annotate glimmer_wo_icm.py @ 0:9c195b26a5ac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author bgruening
date Tue, 28 Nov 2017 10:08:06 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
2 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
3 Input: DNA Fasta File
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
4 Output: Tabular
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
5 Return Tabular File with predicted ORF's
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
6 Bjoern Gruening
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
7 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
8 import os
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
9 import shutil
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
10 import subprocess
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
11 import sys
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
12 import tempfile
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
13
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
14 from glimmer2seq import glimmer2seq
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
15
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
16
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
17 def main():
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
18 genome_seq_file = sys.argv[1]
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
19 outfile_classic_glimmer = sys.argv[2]
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
20 outfile_ext_path = sys.argv[3]
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
21 oufile_genes = sys.argv[8]
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
22
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
23 tag = 'glimmer_non_knowlegde_based_prediction'
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
24 tempdir = tempfile.gettempdir()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
25
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
26 trainingset = os.path.join(tempdir, tag + ".train")
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
27 icm = os.path.join(tempdir, tag + ".icm")
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
28
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
29 longorfs = tempfile.NamedTemporaryFile()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
30 trainingset = tempfile.NamedTemporaryFile()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
31 icm = tempfile.NamedTemporaryFile()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
32
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
33 # glimmeropts = "-o0 -g110 -t30 -l"
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
34 glimmeropts = "-o%s -g%s -t%s" % (sys.argv[4], sys.argv[5], sys.argv[6])
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
35 if sys.argv[7] == "true":
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
36 glimmeropts += " -l"
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
37
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
38 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
39 1. Find long, non-overlapping orfs to use as a training set
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
40 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
41 subprocess.Popen(["long-orfs", "-n", "-t", "1.15",
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
42 genome_seq_file, "-"], stdout=longorfs,
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
43 stderr=subprocess.PIPE).communicate()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
44
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
45 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
46 2. Extract the training sequences from the genome file
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
47 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
48 subprocess.Popen(["extract", "-t",
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
49 genome_seq_file, longorfs.name], stdout=trainingset,
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
50 stderr=subprocess.PIPE).communicate()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
51
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
52 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
53 3. Build the icm from the training sequences
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
54 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
55
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
56 # the "-" parameter is used to redirect the output to stdout
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
57 subprocess.Popen(["build-icm", "-r", "-"],
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
58 stdin=open(trainingset.name), stdout=icm,
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
59 stderr=subprocess.PIPE).communicate()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
60
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
61 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
62 Run Glimmer3
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
63 """
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
64 subprocess.Popen(["glimmer3", glimmeropts,
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
65 genome_seq_file, icm.name, os.path.join(tempdir, tag)],
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
66 stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
67
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
68 if outfile_classic_glimmer.strip() != 'None':
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
69 shutil.copyfile(os.path.join(tempdir, tag + ".predict"), outfile_classic_glimmer)
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
70 if outfile_ext_path.strip() != 'None':
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
71 shutil.copyfile(os.path.join(tempdir, tag + ".detail"), outfile_ext_path)
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
72
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
73 glimmer2seq(os.path.join(tempdir, tag + ".predict"), genome_seq_file, oufile_genes)
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
74
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
75
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
76 if __name__ == "__main__":
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
bgruening
parents:
diff changeset
77 main()