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annotate glimmer_wo_icm.py @ 0:49cf6416bd2b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author bgruening
date Tue, 28 Nov 2017 10:17:37 -0500
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49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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1 #!/usr/bin/env python
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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2 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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3 Input: DNA Fasta File
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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4 Output: Tabular
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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5 Return Tabular File with predicted ORF's
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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6 Bjoern Gruening
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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7 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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8 import os
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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9 import shutil
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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10 import subprocess
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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11 import sys
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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12 import tempfile
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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14 from glimmer2seq import glimmer2seq
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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17 def main():
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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18 genome_seq_file = sys.argv[1]
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19 outfile_classic_glimmer = sys.argv[2]
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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20 outfile_ext_path = sys.argv[3]
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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21 oufile_genes = sys.argv[8]
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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23 tag = 'glimmer_non_knowlegde_based_prediction'
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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24 tempdir = tempfile.gettempdir()
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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26 trainingset = os.path.join(tempdir, tag + ".train")
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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27 icm = os.path.join(tempdir, tag + ".icm")
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28
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29 longorfs = tempfile.NamedTemporaryFile()
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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30 trainingset = tempfile.NamedTemporaryFile()
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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31 icm = tempfile.NamedTemporaryFile()
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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32
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33 # glimmeropts = "-o0 -g110 -t30 -l"
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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34 glimmeropts = "-o%s -g%s -t%s" % (sys.argv[4], sys.argv[5], sys.argv[6])
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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35 if sys.argv[7] == "true":
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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36 glimmeropts += " -l"
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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38 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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39 1. Find long, non-overlapping orfs to use as a training set
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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40 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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41 subprocess.Popen(["long-orfs", "-n", "-t", "1.15",
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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42 genome_seq_file, "-"], stdout=longorfs,
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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43 stderr=subprocess.PIPE).communicate()
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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45 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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46 2. Extract the training sequences from the genome file
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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47 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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48 subprocess.Popen(["extract", "-t",
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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49 genome_seq_file, longorfs.name], stdout=trainingset,
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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50 stderr=subprocess.PIPE).communicate()
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51
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52 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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53 3. Build the icm from the training sequences
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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54 """
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55
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56 # the "-" parameter is used to redirect the output to stdout
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57 subprocess.Popen(["build-icm", "-r", "-"],
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58 stdin=open(trainingset.name), stdout=icm,
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59 stderr=subprocess.PIPE).communicate()
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60
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61 """
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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62 Run Glimmer3
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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63 """
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64 subprocess.Popen(["glimmer3", glimmeropts,
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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65 genome_seq_file, icm.name, os.path.join(tempdir, tag)],
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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66 stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
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67
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68 if outfile_classic_glimmer.strip() != 'None':
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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69 shutil.copyfile(os.path.join(tempdir, tag + ".predict"), outfile_classic_glimmer)
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70 if outfile_ext_path.strip() != 'None':
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71 shutil.copyfile(os.path.join(tempdir, tag + ".detail"), outfile_ext_path)
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72
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73 glimmer2seq(os.path.join(tempdir, tag + ".predict"), genome_seq_file, oufile_genes)
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75
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76 if __name__ == "__main__":
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77 main()