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