Mercurial > repos > rnateam > graphprot_predict_profile

annotate graphprot_predict_wrapper.py @ 1:20429f4c1b95 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
author bgruening
date Wed, 22 Jan 2020 10:14:41 -0500
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children 7bbb7bf6304f
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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1 #!/usr/bin/env python3
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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3 import subprocess
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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4 import argparse
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5 import shutil
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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6 import gplib
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7 import gzip
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8 import sys
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9 import os
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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12 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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14 TOOL DEPENDENCIES
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15 =================
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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17 GraphProt 1.1.7
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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18 Best install via:
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19 https://anaconda.org/bioconda/graphprot
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20 Tested with: miniconda3, conda 4.7.12
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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23 Script: What's my job this time, master?
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24 Author: It'll be a though one.
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25 Script: I take this as a given.
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26 Author: Oh yeah?
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27 Script: ... I'm ready.
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30 OUTPUT FILES
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31 ============
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33 data_id.avg_profile
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34 data_id.avg_profile.peaks.bed
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35 --conf-out
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36 data_id.avg_profile.p50.peaks.bed
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37 --gen-site-bed
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38 data_id.avg_profile.genomic_peaks.bed
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39 --conf-out --gen-site-bed
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40 data_id.avg_profile.p50.genomic_peaks.bed
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41 --ws-pred
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42 data_id.predictions
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43 --ws-pred --conf-out
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44 data_id.predictions
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45 data_id.p50.predictions
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48 EXAMPLE CALLS
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49 =============
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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51 python graphprot_predict_wrapper.py --model test2.model --params test2.params --fasta gp_data/test10_predict.fa --data-id test2pred --gp-output
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52 python graphprot_predict_wrapper.py --model test2.model --params test2.params --fasta gp_data/test10_predict.fa --data-id test2pred --gen-site-bed gp_data/test10_predict.bed
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53 python graphprot_predict_wrapper.py --model test2.model --params test2.params --fasta gp_data/test10_predict.fa --data-id test2pred --gen-site-bed gp_data/test10_predict.bed --conf-out
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54 python graphprot_predict_wrapper.py --model test2.model --params test2.params --fasta gp_data/test10_predict.fa --data-id test2pred --conf-out --ws-pred
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56 python graphprot_predict_wrapper.py --model test-data/test.model --params test-data/test.params --fasta test-data/test_predict.fa --data-id predtest
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58 python graphprot_predict_wrapper.py --model test-data/test.model --params test-data/test.params --fasta test-data/test_predict.fa --data-id predtest --gen-site-bed test-data/test_predict.bed --sc-thr 0.0 --max-merge-dist 0 --conf-out --ap-extlr 5
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60 python graphprot_predict_wrapper.py --data-id GraphProt --fasta test-data/test_predict.fa --model test-data/test.model --params test-data/test.params --gen-site-bed test-data/test_predict.bed --sc-thr 0.0 --max-merge-dist 0 --conf-out --ap-extlr 5
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63 pwd && python '/home/uhlm/Dokumente/Projekte/GraphProt_galaxy_new/galaxytools/tools/rna_tools/graphprot/graphprot_predict_wrapper.py' --data-id GraphProt --fasta /tmp/tmpmuslpc1h/files/0/8/c/dataset_08c48d88-e3b5-423b-acf6-bf89b8c60660.dat --model /tmp/tmpmuslpc1h/files/e/6/4/dataset_e6471bb4-e74c-4372-bc49-656f900e7191.dat --params /tmp/tmpmuslpc1h/files/b/6/5/dataset_b65e8cf4-d3e6-429e-8d57-1d401adf4b3c.dat --gen-site-bed /tmp/tmpmuslpc1h/files/5/1/a/dataset_51a38b65-5943-472d-853e-5d845fa8ac3e.dat --sc-thr 0.0 --max-merge-dist 0 --conf-out --ap-extlr 5
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66 """
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68 ################################################################################
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70 def setup_argument_parser():
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71 """Setup argparse parser."""
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72 help_description = """
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73 Galaxy wrapper script for GraphProt (-action predict and -action
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74 predict_profile) to compute whole site or position-wise scores for input
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75 FASTA sequences.
