Mercurial > repos > bjoern-gruening > antismash

comparison antiSMASH_wrapper.py @ 0:6a37d0a4510a default tip

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initial uploaded
author bjoern-gruening
date Thu, 15 Mar 2012 05:23:03 -0400
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-1:000000000000 0:6a37d0a4510a
1 #!/usr/bin/env python
2 # -*- coding: UTF-8 -*-
3
4 import os, sys, subprocess, commands
5 import random, shutil
6 import zipfile
7
8
9 blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
10 pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
11 antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py'
12
13
14 def zipper(dir, zip_file):
15 zip = zipfile.ZipFile(zip_file, 'w', compression=zipfile.ZIP_DEFLATED)
16 root_len = len(os.path.abspath(dir))
17 for root, dirs, files in os.walk(dir):
18 # only inlcude the result directory
19 # assumption, each galaxy file and so the result directory starts with dataset_xxx
20 if root.find('dataset_') != -1:
21 archive_root = os.path.abspath(root)[root_len:]
22 for f in files:
23 fullpath = os.path.join(root, f)
24 archive_name = os.path.join(archive_root, f)
25 zip.write(fullpath, archive_name, zipfile.ZIP_DEFLATED)
26 zip.close()
27 return zip_file
28
29
30 def anitSMASH(args):
31 #./antismash.py Tue6071_genome.fasta --geneclustertypes 1 --fullhmm y
32 rint = random.randint(1,10000000)
33 tmp_dir = '/tmp/galaxy_%s' % rint
34 os.mkdir(tmp_dir)
35 os.mkdir(os.path.join( tmp_dir, 'geneprediction' ))
36 os.chdir(tmp_dir)
37 new_input_path = os.path.join(tmp_dir, os.path.basename(args.input) + '.fasta')
38
39 # try to generate the same name as in antismash.py
40 genomename = ".".join( (os.path.basename(args.input) + '.fasta').split(".")[:-1] )
41 for i in """!"#$%&()*+,./:;=>?@[]^`{|}'""":
42 genomename = genomename.replace(i,"")
43 result_path = os.path.join( tmp_dir, genomename )
44
45 shutil.copy(args.input, new_input_path )
46
47 if args.eukaryotic:
48 taxon = '--taxon e'
49 else:
50 taxon = '--taxon p'
51
52 if args.clusterblast:
53 clusterblast = '--clusterblast y'
54 else:
55 clusterblast = '--clusterblast n'
56
57 if args.smcogs:
58 smcogs = '--smcogs y'
59 else:
60 smcogs = '--smcogs n'
61
62 if args.fullhmm:
63 fullhmm = '--fullhmm y'
64 else:
65 fullhmm = '--fullhmm n'
66
67 if args.fullblast:
68 fullblast = '--fullblast y'
69 else:
70 fullblast = '--fullblast n'
71
72 h = [antismash_path, new_input_path,
73 '--geneclustertypes %s' % args.geneclustertypes,
74 taxon,
75 clusterblast,
76 smcogs,
77 fullhmm,
78 fullblast,
79 '--glimmer_prediction %s' % args.glimmer_prediction,
80 '--blastdbpath %s' % blastdbpath,
81 '--pfamdbpath %s' % pfamdbpath,
82 '--cores 10',
83 ]
84 a = ' '.join(h)
85 subprocess.call(a, shell=True)
86
87
88 shutil.copy(os.path.join(result_path, '%s.final.embl' % genomename), args.embl_path)
89
90 clustername_mapping = {}
91 for line in open( os.path.join(result_path, 'clusterblast/geneclusters.txt') ):
92 token = line.split('\t')
93 clustername_mapping[token[2]] = token[3]
94
95 for line in open( os.path.join(result_path, 'clusterblast/geneclusterprots.fasta') ):
96 if line.startswith('>'):
97 for k,v in clustername_mapping.items():
98 if '|%s|' % k in line:
99 args.geneclusterprots.write( line.replace('|%s|' % k, '|%s|%s|' % (k,v)) )
100 else:
101 args.geneclusterprots.write( line )
102
103 zipper(result_path, args.zip)
104
105 # html output
106 shutil.copy( os.path.join(result_path, 'display.xhtml'), args.html_file)
107 os.mkdir( args.html_path )
108 html_dest_path = os.path.join(args.html_path, 'html/')
109 images_dest_path = os.path.join(args.html_path, 'images/')
110 svg_dest_path = os.path.join(args.html_path, 'svg/')
111 substrspecs_dest_path = os.path.join(args.html_path, 'substrspecs/')
112 shutil.copytree( os.path.join(result_path, 'html/'), html_dest_path)
113 shutil.copytree( os.path.join(result_path, 'images/'), images_dest_path)
114 shutil.copytree( os.path.join(result_path, 'svg/'), svg_dest_path)
115 shutil.copytree( os.path.join(result_path, 'substrspecs/'), substrspecs_dest_path)
116 shutil.copy( os.path.join(result_path, 'jquery.svg.js'), args.html_path )
117 shutil.copy( os.path.join(result_path, 'jquery.svgdom.js'), args.html_path )
118 shutil.copy( os.path.join(result_path, 'jquery-1.4.2.min.js'), args.html_path )
119 shutil.copy( os.path.join(result_path, 'style.css'), args.html_path )
120
121 # remove tmp directory
122 shutil.rmtree(tmp_dir)
123
124
125 def arg_parse():
126 import argparse
127 parser = argparse.ArgumentParser(prog = 'antiSMASH-Wrapper')
128 parser.add_argument('--version', action='version', version='%(prog)s 0.01')
129 parser.add_argument('--geneclustertypes',
130 help='Fingerprint Type, currently FP2, FP3, FP4')
131 parser.add_argument('--clusterblast', action='store_true')
132 parser.add_argument('--eukaryotic', action='store_true')
133 parser.add_argument('--fullhmm', action='store_true')
134 parser.add_argument('--smcogs', action='store_true')
135 parser.add_argument('--fullblast', action='store_true')
136
137 parser.add_argument('--input', '-i', help='FASTA Sequence File')
138 parser.add_argument('--glimmer_prediction', help='Glimmer Prediction File')
139
140 parser.add_argument('--zip', help='output: all files as zip file')
141 parser.add_argument('--html_file', help='output: the path to the index html file')
142 parser.add_argument('--html_path', help='output: the path to the output html dir')
143 parser.add_argument('--embl_path', help='output: the path to the embl output file')
144 parser.add_argument('--geneclusterprots', help='output: Genecluster Fasta File', type=argparse.FileType('w'))
145
146 args = parser.parse_args()
147 return args
148
149
150 if __name__ == '__main__':
151 args = arg_parse()
152 anitSMASH(args)
153