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