Mercurial > repos > fubar > rg_gsea
diff rgGSEA/makeGSEAloc.py @ 4:89e89b70a867 draft default tip
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| author | fubar |
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| date | Sun, 09 Jun 2013 23:09:34 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgGSEA/makeGSEAloc.py Sun Jun 09 23:09:34 2013 -0400 @@ -0,0 +1,146 @@ +#!/bin/env python +# make the gsea loc files needed for the rgGSEA tool from a directory +# containing gmt and chip files downloaded from the gsea site +# Copyright ross lazarus feb 2012 +# all rights reserved +# licensed under the LGPL + +import os,sys,glob,time + +notes = """ + + <table name="gseaChip" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/gseaChip_%s.loc" /> + </table> + <table name="gseaGMT" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/gseaGMTsymbols%s.loc" /> + </table> + +""" + +def timenow(): + """return current time as a string + """ + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + +def makeLoc(paths=[],head=[],outpath='gseaChip.loc',): + """ + write a 3 column loc file - name, value, path from a glob list + """ + paths.sort() + loc = [[os.path.basename(x),x] for x in paths] + loc = [[os.path.splitext(x[0])[0],os.path.splitext(x[0])[0],x[1]] for x in loc] + loc = ['\t'.join(x) for x in loc] + loc.sort() + f = open(outpath,'w') + f.write('\n'.join(head)) + f.write('\n') + f.write('\n'.join(loc)) + f.write('\n') + f.close() + +""" +AgoodchoiceC2_c3_c5_entrez_all.gmt Clontech_BD_Atlas.chip MOE430B.chip +AgoodchoiceC2_c3_c5_orig_all.gmt CNMCMuscleChip.chip MoEx_1_0_st.chip +AgoodchoiceC2_c3_c5_symbols_all.gmt CodeLink_Human_Whole_Genome.chip MoGene_1_0_st.chip +APPLERA_ABI1700.chip CodeLink_UniSet_Human_20K_I_Bioarray.chip MoGene_1_1_st.chip +ATH1_121501.chip CodeLink_UniSet_Human_I_Bioarray.chip Mouse430_2.chip +AtlasMouse1.2.chip CodeLink_UniSet_Human_II_Bioarray.chip Mouse430A_2.chip +AtlasRat1.2.chip CodeLink_UniSet_Rat_I_Bioarray.chip msigdb.v3.1.entrez.gmt +BIAO.chip DrosGenome1.chip msigdb_v3.1_files_to_download_locally +Bovine.chip Drosophila_2.chip msigdb.v3.1.orig.gmt +c1.all.v3.1.entrez.gmt G4110A.chip msigdb.v3.1.symbols.gmt +c1.all.v3.1.orig.gmt G4110Av2.chip msigdb_v3.1.xml +c1.all.v3.1.symbols.gmt GENE_SYMBOL.chip Mu11KsubA.chip +c2.all.v3.1.entrez.gmt GenosysCytokineV2.chip Mu11KsubB.chip +c2.all.v3.1.orig.gmt gseaChip3.1.loc Mu19KsubA.chip +c2.all.v3.1.symbols.gmt gseaGMTsymbols_3.1.loc Mu19KsubB.chip +c2.cgp.v3.1.entrez.gmt HC_G110.chip Mu19KsubC.chip +c2.cgp.v3.1.orig.gmt HG_Focus.chip MWG_Human_30K_A.chip +c2.cgp.v3.1.symbols.gmt HG_U133A_2.chip MWG_Human_30K_B.chip +c2.cp.biocarta.v3.1.entrez.gmt HG_U133AAOFAV2.chip Netherland_cancer_institute_operon_human_35k.chip +c2.cp.biocarta.v3.1.orig.gmt HG_U133A.chip Netherland_cancer_institute_operon_mouse_FOOk.chip +c2.cp.biocarta.v3.1.symbols.gmt HG_U133B.chip NIA15k.chip +c2.cp.kegg.v3.1.entrez.gmt HG_U133_Plus_2.chip OPERON_HUMANv2.chip +c2.cp.kegg.v3.1.orig.gmt HG_U95Av2.chip OPERON_HUMANv3.chip +c2.cp.kegg.v3.1.symbols.gmt HG_U95B.chip Ortholog_SEQ_ACCESSION_MOUSE.chip +c2.cp.reactome.v3.1.entrez.gmt HG_U95C.chip RAE230A.chip +c2.cp.reactome.v3.1.orig.gmt HG_U95D.chip RAE230B.chip +c2.cp.reactome.v3.1.symbols.gmt HG_U95E.chip Rat230_2.chip +c2.cp.v3.1.entrez.gmt