Mercurial > repos > rnateam > graphprot_predict_profile

annotate graphprot_predict_wrapper.py @ 4:2d6de5b769e6 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
author bgruening
date Thu, 28 Jan 2021 15:05:38 +0000
parents 9a83a84a25a7
children 58ebf089377e
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adcc4c457c3c "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
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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3 import argparse as ap
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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4 import os
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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5 import subprocess
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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6 import sys
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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8 import gplib
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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11 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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13 TOOL DEPENDENCIES
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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14 =================
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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16 GraphProt 1.1.7
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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17 Best install via:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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18 https://anaconda.org/bioconda/graphprot
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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19 Tested with: miniconda3, conda 4.7.12
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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22 Script: What's my job this time, master?
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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23 Author: It'll be a though one.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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24 Script: I take this as a given.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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25 Author: Oh yeah?
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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26 Script: ... I'm ready.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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29 OUTPUT FILES
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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30 ============
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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32 data_id.avg_profile
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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33 data_id.avg_profile.peaks.bed
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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34 --conf-out
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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35 data_id.avg_profile.p50.peaks.bed
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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36 --gen-site-bed
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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37 data_id.avg_profile.genomic_peaks.bed
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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38 --conf-out --gen-site-bed
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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39 data_id.avg_profile.p50.genomic_peaks.bed
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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40 --ws-pred
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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41 data_id.predictions
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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42 --ws-pred --conf-out
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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43 data_id.predictions
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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44 data_id.p50.predictions
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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47 EXAMPLE CALLS
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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48 =============
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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49
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50 flake8 coming out of hotel room. FB enters.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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51 FB: Who is this f*** ???
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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54 python graphprot_predict_wrapper.py --model test2.model --params test2.params
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55 --fasta gp_data/test10_predict.fa --data-id test2pred --gp-output
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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56 python graphprot_predict_wrapper.py --model test2.model --params test2.params
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57 --fasta gp_data/test10_predict.fa --data-id test2pred
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58 --gen-site-bed gp_data/test10_predict.bed
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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60 python graphprot_predict_wrapper.py --model test2.model --params test2.params
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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61 --fasta gp_data/test10_predict.fa --data-id test2pred
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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62 --gen-site-bed gp_data/test10_predict.bed --conf-out
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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64 python graphprot_predict_wrapper.py --model test2.model --params test2.params
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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65 --fasta gp_data/test10_predict.fa --data-id test2pred --conf-out --ws-pred
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66
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67 python graphprot_predict_wrapper.py --model test-data/test.model
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68 --params test-data/test.params --fasta test-data/test_predict.fa
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69 --data-id predtest
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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71 python graphprot_predict_wrapper.py --model test-data/test.model
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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72 --params test-data/test.params --fasta test-data/test_predict.fa
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73 --data-id predtest --gen-site-bed test-data/test_predict.bed
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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74 --sc-thr 0.0 --max-merge-dist 0 --conf-out --ap-extlr 5
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75
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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76 python graphprot_predict_wrapper.py --data-id GraphProt
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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77 --fasta test-data/test_predict.fa --model test-data/test.model
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78 --params test-data/test.params --gen-site-bed test-data/test_predict.bed
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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79 --sc-thr 0.0 --max-merge-dist 0 --conf-out --ap-extlr 5
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80
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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81 """
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82
3
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83
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84 ###############################################################################
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85
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86 def setup_argument_parser():
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87 """Setup argparse parser."""
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88 help_description = """
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89 Galaxy wrapper script for GraphProt (-action predict and -action
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90 predict_profile) to compute whole site or position-wise scores for input
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91 FASTA sequences.
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92 By default, profile predictions are calculated, followed by average
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93 profiles computions and peak regions extraction from average profiles.
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94 If --ws-pred is set, whole site score predictions on input sequences
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95 will be run instead.
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96 If --conf-out is set, sites or peak regions with a score >= the median
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97 score of positive training sites will be output.
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98 If --gen-site-bed .bed file is provided, peak regions will be output
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99 with genomic coordinates too.
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100
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101 """
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102 # Define argument parser.
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103 p = ap.ArgumentParser(add_help=False,
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104 prog="graphprot_predict_wrapper.py",
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105 description=help_description,
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106 formatter_class=ap.MetavarTypeHelpFormatter)
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107
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108 # Argument groups.
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109 p_man = p.add_argument_group("REQUIRED ARGUMENTS")
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110 p_opt = p.add_argument_group("OPTIONAL ARGUMENTS")
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111
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112 # Required arguments.