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76 By default, profile predictions are calculated, followed by average
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77 profiles computions and peak regions extraction from average profiles.
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78 If --ws-pred is set, whole site score predictions on input sequences
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79 will be run instead.
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80 If --conf-out is set, sites or peak regions with a score >= the median
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81 score of positive training sites will be output.
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82 If --gen-site-bed .bed file is provided, peak regions will be output
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83 with genomic coordinates too.
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84
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85 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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86 # Define argument parser.
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87 p = argparse.ArgumentParser(add_help=False,
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88 prog="graphprot_predict_wrapper.py",
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89 description=help_description,
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90 formatter_class=argparse.MetavarTypeHelpFormatter)
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91
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92 # Argument groups.
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93 p_man = p.add_argument_group("REQUIRED ARGUMENTS")
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94 p_opt = p.add_argument_group("OPTIONAL ARGUMENTS")
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95
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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96 # Required arguments.
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97 p_opt.add_argument("-h", "--help",
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98 action="help",
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99 help="Print help message")
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100 p_man.add_argument("--fasta",
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101 dest="in_fa",
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102 type=str,
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103 required = True,
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104 help = "Sequences .fa file to predict on (option -fasta)")
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105 p_man.add_argument("--model",
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106 dest="in_model",
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107 type=str,
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108 required = True,
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109 help = "GraphProt model file to use for predictions (option -model)")
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110 p_man.add_argument("--params",
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111 dest="in_params",
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112 type=str,
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113 required = True,
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114 help = "Parameter file for given model")
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115 p_man.add_argument("--data-id",
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116 dest="data_id",
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117 type=str,
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118 required = True,
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119 help = "Data ID (option -prefix)")
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120 # ---> I'm a conditional argument <---
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121 p_opt.add_argument("--ws-pred",
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122 dest = "ws_pred",
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123 default = False,
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124 action = "store_true",
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125 help = "Run a whole site prediction instead of calculating profiles (default: false)")
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126 # Additional arguments.
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127 p_opt.add_argument("--sc-thr",
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128 dest="score_thr",
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129 type = float,
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130 default = 0,
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131 help = "Score threshold for extracting average profile peak regions (default: 0)")
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132 p_opt.add_argument("--max-merge-dist",
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133 dest="max_merge_dist",
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134 type = int,
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135 default = 0,
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136 choices = [0,1,2,3,4,5,6,7,8,9,10],
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137 help = "Maximum merge distance for nearby peak regions (default: report all non-overlapping regions)")
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138 p_opt.add_argument("--gen-site-bed",
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139 dest="genomic_sites_bed",
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140 type=str,
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141 help = ".bed file specifying the genomic regions of the input .fa sequences. Corrupt .bed information will be punished (default: false)")
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142 p_opt.add_argument("--conf-out",
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143 dest="conf_out",
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144 default = False,
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145 action = "store_true",
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146 help = "Output filtered peak regions BED file or predictions file (if --ws-pred) using the median positive training site score for filtering (default: false)")
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147 p_opt.add_argument("--gp-output",
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148 dest = "gp_output",
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149 default = False,
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150 action = "store_true",
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151 help = "Print output produced by GraphProt (default: false)")
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152 p_opt.add_argument("--ap-extlr",
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153 dest="ap_extlr",
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154 type = int,
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155 default = 5,
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156 choices = [0,1,2,3,4,5,6,7,8,9,10],
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157 help = "Define average profile up- and downstream extension to produce the average profile. The mean over small sequence windows (window length = --ap-extlr*2 + 1) is used to get position scores, thus the average profile is more smooth than the initial profile output by GraphProt (default: 5)")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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158 return p
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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159
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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parents:
diff changeset
160
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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161 ################################################################################
