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annotate rgWebLogo3.py @ 5:dc25a5169a91 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 commit d0f167e74e705788adcd9c846db011aee490074b
author iuc
date Fri, 17 Nov 2017 10:19:39 -0500
parents c1a9e644d580
children
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1 # modified june 2 ross lazarus to add units option at Assaf Gordon's suggestion
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2 # rgWebLogo3.py
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3 # wrapper to check that all fasta files are same length
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4
5
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5 from __future__ import print_function
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6
5
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7 import optparse
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8 import os
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9 import subprocess
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10 import sys
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11 import tempfile
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12
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13 WEBLOGO = 'weblogo' # executable name for weblogo3 - confusing isn't it?
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14
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15
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16 class WL3:
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17 """
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18 simple wrapper class to check fasta sequence lengths are all identical
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19 """
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20 FASTASTARTSYM = '>'
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21 badseq = '## error - sequences in file %s are not all the same length - cannot proceed. Please read the tool documentation carefully'
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22
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23 def __init__(self, opts=None):
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24 assert opts is not None, 'WL3 class needs opts passed in - got None'
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25 self.opts = opts
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26 self.fastaf = open(self.opts.input, 'r')
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27 self.clparams = {}
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28
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29 def whereis(self, program):
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30 for path in os.environ.get('PATH', '').split(':'):
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31 if os.path.exists(os.path.join(path, program)) and not os.path.isdir(os.path.join(path, program)):
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32 return os.path.join(path, program)
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33 return None
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34
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35 def runCL(self):
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36 """ construct and run a command line
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37 """
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38 wl = self.whereis(WEBLOGO)
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39 if not wl:
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40 print('## rgWebLogo3.py error - cannot locate the weblogo binary %s on the current path' % (WEBLOGO), file=sys.stderr)
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41 print('## Please ensure it is installed and working from https://github.com/weblogo/weblogo', file=sys.stderr)
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42 sys.exit(1)
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43 cll = [WEBLOGO, ]
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44 cll += [' '.join(it) for it in list(self.clparams.items())]
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45 cl = ' '.join(cll)
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46 assert cl > '', 'runCL needs a command line as clparms'
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47 fd, templog = tempfile.mkstemp(suffix='rgtempRun.txt')
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48 tlf = open(templog, 'w')
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49 process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf)
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50 rval = process.wait()
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51 tlf.close()
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52 tlogs = ''.join(open(templog, 'r').readlines())
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53 if len(tlogs) > 1:
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54 s = '## executing %s returned status %d and log (stdout/stderr) records: \n%s\n' % (cl, rval, tlogs)
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55 else:
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56 s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl, rval)
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57 os.unlink(templog) # always
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58 if rval != 0:
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59 print('## rgWebLogo3.py error - executing %s returned error code %d' % (cl, rval), file=sys.stderr)
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60 print('## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO, file=sys.stderr)
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61 print('## Please ensure %s is correctly installed and working on the command line -see https://github.com/weblogo/weblogo' % WEBLOGO, file=sys.stderr)
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62 sys.exit(1)
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63 return s
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64
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65 def iter_fasta(self):
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66 """
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67 generator for fasta sequences from a file
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68 """
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69 aseq = []
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70 seqname = None
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71 for i, row in enumerate(self.fastaf):
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72 if row.startswith(self.FASTASTARTSYM):
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73 if seqname is not None: # already in a sequence
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74 s = ''.join(aseq)
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75 ls = len(s)
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76 yield (seqname, ls)
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77 seqname = row[1:].strip()
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78 aseq = []
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79 else:
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80 if i > 0:
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81 print('Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input, self.FASTASTARTSYM), file=sys.stderr)
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82 sys.exit(1)
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83 else:
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84 seqname = row[1:].strip()
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85 else: # sequence row
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86 if seqname is None:
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87 print('Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input, self.FASTASTARTSYM), file=sys.stderr)
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88 sys.exit(1)
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89 else:
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90 aseq.append(row.strip())
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91
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92 if seqname is not None: # last one
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93 las = len(''.join(aseq))
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94 yield (seqname, las)
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95
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96 def fcheck(self):
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97 """ are all fasta sequence same length?
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98 might be mongo big
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99 """
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100 flen = None
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101 lasti = None
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102 f = self.iter_fasta()
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103 for i, (seqname, seqlen) in enumerate(f):
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104 lasti = i
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105 if i == 0:
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106 flen = seqlen
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107 else:
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108 if seqlen != flen:
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109 print(self.badseq % self.opts.input, file=sys.stderr)
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110 sys.exit(1)
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111 return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input, lasti + 1, flen)
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112
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113 def run(self):
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114 check = self.fcheck()
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115 self.clparams['-f'] = self.opts.input
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116 self.clparams['-o'] = self.opts.output
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117 self.clparams['-t'] = '"%s"' % self.opts.logoname # must be wrapped as a string
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118 self.clparams['-F'] = self.opts.outformat
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119 if self.opts.size is not None:
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120 self.clparams['-s'] = self.opts.size
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121 if self.opts.lower is not None:
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122 self.clparams['-l'] = self.opts.lower
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123 if self.opts.upper is not None:
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124 self.clparams['-u'] = self.opts.upper
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125 if self.opts.colours is not None:
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126 self.clparams['-c'] = self.opts.colours
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127 if self.opts.units is not None:
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128 self.clparams['-U'] = self.opts.units
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129 s = self.runCL()
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130 return check, s
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131
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132
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133 if __name__ == '__main__':
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134 op = optparse.OptionParser()
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135 op.add_option('-i', '--input', default=None)
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136 op.add_option('-F', '--outformat', default='png')
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137 op.add_option('-s', '--size', default=None)
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138 op.add_option('-o', '--output', default='rgWebLogo3')
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139 op.add_option('-t', '--logoname', default='rgWebLogo3')
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140 op.add_option('-c', '--colours', default=None)
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141 op.add_option('-l', '--lower', default=None)
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142 op.add_option('-u', '--upper', default=None)
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143 op.add_option('-U', '--units', default=None)
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144 opts, args = op.parse_args()
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145 assert opts.input is not None, 'weblogo3 needs a -i parameter with a fasta input file - cannot open'
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146 assert os.path.isfile(opts.input), 'weblogo3 needs a valid fasta input file - cannot open %s' % opts.input
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147 w = WL3(opts)
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148 checks, s = w.run()
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149 print(checks, file=sys.stdout) # for info