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113 p_opt.add_argument("-h", "--help",
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114 action="help",
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115 help="Print help message")
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116 p_man.add_argument("--fasta",
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117 dest="in_fa",
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118 type=str,
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119 required=True,
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120 help="Sequences .fa file to predict"
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121 " on (option -fasta)")
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122 p_man.add_argument("--model",
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123 dest="in_model",
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124 type=str,
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125 required=True,
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126 help="GraphProt model file to use for predictions"
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127 " (option -model)")
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128 p_man.add_argument("--params",
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129 dest="in_params",
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130 type=str,
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131 required=True,
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132 help="Parameter file for given model")
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133 p_man.add_argument("--data-id",
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134 dest="data_id",
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135 type=str,
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136 required=True,
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137 help="Data ID (option -prefix)")
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138 # ---> I'm a conditional argument <---
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139 p_opt.add_argument("--ws-pred",
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140 dest="ws_pred",
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141 default=False,
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142 action="store_true",
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143 help="Run a whole site prediction instead "
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144 "of calculating profiles (default: false)")
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145 # Additional arguments.
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146 p_opt.add_argument("--sc-thr",
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147 dest="score_thr",
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148 type=float,
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149 default=0,
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150 help="Score threshold for extracting "
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151 "average profile peak regions (default: 0)")
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152 p_opt.add_argument("--max-merge-dist",
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153 dest="max_merge_dist",
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154 type=int,
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155 default=0,
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156 choices=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
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157 help="Maximum merge distance for nearby peak regions"
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158 " (default: report all non-overlapping regions)")
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159 p_opt.add_argument("--gen-site-bed",
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160 dest="genomic_sites_bed",
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161 type=str,
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162 help=".bed file specifying the genomic regions of "
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163 "the input .fa sequences. Corrupt .bed "
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164 "information will be punished (default: false)")
1
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165 p_opt.add_argument("--conf-out",
3
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166 dest="conf_out",
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167 default=False,
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168 action="store_true",
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169 help="Output filtered peak regions BED file or "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
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170 "predictions file (if --ws-pred) using the median "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
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diff changeset
171 "positive training site score for filtering "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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172 "(default: false)")
1
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173 p_opt.add_argument("--gp-output",
3
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174 dest="gp_output",
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175 default=False,
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176 action="store_true",
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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177 help="Print output produced by GraphProt "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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178 "(default: false)")
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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179 p_opt.add_argument("--ap-extlr",
3
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180 dest="ap_extlr",
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181 type=int,
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182 default=5,
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183 choices=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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184 help="Define average profile up- and downstream "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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185 "extension to produce the average profile. "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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186 "The mean over small sequence windows "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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187 "(window length = --ap-extlr*2 + 1) is used to "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
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188 "get position scores, thus the average profile "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
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189 "is more smooth than the initial profile output "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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190 "by GraphProt (default: 5)")
1
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191 return p
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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192
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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193
3
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194 ###############################################################################
1
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195
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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196 if __name__ == '__main__':
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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197
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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198 # Setup argparse.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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199 parser = setup_argument_parser()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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200 # Read in command line arguments.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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201 args = parser.parse_args()
3
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202
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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203 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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204 Do all sorts of sanity checking.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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205
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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206 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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207 # Check for Linux.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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208 assert "linux" in sys.platform, "please use Linux"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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209 # Check tool availability.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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210 assert gplib.is_tool("GraphProt.pl"), "GraphProt.pl not in PATH"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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211 # Check file inputs.
3
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212 assert os.path.exists(args.in_fa), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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213 "input .fa file \"%s\" not found" % (args.in_fa)
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214 assert os.path.exists(args.in_model), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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215 "input .model file \"%s\" not found" % (args.in_model)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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216 assert os.path.exists(args.in_params), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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217 "input .params file \"%s\" not found" % (args.in_params)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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218 # Count .fa entries.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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219 c_in_fa = gplib.count_fasta_headers(args.in_fa)
3
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220 assert c_in_fa, "input .fa file \"%s\" no headers found" % (args.in_fa)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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221 print("# input .fa sequences: %i" % (c_in_fa))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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222 # Read in FASTA sequences to check for uppercase sequences.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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223 seqs_dic = gplib.read_fasta_into_dic(args.in_fa)
4
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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diff changeset
224 # Check for lowercase only sequences, which cause GP to crash.
