root/galaxy-central/tools/rgenetics/listFiles.py

リビジョン 2, 7.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#Provides Upload tool with access to list of available files
2import glob,sys
3import galaxy.app as thisapp
4import galaxy.util
5
6from elementtree.ElementTree import XML
7
8librepos = '/usr/local/galaxy/data/rg'
9myrepos = '/home/rerla/galaxy'
10marchinirepos = '/usr/local/galaxy/data/rg/snptest'
11
12from galaxy.tools.parameters import DataToolParameter
13
14#Provides Upload tool with access to list of available builds
15
16builds = []
17#Read build names and keys from galaxy.util
18for dbkey, build_name in galaxy.util.dbnames:
19    builds.append((build_name,dbkey,False))
20
21#Return available builds
22def get_available_builds(defval='hg18'):
23    for i,x in enumerate(builds):
24        if x[1] == defval:
25           x = list(x)
26           x[2] = True
27           builds[i] = tuple(x)
28    return builds
29
30
31
32def get_tabular_cols( input, outformat='gg' ):
33    """numeric only other than rs for strict genome graphs
34    otherwise tabular. Derived from galaxy tool source around August 2007 by Ross"""
35    columns = []
36    seenCnames = {}
37    elems = []
38    colnames = ['Col%d' % x for x in range(input.metadata.columns+1)]
39    strict = (outformat=='gg')
40    for i, line in enumerate( file ( input.file_name ) ):
41        if line and not line.startswith( '#' ):
42            line = line.rstrip('\r\n')
43            elems = line.split( '\t' )
44   
45            """
46            Strict gg note:
47            Since this tool requires users to select only those columns
48            that contain numerical values, we'll restrict the column select
49            list appropriately other than the first column which must be a marker
50            """
51            if len(elems) > 0:
52                for col in range(1, input.metadata.columns+1):
53                    isFloat = False # short circuit common result
54                    try:
55                        val = float(elems[col-1])
56                        isFloat = True
57                    except:
58                        val = elems[col-1]
59                        if val:
60                            if i == 0: # header row
61                               colnames[col] = val
62                    if isFloat or (not strict) or (col == 1): # all in if not GG
63                        option = colnames[col]
64                        if not seenCnames.get(option,None): # new
65                              columns.append((option,str(col),False))
66                              seenCnames[option] = option
67            #print 'get_tab: %d=%s. Columns=%s' % (i,line,str(columns))
68            if len(columns) > 0 and i > 10:
69                """
70                We have our select list built, so we can break out of the outer most for loop
71                """
72                break
73        if i == 30:
74            break # Hopefully we never get here...
75    for option in range(min(5,len(columns))):
76      (x,y,z) = columns[option]
77      columns[option] = (x,y,True)
78    return columns # sorted select options
79
80def get_marchini_dir():
81    """return the filesystem directory for snptest style files"""
82    return marchinirepos
83
84
85def get_lib_SNPTESTCaCofiles():
86    """return a list of file names - without extensions - available for caco studies
87    These have a common file name with both _1 and _2 suffixes"""
88    d = get_marchini_dir()
89    testsuffix = '.gen_1' # glob these
90    flist = glob.glob('%s/*%s' % (d,testsuffix))
91    flist = [x.split(testsuffix)[0] for x in flist] # leaves with a list of file set names
92    if len(flist) > 0:
93        dat = [(flist[0],flist[0],True),]
94        dat += [(x,x,False) for x in flist[1:]]
95    else:
96        dat = [('No Marchini CaCo files found in %s - convert some using the Marchini converter tool' % d,'None',True),]
97    return dat
98
99def getChropt():
100    """return dynamic chromosome select options
101    """
102    c = ['X','Y']
103    c += ['%d' % x for x in range(1,23)]
