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comparison rgweblogo/rgWebLogo3.py @ 3:fad187cb76fe draft

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author fubar
date Thu, 05 Dec 2013 00:56:04 -0500
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2:ef1f89257fdb 3:fad187cb76fe
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