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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225 error_mess = "input sequences encountered containing "\
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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226 "only lowercase characters or lowercase characters in between "\
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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227 "uppercase characters. Please provide either all uppercase "\
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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diff changeset
228 "sequences or sequences containing uppercase regions surrounded "\
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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229 "by lowercase context regions for structure calculation (see "\
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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diff changeset
230 "viewpoint concept in original GraphProt publication "\
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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diff changeset
231 "for more details)"
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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232 if args.ws_pred:
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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diff changeset
233 bad_ids = gplib.check_seqs_dic_format(seqs_dic)
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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diff changeset
234 assert not bad_ids, "%s" % (error_mess)
2d6de5b769e6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"
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diff changeset
235
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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236 c_uc_nt = gplib.seqs_dic_count_uc_nts(seqs_dic)
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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diff changeset
237 assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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diff changeset
238 "Please change sequences to uppercase (keep in mind "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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diff changeset
239 "GraphProt only scores uppercase regions (according "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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diff changeset
240 "to its viewpoint concept)"
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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241 if not args.ws_pred:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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242 # Check for lowercase sequences.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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243 c_lc_nt = gplib.seqs_dic_count_lc_nts(seqs_dic)
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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244 assert not c_lc_nt, "lowercase nucleotides in input .fa not allowed"\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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diff changeset
245 " in profile predictions, since GraphProt only scores "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
246 "uppercase regions (according to its viewpoint concept)"
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
247 # Check .bed.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
248 if args.genomic_sites_bed:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
249 # An array of checks, marvelous.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
250 assert \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
251 os.path.exists(args.genomic_sites_bed), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
252 "genomic .bed file \"%s\" not found" % (args.genomic_sites_bed)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
253 # Check .bed for content.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
254 assert gplib.count_file_rows(args.genomic_sites_bed), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
255 "genomic .bed file \"%s\" is empty" % (args.genomic_sites_bed)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
256 # Check .bed for 6-column format.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
257 assert gplib.bed_check_six_col_format(args.genomic_sites_bed), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
258 "genomic .bed file \"%s\" appears to not "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
259 "be in 6-column .bed format" % (args.genomic_sites_bed)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
260 # Check for unique column 4 IDs.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
261 assert gplib.bed_check_unique_ids(args.genomic_sites_bed), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
262 "genomic .bed file \"%s\" column 4 IDs not unique" % \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
263 (args.genomic_sites_bed)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
264 # Read in .bed regions, compare to FASTA sequences.
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
265 seq_len_dic = gplib.get_seq_lengths_from_seqs_dic(seqs_dic)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
266 reg_len_dic = gplib.bed_get_region_lengths(args.genomic_sites_bed)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
267 for seq_id in seq_len_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
268 seq_l = seq_len_dic[seq_id]
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
269 assert seq_id in reg_len_dic, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
270 "sequence ID \"%s\" missing in input .bed \"%s\"" % \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
271 (seq_id, args.genomic_sites_bed)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
272 reg_l = reg_len_dic[seq_id]
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
273 assert seq_l == reg_l, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
274 "sequence length differs from .bed region length (%i != %i)" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
275 % (seq_l, reg_l)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
276 # Read in model parameters.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
277 param_dic = gplib.graphprot_get_param_dic(args.in_params)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
278 # Create GraphProt parameter string.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
279 param_string = gplib.graphprot_get_param_string(args.in_params)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
280
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
281 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
282 Run predictions.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
283
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
284 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
285 if args.ws_pred:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
286 # Do whole site prediction.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
287 print("Starting whole site predictions on input .fa file"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
288 " (-action predict) ... ")
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
289 check_cmd = "GraphProt.pl -action predict -prefix " \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
290 + args.data_id + " -fasta " + args.in_fa + " " \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
291 + param_string + " -model " + args.in_model
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
292 output = subprocess.getoutput(check_cmd)
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
293 assert output, "the following call of GraphProt.pl "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
294 "produced no output:\n%s" % (check_cmd)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
295 if args.gp_output:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
296 print(output)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
297 ws_predictions_file = args.data_id + ".predictions"
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
298 assert os.path.exists(ws_predictions_file), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
299 "Whole site prediction output .predictions file \"%s\" not found" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
300 % (ws_predictions_file)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
