCAAATGCGGCCAGGAACATCGCGAGCGGGGACCAATCAG +AGAGTAGCTTTGCCTCTATAACGGCGCGAGAGTGAGACGTCATCGGTGAGCGACTAACGC +TAGAAACAGTGGTGCGCGGAGAGGAGAGGCCTCGGGATGTCTCTGGCAGATGAGCTCTTA +GCTGATCTCGAAGAGGCAGCAGAAGAGGAGGAAGGAGGAAGCTATGGGGAGGAAGAAGAG +GAGCCAGCGATCGAGGATGTGCAGGAGGAGACACAGCTGGATCTTTCCGGGGATTCAGTC +AAGACCATCGCCAAGCTATGGGATAGTAAGATGTTTGCTGAGATTATGATGAAGATTGAG +GAGTATATCAGCAAGCAAGCCAAAGCTTCAGAAGTGATGGGACCAGTGGAGGCCGCGCCT +GAATACCGCGTCATCGTGGATGCCAACAACCTGACCGTGGAGATCGAAAACGAGCTGAAC +ATCATCCATAAGTTCATCCGGGATAAGTACTCAAAGAGATTCCCTGAACTGGAGTCCTTG +GTCCCCAATGCACTGGATTACATCCGCACGGTCAAGGAGCTGGGCAACAGCCTGGACAAG +TGCAAGAACAATGAGAACCTGCAGCAGATCCTCACCAATGCCACCATCATGGTCGTCAGC +GTCACCGCCTCCACCACCCAGGGGCAGCAGCTGTCGGAGGAGGAGCTGGAGCGGCTGGAG +GAGGCCTGCGACATGGCGCTGGAGCTGAACGCCTCCAAGCACCGCATCTACGAGTATGTG +GAGTCCCGGATGTCCTTCATCGCACCCAACCTGTCCATCATTATCGGGGCATCCACGGCC +GCCAAGATCATGGGTGTGGCCGGCGGCCTGACCAACCTCTCCAAGATGCCCGCCTGCAAC +ATCATGCTGCTCGGGGCCCAGCGCAAGACGCTGTCGGGCTTCTCGTCTACCTCAGTGCTG +CCCCACACCGGCTACATCTACCACAGTGACATCGTGCAGTCCCTGCCACCGGATCTGCGG +CGGAAAGCGGCCCGGCTGGTGGCCGCCAAGTGCACACTGGCAGCCCGTGTGGACAGTTTC +CACGAGAGCACAGAAGGGAAGGTGGGCTACGAACTGAAGGATGAGATCGAGCGCAAATTC +GACAAGTGGCAGGAGCCGCCGCCTGTGAAGCAGGTGAAGCCGCTGCCTGCGCCCCTGGAT +GGACAGCGGAAGAAGCGAGGCGGCCGCAGGTACCGCAAGATGAAGGAGCGGCTGGGGCTG +ACGGAGATCCGGAAGCAGGCCAACCGTATGAGCTTCGGAGAGATCGAGGAGGACGCCTAC +CAGGAGGACCTGGGATTCAGCCTGGGCCACCTGGGCAAGTCGGGCAGTGGGCGTGTGCGG +CAGACACAGGTAAACGAGGCCACCAAGGCCAGGATCTCCAAGACGCTGCAGCGGACCCTG +CAGAAGCAGAGCGTCGTATATGGCGGGAAGTCCACCATCCGCGACCGCTCCTCGGGCACG +GCCTCCAGCGTGGCCTTCACCCCACTCCAGGGCCTGGAGATTGTGAACCCACAGGCGGCA +GAGAAGAAGGTGGCTGAGGCCAACCAGAAGTATTTCTCCAGCATGGCTGAGTTCCTCAAG +GTCAAGGGCGAGAAGAGTGGCCTTATGTCCACCTGAATGACTGCGTGTGTCCAAGGTGGC +TTCCCACTGAAGGGACACAGAGGTCCAGTCCTTCTGAAGGGCTAGGATCGGGTTCTGGCA +GGGAGAACCTGCCCTGCCACTGGCCCCATTGCTGGGACTGCCCAGGGAGGAGGCCTTGGA +AGAGTCCGGCCTGGCCTCCCCCAGGACCGAGATCACCGCCCAGTATGGGCTAGAGCAGGT +CTTCATCATGCCTTGTCTTTTTTAACTGAGAAAGGAGATTTTTTGAAAAGAGTACAATTA +AAAGGACATTGTCAAGATCTGTC |
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/test.model --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.model Fri May 25 12:17:44 2018 -0400 |
| b |
| b'@@ -0,0 +1,3 @@\n+bias 0.0990594\n+wscale 0.000419047\n+w 3:-2.6323795e+02 7:-1.5498299e+02 39:3.2710247e+01 90:-9.6892609e+01 92:-6.2059918e+02 102:2.7361217e+01 108:-1.8683072e+02 111:9.2224388e+01 121:4.4261597e+01 127:-2.9686353e+02 148:-2.4798018e+02 155:1.0929895e+02 212:-3.0733829e+02 217:-3.6330551e+02 219:4.3392648e+02 220:-4.3969490e+01 223:-1.2370902e+03 235:-2.5857092e+02 286:-4.4877792e+01 306:-3.2496075e+02 308:-2.0045505e+02 375:-2.3125467e+02 396:-6.7614136e+02 400:1.1828072e+02 408:4.3950644e+00 414:2.0196147e+03 421:-3.3002304e+01 431:-4.0940579e+02 432:-5.0269598e+02 434:-1.4379294e+02 469:-4.2782242e+02 486:1.9116473e+02 492:-1.6351070e+02 496:-3.4013925e+02 502:1.6938168e+02 524:9.0154556e+01 541:-3.2447818e+02 542:-3.8114508e+02 546:1.8973650e+02 605:2.8628244e+02 609:-2.4498466e+02 615:4.9888785e+02 617:-7.0967567e+01 626:-7.4189880e+01 635:-4.8810840e+02 638:-3.8662479e+02 703:-6.1965290e+01 718:-2.5008917e+02 752:4.7394373e+02 778:3.6091281e+02 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16321:-5.4178558e+01 16328:-7.2517517e+02 16334:7.0763763e+02 16377:1.2659835e+03\n' |
| b |
| diff -r 000000000000 -r 215925e588c4 test-data/test.params --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.params Fri May 25 12:17:44 2018 -0400 |
| b |
| @@ -0,0 +1,19 @@ +epochs: 20 +lambda: 0.001 +R: 1 +D: 4 +bitsize: 14 +model_type: sequence +#ADDITIONAL MODEL PARAMETERS +ap_extlr: 5 +gev_my: -2.5408 +gev_sigma: 1.6444 +gev_xi: -0.1383 +p50_score: 6.51534 +p50_p_val: 0.0009059744 +# ADDITIONAL MODEL INFO +organism: hsa +rbp_ens_gene_id: ENSG00000011304 +rbp_gene_name: PTBP1 +clip_method: eCLIP +pubmed_id: 27018577 |