Mercurial > repos > devteam > weblogo3
annotate rgWebLogo3.py @ 4:c1a9e644d580 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weblogo3 commit b3b7a9898eb2b5d12745ef96250b04955bd1e209
| author | devteam |
|---|---|
| date | Thu, 03 Dec 2015 15:55:38 -0500 |
| parents | 66253fc0a69b |
| children | dc25a5169a91 |
| rev | line source |
|---|---|
| 0 | 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) | |
|
4
c1a9e644d580
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weblogo3 commit b3b7a9898eb2b5d12745ef96250b04955bd1e209
devteam
parents:
0
diff
changeset
|
108 return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input, lasti+1, flen) |
| 0 | 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 |