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1 #!/bin/env python
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2 # make the gsea loc files needed for the rgGSEA tool from a directory
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3 # containing gmt and chip files downloaded from the gsea site
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4 # Copyright ross lazarus feb 2012
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5 # all rights reserved
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6 # licensed under the LGPL
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7
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8 import os,sys,glob,time
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9
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10 notes = """
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11
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12 <table name="gseaChip" comment_char="#">
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13 <columns>value, name, path</columns>
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14 <file path="tool-data/gseaChip_%s.loc" />
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15 </table>
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16 <table name="gseaGMT" comment_char="#">
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17 <columns>value, name, path</columns>
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18 <file path="tool-data/gseaGMTsymbols%s.loc" />
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19 </table>
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20
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21 """
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22
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23 def timenow():
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24 """return current time as a string
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25 """
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26 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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27
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28 def makeLoc(paths=[],head=[],outpath='gseaChip.loc',):
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29 """
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30 write a 3 column loc file - name, value, path from a glob list
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31 """
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32 paths.sort()
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33 loc = [[os.path.basename(x),x] for x in paths]
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34 loc = [[os.path.splitext(x[0])[0],os.path.splitext(x[0])[0],x[1]] for x in loc]
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35 loc = ['\t'.join(x) for x in loc]
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36 loc.sort()
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37 f = open(outpath,'w')
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38 f.write('\n'.join(head))
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39 f.write('\n')
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40 f.write('\n'.join(loc))
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41 f.write('\n')
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42 f.close()
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43
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44 """
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45 AgoodchoiceC2_c3_c5_entrez_all.gmt Clontech_BD_Atlas.chip MOE430B.chip
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46 AgoodchoiceC2_c3_c5_orig_all.gmt CNMCMuscleChip.chip MoEx_1_0_st.chip
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47 AgoodchoiceC2_c3_c5_symbols_all.gmt CodeLink_Human_Whole_Genome.chip MoGene_1_0_st.chip
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48 APPLERA_ABI1700.chip CodeLink_UniSet_Human_20K_I_Bioarray.chip MoGene_1_1_st.chip
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49 ATH1_121501.chip CodeLink_UniSet_Human_I_Bioarray.chip Mouse430_2.chip
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50 AtlasMouse1.2.chip CodeLink_UniSet_Human_II_Bioarray.chip Mouse430A_2.chip
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51 AtlasRat1.2.chip CodeLink_UniSet_Rat_I_Bioarray.chip msigdb.v3.1.entrez.gmt
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52 BIAO.chip DrosGenome1.chip msigdb_v3.1_files_to_download_locally
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53 Bovine.chip Drosophila_2.chip msigdb.v3.1.orig.gmt
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54 c1.all.v3.1.entrez.gmt G4110A.chip msigdb.v3.1.symbols.gmt
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55 c1.all.v3.1.orig.gmt G4110Av2.chip msigdb_v3.1.xml
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56 c1.all.v3.1.symbols.gmt GENE_SYMBOL.chip Mu11KsubA.chip
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57 c2.all.v3.1.entrez.gmt GenosysCytokineV2.chip Mu11KsubB.chip
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58 c2.all.v3.1.orig.gmt gseaChip3.1.loc Mu19KsubA.chip
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59 c2.all.v3.1.symbols.gmt gseaGMTsymbols_3.1.loc Mu19KsubB.chip
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60 c2.cgp.v3.1.entrez.gmt HC_G110.chip Mu19KsubC.chip
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61 c2.cgp.v3.1.orig.gmt HG_Focus.chip MWG_Human_30K_A.chip
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62 c2.cgp.v3.1.symbols.gmt HG_U133A_2.chip MWG_Human_30K_B.chip
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63 c2.cp.biocarta.v3.1.entrez.gmt HG_U133AAOFAV2.chip Netherland_cancer_institute_operon_human_35k.chip
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64 c2.cp.biocarta.v3.1.orig.gmt HG_U133A.chip Netherland_cancer_institute_operon_mouse_FOOk.chip
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65 c2.cp.biocarta.v3.1.symbols.gmt HG_U133B.chip NIA15k.chip
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66 c2.cp.kegg.v3.1.entrez.gmt HG_U133_Plus_2.chip OPERON_HUMANv2.chip
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67 c2.cp.kegg.v3.1.orig.gmt HG_U95Av2.chip OPERON_HUMANv3.chip
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68 c2.cp.kegg.v3.1.symbols.gmt HG_U95B.chip Ortholog_SEQ_ACCESSION_MOUSE.chip
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69 c2.cp.reactome.v3.1.entrez.gmt HG_U95C.chip RAE230A.chip
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70 c2.cp.reactome.v3.1.orig.gmt HG_U95D.chip RAE230B.chip
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71 c2.cp.reactome.v3.1.symbols.gmt HG_U95E.chip Rat230_2.chip
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72 c2.cp.v3.1.entrez.gmt HPCGGCompugenAnnotations.chip RefSeq_human.chip
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73 c2.cp.v3.1.orig.gmt HT_HG_U133A.chip RefSeq_NP_Human.chip
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74 c2.cp.v3.1.symbols.gmt HT_HG_U133A_EA.chip RefSeq_NP_Mouse.chip
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75 c3.all.v3.1.entrez.gmt Hu35KsubA.chip RefSeq_NP_Rat.chip
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76 c3.all.v3.1.orig.gmt Hu35KsubB.chip Research_Genetics.chip
