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