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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162
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
163 if __name__ == '__main__':
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
164
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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165 # Setup argparse.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
166 parser = setup_argument_parser()
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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167 # Read in command line arguments.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
168 args = parser.parse_args()
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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169
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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170 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
171 Do all sorts of sanity checking.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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172
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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173 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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174 # Check for Linux.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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175 assert "linux" in sys.platform, "please use Linux"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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176 # Check tool availability.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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177 assert gplib.is_tool("GraphProt.pl"), "GraphProt.pl not in PATH"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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178 # Check file inputs.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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179 assert os.path.exists(args.in_fa), "input .fa file \"%s\" not found" %(args.in_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
180 assert os.path.exists(args.in_model), "input .model file \"%s\" not found" %(args.in_model)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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181 assert os.path.exists(args.in_params), "input .params file \"%s\" not found" %(args.in_params)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
182 # Count .fa entries.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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183 c_in_fa = gplib.count_fasta_headers(args.in_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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184 assert c_in_fa, "input .fa file \"%s\" no headers found" %(args.in_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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185 print("# input .fa sequences: %i" %(c_in_fa))
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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186 # Read in FASTA sequences to check for uppercase sequences.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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187 seqs_dic = gplib.read_fasta_into_dic(args.in_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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188 c_uc_nt = gplib.seqs_dic_count_uc_nts(seqs_dic)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
189 assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. Please change sequences to uppercase (keep in mind GraphProt only scores uppercase regions (according to its viewpoint concept))"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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190 if not args.ws_pred:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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191 # Check for lowercase sequences.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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192 c_lc_nt = gplib.seqs_dic_count_lc_nts(seqs_dic)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
193 assert not c_lc_nt, "lowercase nucleotides not allowed in profile predictions, since GraphProt only scores uppercase regions (according to its viewpoint concept))"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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194 # Check .bed.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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195 if args.genomic_sites_bed:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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196 # An array of checks, marvelous.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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197 assert os.path.exists(args.genomic_sites_bed), "genomic .bed file \"%s\" not found" %(args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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198 # Check .bed for content.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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199 assert gplib.count_file_rows(args.genomic_sites_bed), "genomic .bed file \"%s\" is empty" %(args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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200 # Check .bed for 6-column format.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
201 assert gplib.bed_check_six_col_format(args.genomic_sites_bed), "genomic .bed file \"%s\" appears to not be in 6-column .bed format" %(args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
202 # Check for unique column 4 IDs.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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203 assert gplib.bed_check_unique_ids(args.genomic_sites_bed), "genomic .bed file \"%s\" column 4 IDs not unique" %(args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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204 # Read in .bed regions, compare to FASTA sequences (compare IDs + lengths)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
205 seq_len_dic = gplib.get_seq_lengths_from_seqs_dic(seqs_dic)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
206 reg_len_dic = gplib.bed_get_region_lengths(args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
207 for seq_id in seq_len_dic:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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208 seq_l = seq_len_dic[seq_id]
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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209 assert seq_id in reg_len_dic, "sequence ID \"\" missing in input .bed \"\"" %(seq_id, args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
210 reg_l = reg_len_dic[seq_id]
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
211 assert seq_l == reg_l, "sequence length differs from .bed region length (%i != %i)" %(seq_l, reg_l)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
212 # Read in model parameters.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
213 param_dic = gplib.graphprot_get_param_dic(args.in_params)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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214 # Create GraphProt parameter string.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
215 param_string = gplib.graphprot_get_param_string(args.in_params)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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parents:
diff changeset
216
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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217 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
218 Run predictions.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
219
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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220 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
221 if args.ws_pred:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
222 # Do whole site prediction.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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223 print("Starting whole site predictions on input .fa file (-action predict) ... ")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