301 if args.conf_out:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
302 # Filter by pos_train_ws_pred_median median.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
303 assert "pos_train_ws_pred_median" in param_dic, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
304 "whole site top scores median information "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
305 "missing in .params file"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
306 pos_tr_ws_pred_med = \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
307 float(param_dic["pos_train_ws_pred_median"])
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
308 # Filtered file.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
309 filt_ws_predictions_file = args.data_id + ".p50.predictions"
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
310 print("Extracting p50 sites from whole site predictions"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
311 " (score threshold = %f) ... " % (pos_tr_ws_pred_med))
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
312 gplib.graphprot_filter_predictions_file(ws_predictions_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
313 filt_ws_predictions_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
314 sc_thr=pos_tr_ws_pred_med)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
315 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
316 # Do profile prediction.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
317 print("Starting profile predictions on on input .fa file "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
318 "(-action predict_profile) ... ")
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
319 check_cmd = "GraphProt.pl -action predict_profile -prefix " \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
320 + args.data_id + " -fasta " + args.in_fa + " " + \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
321 param_string + " -model " + args.in_model
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
322 output = subprocess.getoutput(check_cmd)
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
323 assert output, "the following call of GraphProt.pl produced "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
324 "no output:\n%s" % (check_cmd)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
325 if args.gp_output:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
326 print(output)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
327 profile_predictions_file = args.data_id + ".profile"
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
328 assert os.path.exists(profile_predictions_file), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
329 "Profile prediction output .profile file \"%s\" not found" % \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
330 (profile_predictions_file)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
331
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
332 # Profile prediction output files.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
333 avg_prof_file = args.data_id + ".avg_profile"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
334 avg_prof_peaks_file = args.data_id + ".avg_profile.peaks.bed"
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
335 avg_prof_gen_peaks_file = args.data_id + \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
336 ".avg_profile.genomic_peaks.bed"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
337 avg_prof_peaks_p50_file = args.data_id + \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
338 ".avg_profile.p50.peaks.bed"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
339 avg_prof_gen_peaks_p50_file = args.data_id + \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
340 ".avg_profile.p50.genomic_peaks.bed"
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
341
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
342 # Get sequence IDs in order from input .fa file.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
343 seq_ids_list = gplib.fasta_read_in_ids(args.in_fa)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
344 # Calculate average profiles.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
345 print("Getting average profile from profile "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
346 "(extlr for smoothing: %i) ... " % (args.ap_extlr))
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
347 gplib.graphprot_profile_calc_avg_profile(profile_predictions_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
348 avg_prof_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
349 ap_extlr=args.ap_extlr,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
350 seq_ids_list=seq_ids_list,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
351 method=2)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
352 # Extract peak regions on sequences with threshold score 0.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
353 print("Extracting peak regions from average profile "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
354 "(score threshold = 0) ... ")
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
355 killpep8 = args.max_merge_dist
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
356 gplib.graphprot_profile_extract_peak_regions(avg_prof_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
357 avg_prof_peaks_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
358 max_merge_dist=killpep8,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
359 sc_thr=args.score_thr)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
360 # Convert peaks to genomic coordinates.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
361 if args.genomic_sites_bed:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
362 print("Converting peak regions to genomic coordinates ... ")
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
363 killit = args.genomic_sites_bed
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
364 gplib.bed_peaks_to_genomic_peaks(avg_prof_peaks_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
365 avg_prof_gen_peaks_file,
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
366 print_rows=False,
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
367 genomic_sites_bed=killit)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
368 # Extract peak regions with threshold score p50.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
369 if args.conf_out:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
370 sc_id = "pos_train_avg_profile_median_%i" % (args.ap_extlr)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
371 # Filter by pos_tr_ws_pred_med median.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
372 assert sc_id in param_dic, "average profile extlr %i median "\
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
373 "information missing in .params file" % (args.ap_extlr)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
374 p50_sc_thr = float(param_dic[sc_id])
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
375 print("Extracting p50 peak regions from average profile "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
376 "(score threshold = %f) ... " % (p50_sc_thr))
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
377 despair = avg_prof_peaks_p50_file
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
378 pain = args.max_merge_dist
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
379 gplib.graphprot_profile_extract_peak_regions(avg_prof_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
380 despair,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
381 max_merge_dist=pain,
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
382 sc_thr=p50_sc_thr)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
383 # Convert peaks to genomic coordinates.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
384 if args.genomic_sites_bed:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
385 print("Converting p50 peak regions to "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
386 "genomic coordinates ... ")
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
387 madness = args.genomic_sites_bed
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
388 gplib.bed_peaks_to_genomic_peaks(avg_prof_peaks_p50_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
389 avg_prof_gen_peaks_p50_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 2
diff changeset
390 genomic_sites_bed=madness)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
391 # Done.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
392 print("Script: I'm done.")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
393 print("Author: ... ")