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77 c3.all.v3.1.symbols.gmt Hu35KsubC.chip RG_U34A.chip
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78 c3.mir.v3.1.entrez.gmt Hu35KsubD.chip RG_U34B.chip
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79 c3.mir.v3.1.orig.gmt HU6800.chip RG_U34C.chip
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80 c3.mir.v3.1.symbols.gmt HuEx_1_0_STv2.chip RN_U34.chip
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81 c3.tft.v3.1.entrez.gmt HuGene_1_0_st.chip Rosetta50K.chip
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82 c3.tft.v3.1.orig.gmt Illimina_Mus6_v1_1.chip Rosetta.chip
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83 c3.tft.v3.1.symbols.gmt Illimuna_Mus6_v1.chip RT_U34.chip
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84 c4.all.v3.1.entrez.gmt Illumina_Hum6_v1.chip RZPD_Human_Ensembl1.1.chip
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85 c4.all.v3.1.orig.gmt Illumina_Hum6_v2.chip RZPD_Human_ORF_Clones_Gateway.chip
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86 c4.all.v3.1.symbols.gmt Illumina_Human.chip RZPD_Human_Unigene3.1.chip
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87 c4.cgn.v3.1.entrez.gmt Illumina_HumRef8_v1.chip Seq_Accession.chip
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88 c4.cgn.v3.1.orig.gmt Illumina_HumRef8_v2.chip Stanford.chip
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89 c4.cgn.v3.1.symbols.gmt Illumina_Mus6_v2.chip Stanford_Source_Accessions.chip
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90 c4.cm.v3.1.entrez.gmt Illumina_MusRef8_v1_1.chip TIGR_31K_Human_Set.chip
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91 c4.cm.v3.1.orig.gmt Illumina_MusRef8_v1.chip TIGR_40K_Human_Set.chip
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92 c4.cm.v3.1.symbols.gmt Illumina_RatRef12_v1.chip TRC.chip
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93 c5.all.v3.1.entrez.gmt ilmn_HumanHT_12_V3_0_R3_11283641_A.chip TRC_DB.chip
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94 c5.all.v3.1.orig.gmt ilmn_HumanHT_12_V4_0_R1_15002873_B.chip TRC_DB_v1.chip
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95 c5.all.v3.1.symbols.gmt ilmn_HumanRef_8_V2_0_R4_11223162_A.chip U133_X3P.chip
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96 c5.bp.v3.1.entrez.gmt ilmn_HUMANREF_8_V3_0_R1_11282963_A_WGDASL.chip UCLA_NIH_33K.chip
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97 c5.bp.v3.1.orig.gmt ilmn_HumanRef_8_V3_0_R3_11282963_A.chip Zebrafish.chip
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98 c5.bp.v3.1.symbols.gmt
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99 """
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100 import subprocess
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101
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102 def makeRoss():
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103 for kind in ['orig','symbols','entrez']:
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104 outf = 'Abetterchoice_nocgp_c2_c3_c5_%s_all.gmt' % kind
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105 o = open(outf,'w')
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106 s = 'cat c2.cp.biocarta.v3.1.%s.gmt c2.cp.kegg.v3.1.%s.gmt c2.cp.reactome.v3.1.%s.gmt c3.all.v3.1.%s.gmt c5.all.v3.1.%s.gmt' \
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107 % (kind,kind,kind,kind,kind)
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108 cl = s.split(' ')
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109 print 'running',cl
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110 p = subprocess.check_call(cl,shell=False,stdout=o)
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111 o.close()
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112 outf = 'Agoodchoice_c2_c3_c5_%s_all.gmt' % kind
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113 o = open(outf,'w')
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114 s = 'cat c2.all.v3.1.%s.gmt c3.all.v3.1.%s.gmt c5.all.v3.1.%s.gmt' \
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115 % (kind,kind,kind)
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116 cl = s.split(' ')
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117 print 'running',cl
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118 p = subprocess.check_call(cl,shell=False,stdout=o)
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119 o.close()
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120
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121
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122 def main():
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123 if len(sys.argv) >= 1:
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124 usedir = os.path.abspath(sys.argv[1])
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125 vers = sys.argv[2] or '3.1'
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126 print 'Using supplied path',usedir,'and vers',vers
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127 else: # default at BakerIDI
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128 usedir = '/data/genomes/gsea'
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129 vers = '3.1'
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130 print 'Using default path',usedir,'and vers',vers
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131 assert os.path.isdir(usedir),'## unable to open %s - please pass the path to a directory containing all gsea chip/gmt downloaded from ftp://gseaftp.broadinstitute.org/pub/gsea/annotations on the command line' % usedir
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132 progName = os.path.basename(sys.argv[0])
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133 h = ['# generated by %s at %s from path = %s' % (progName,timenow(),usedir),'# loc file for the rgGSEA tool pointing to files from ftp://gseaftp.broadinstitute.org/pub/gsea/annotations','# name value path']
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134 makeRoss()
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135 chips = glob.glob(os.path.join(usedir,'*.chip'))
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136 makeLoc(paths=chips,head=h,outpath=os.path.join(usedir,'gseaChip%s.loc' % vers))
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137 for kind in ['orig','symbols','entrez']:
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138 gmt = glob.glob(os.path.join(usedir,'*.gmt'))
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139 gmt = [x for x in gmt if x.find(kind) <> -1]
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140 makeLoc(paths=gmt,head=h,outpath=os.path.join(usedir,'gseaGMT%s_%s.loc' % (kind,vers)))
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141 print '## %s done. copy the new .loc files in %s to your galaxy tool-data directory, add them to your tool_data_tables.xml file and restart Galaxy' % (progName,usedir)
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142 print '## something like:'
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143 print notes % (vers,vers)
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144 print '## should do for tool_data_tables.xml'
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145 if __name__=="__main__":
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146 main()
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