224 check_cmd = "GraphProt.pl -action predict -prefix " + args.data_id + " -fasta " + args.in_fa + " " + param_string + " -model " + args.in_model
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
225 output = subprocess.getoutput(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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226 assert output, "the following call of GraphProt.pl produced no output:\n%s" %(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
227 if args.gp_output:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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228 print(output)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
229 ws_predictions_file = args.data_id + ".predictions"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
230 assert os.path.exists(ws_predictions_file), "Whole site prediction output .predictions file \"%s\" not found" %(ws_predictions_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
231 if args.conf_out:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
232 # Filter by pos_train_ws_pred_median median.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
233 assert "pos_train_ws_pred_median" in param_dic, "whole site top scores median information missing in .params file"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
234 pos_train_ws_pred_median = float(param_dic["pos_train_ws_pred_median"])
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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diff changeset
235 # Filtered file.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
236 filt_ws_predictions_file = args.data_id + ".p50.predictions"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
237 print("Extracting p50 sites from whole site predictions (score threshold = %f) ... " %(pos_train_ws_pred_median))
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
238 gplib.graphprot_filter_predictions_file(ws_predictions_file, filt_ws_predictions_file,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
239 sc_thr=pos_train_ws_pred_median)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
240 else:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
241 # Do profile prediction.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
242 print("Starting profile predictions on on input .fa file (-action predict_profile) ... ")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
243 check_cmd = "GraphProt.pl -action predict_profile -prefix " + args.data_id + " -fasta " + args.in_fa + " " + param_string + " -model " + args.in_model
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
244 output = subprocess.getoutput(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
245 assert output, "the following call of GraphProt.pl produced no output:\n%s" %(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
246 if args.gp_output:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
247 print(output)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
248 profile_predictions_file = args.data_id + ".profile"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
249 assert os.path.exists(profile_predictions_file), "Profile prediction output .profile file \"%s\" not found" %(profile_predictions_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
250
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
251 # Profile prediction output files.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
252 avg_prof_file = args.data_id + ".avg_profile"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
253 avg_prof_peaks_file = args.data_id + ".avg_profile.peaks.bed"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
254 avg_prof_gen_peaks_file = args.data_id + ".avg_profile.genomic_peaks.bed"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
255 avg_prof_peaks_p50_file = args.data_id + ".avg_profile.p50.peaks.bed"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
256 avg_prof_gen_peaks_p50_file = args.data_id + ".avg_profile.p50.genomic_peaks.bed"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
257
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
258 # Get sequence IDs in order from input .fa file.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
259 seq_ids_list = gplib.fasta_read_in_ids(args.in_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
260 # Calculate average profiles.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
261 print("Getting average profile from profile (extlr for smoothing: %i) ... " %(args.ap_extlr))
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
262 gplib.graphprot_profile_calculate_avg_profile(profile_predictions_file,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
263 avg_prof_file,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
264 ap_extlr=args.ap_extlr,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
265 seq_ids_list=seq_ids_list,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
266 method=2)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
267 # Extract peak regions on sequences with threshold score 0.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
268 print("Extracting peak regions from average profile (score threshold = 0) ... ")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
269 gplib.graphprot_profile_extract_peak_regions(avg_prof_file, avg_prof_peaks_file,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
270 max_merge_dist=args.max_merge_dist,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
271 sc_thr=args.score_thr)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
272 # Convert peaks to genomic coordinates.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
273 if args.genomic_sites_bed:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
274 print("Converting peak regions to genomic coordinates ... ")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
275 gplib.bed_peaks_to_genomic_peaks(avg_prof_peaks_file, avg_prof_gen_peaks_file,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
276 print_rows=False,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
277 genomic_sites_bed=args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
278 # gplib.make_file_copy(avg_prof_gen_peaks_file, avg_prof_peaks_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
279 # Extract peak regions with threshold score p50.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
280 if args.conf_out:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
281 sc_id = "pos_train_avg_profile_median_%i" %(args.ap_extlr)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
282 # Filter by pos_train_ws_pred_median median.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
283 assert sc_id in param_dic, "average profile extlr %i median information missing in .params file" %(args.ap_extlr)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
284 p50_sc_thr = float(param_dic[sc_id])
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
285 print("Extracting p50 peak regions from average profile (score threshold = %f) ... " %(p50_sc_thr))
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
286 gplib.graphprot_profile_extract_peak_regions(avg_prof_file, avg_prof_peaks_p50_file,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
287 max_merge_dist=args.max_merge_dist,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
288 sc_thr=p50_sc_thr)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
289 # Convert peaks to genomic coordinates.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
290 if args.genomic_sites_bed:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
291 print("Converting p50 peak regions to genomic coordinates ... ")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
292 gplib.bed_peaks_to_genomic_peaks(avg_prof_peaks_p50_file, avg_prof_gen_peaks_p50_file,
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
293 genomic_sites_bed=args.genomic_sites_bed)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
294 # Done.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
295 print("Script: I'm done.")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
296 print("Author: ... ")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
297
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
298