104    dat = [(x,x,False) for x in c]
105    x,y,z = dat[3]
106    dat[3] = (x,y,True)
107    return dat
108
109
110def get_phecols(fname=''):
111   """ return a list of phenotype columns for a multi-select list
112   prototype:
113   foo = ('fake - not yet implemented','not implemented','False')
114   dat = [foo for x in range(5)]
115   return dat
116   """
117   try:
118        header = file(fname,'r').next().split()
119   except:
120        return [('get_phecols unable to open file %s' % fname,'None',False),]
121   dat = [(x,x,False) for x in header]
122   return dat
123
124#Return various kinds of files
125
126def get_lib_pedfiles():
127    dat = glob.glob('%s/ped/*.ped' % librepos)
128    dat += glob.glob('%s/ped/*.ped' % myrepos)
129    dat.sort()
130    if len(dat) > 0:
131        dat = [x.split('.ped')[0] for x in dat]
132        dat = [(x,x,'True') for x in dat]
133    else:
134        dat = [('No ped files - add some to %s/ped or %s/ped' % (librepos,myrepos),'None',True),]
135    return dat
136
137def get_lib_phefiles():
138    ext = 'phe'
139    dat = glob.glob('%s/pheno/*.%s' % (librepos,ext))
140    dat += glob.glob('%s/pheno/*.%s' % (myrepos,ext))
141    dat.sort()
142    if len(dat) > 0:
143        dat = [(x,x,'False') for x in dat]
144    else:
145        dat = [('No %s files - add some to %s/pheno or %s/pheno' % (ext,librepos,myrepos),'None',True),]
146    return dat
147
148def get_lib_bedfiles():
149    dat = glob.glob('%s/plinkbed/*.bed' % librepos)
150    dat += glob.glob('%s/plinkbed/*.bed' % myrepos)
151    dat.sort()
152    if len(dat) > 0:
153        dat = [x.split('.bed')[0] for x in dat]
154        dat = [(x,x,False) for x in dat]
155    else:
156        dat = [('No bed files - Please import some to %s/plinkbed or %s/plinkbed' % (librepos,myrepos),'None',True),]
157    return dat
158
159def get_lib_fbatfiles():
160    dat = glob.glob('%s/plinkfbat/*.ped' % librepos)
161    dat += glob.glob('%s/plinkfbat/*.ped' % myrepos)
162    dat.sort()
163    if len(dat) > 0:
164        dat = [(x,x,False) for x in dat]
165    else:
166        dat = [('No fbat bed files - Please import some to %s/plinkfbat or %s/plinkfbat' % (librepos,myrepos),'None',True),]
167    return dat
168
169def get_lib_mapfiles():
170    dat = glob.glob('%s/ped/*.map' % librepos)
171    dat += glob.glob('%s/ped/*.map' % myrepos)
172    dat.sort()
173    if len(dat) > 0:
174        dat = [(x,x,False) for x in dat]
175    else:
176        dat = [('No map files - add some to %s/ped' % librepos,'None',True),]
177    return dat
178
179def get_my_pedfiles():
180    dat = glob.glob('%s/*.ped' % myrepos)
181    if len(dat) > 0:
182        dat = [(x,x,False) for x in dat]
183    else:
184        dat = [('No ped files - add some to %s' % librepos,'None',True),]
185    return dat
186
187def get_my_mapfiles():
188    dat = glob.glob('%s/*.map' % myrepos)
189    if len(dat) > 0:
190        dat = [(x,x,'True') for x in dat]
191    else:
192        dat = [('No ped files - add some to %s' % librepos,'None',True),]
193    return dat
194
195def get_lib_xlsfiles():
196    dat = glob.glob('%s/*.xls' % librepos)
197    if len(dat) > 0:
198        dat = [(x,x,False) for x in dat]
199    else:
200        dat = [('No ped files - add some to %s' % librepos,'None',True),]
201    return dat
202
203def get_lib_htmlfiles():
204    dat = glob.glob('%s/*.html' % librepos)
205    if len(dat) > 0:
206        dat = [(x,x,False) for x in dat]
207    else:
208        dat = [('No ped files - add some to %s' % librepos,'None',True),]
209    return dat
210
211def get_my_xlsfiles():
212    dat = glob.glob('%s/*.xls' %  myrepos)
213    if len(dat) > 0:
214        dat = [(x,x,False) for x in dat]
215    else:
216        dat = [('No ped files - add some to %s' % librepos,'None',True),]
217    return dat
218
219def get_my_htmlfiles():
220    dat = glob.glob('%s/*.html' % myrepos)
221    if len(dat) > 0:
222        dat = [(x,x,False) for x in dat]
223    else:
224        dat = [('No ped files - add some to %s' % librepos,'None',True),]
225    return dat
226
227
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