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