HPCGGCompugenAnnotations.chip RefSeq_human.chip +c2.cp.v3.1.orig.gmt HT_HG_U133A.chip RefSeq_NP_Human.chip +c2.cp.v3.1.symbols.gmt HT_HG_U133A_EA.chip RefSeq_NP_Mouse.chip +c3.all.v3.1.entrez.gmt Hu35KsubA.chip RefSeq_NP_Rat.chip +c3.all.v3.1.orig.gmt Hu35KsubB.chip Research_Genetics.chip +c3.all.v3.1.symbols.gmt Hu35KsubC.chip RG_U34A.chip +c3.mir.v3.1.entrez.gmt Hu35KsubD.chip RG_U34B.chip +c3.mir.v3.1.orig.gmt HU6800.chip RG_U34C.chip +c3.mir.v3.1.symbols.gmt HuEx_1_0_STv2.chip RN_U34.chip +c3.tft.v3.1.entrez.gmt HuGene_1_0_st.chip Rosetta50K.chip +c3.tft.v3.1.orig.gmt Illimina_Mus6_v1_1.chip Rosetta.chip +c3.tft.v3.1.symbols.gmt Illimuna_Mus6_v1.chip RT_U34.chip +c4.all.v3.1.entrez.gmt Illumina_Hum6_v1.chip RZPD_Human_Ensembl1.1.chip +c4.all.v3.1.orig.gmt Illumina_Hum6_v2.chip RZPD_Human_ORF_Clones_Gateway.chip +c4.all.v3.1.symbols.gmt Illumina_Human.chip RZPD_Human_Unigene3.1.chip +c4.cgn.v3.1.entrez.gmt Illumina_HumRef8_v1.chip Seq_Accession.chip +c4.cgn.v3.1.orig.gmt Illumina_HumRef8_v2.chip Stanford.chip +c4.cgn.v3.1.symbols.gmt Illumina_Mus6_v2.chip Stanford_Source_Accessions.chip +c4.cm.v3.1.entrez.gmt Illumina_MusRef8_v1_1.chip TIGR_31K_Human_Set.chip +c4.cm.v3.1.orig.gmt Illumina_MusRef8_v1.chip TIGR_40K_Human_Set.chip +c4.cm.v3.1.symbols.gmt Illumina_RatRef12_v1.chip TRC.chip +c5.all.v3.1.entrez.gmt ilmn_HumanHT_12_V3_0_R3_11283641_A.chip TRC_DB.chip +c5.all.v3.1.orig.gmt ilmn_HumanHT_12_V4_0_R1_15002873_B.chip TRC_DB_v1.chip +c5.all.v3.1.symbols.gmt ilmn_HumanRef_8_V2_0_R4_11223162_A.chip U133_X3P.chip +c5.bp.v3.1.entrez.gmt ilmn_HUMANREF_8_V3_0_R1_11282963_A_WGDASL.chip UCLA_NIH_33K.chip +c5.bp.v3.1.orig.gmt ilmn_HumanRef_8_V3_0_R3_11282963_A.chip Zebrafish.chip +c5.bp.v3.1.symbols.gmt +""" +import subprocess + +def makeRoss(): + for kind in ['orig','symbols','entrez']: + outf = 'Abetterchoice_nocgp_c2_c3_c5_%s_all.gmt' % kind + o = open(outf,'w') + 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' \ + % (kind,kind,kind,kind,kind) + cl = s.split(' ') + print 'running',cl + p = subprocess.check_call(cl,shell=False,stdout=o) + o.close() + outf = 'Agoodchoice_c2_c3_c5_%s_all.gmt' % kind + o = open(outf,'w') + s = 'cat c2.all.v3.1.%s.gmt c3.all.v3.1.%s.gmt c5.all.v3.1.%s.gmt' \ + % (kind,kind,kind) + cl = s.split(' ') + print 'running',cl + p = subprocess.check_call(cl,shell=False,stdout=o) + o.close() + + +def main(): + if len(sys.argv) >= 1: + usedir = os.path.abspath(sys.argv[1]) + vers = sys.argv[2] or '3.1' + print 'Using supplied path',usedir,'and vers',vers + else: # default at BakerIDI + usedir = '/data/genomes/gsea' + vers = '3.1' + print 'Using default path',usedir,'and vers',vers + 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 + progName = os.path.basename(sys.argv[0]) + 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'] + makeRoss() + chips = glob.glob(os.path.join(usedir,'*.chip')) + makeLoc(paths=chips,head=h,outpath=os.path.join(usedir,'gseaChip%s.loc' % vers)) + for kind in ['orig','symbols','entrez']: + gmt = glob.glob(os.path.join(usedir,'*.gmt')) + gmt = [x for x in gmt if x.find(kind) <> -1] + makeLoc(paths=gmt,head=h,outpath=os.path.join(usedir,'gseaGMT%s_%s.loc' % (kind,vers))) + 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) + print '## something like:' + print notes % (vers,vers) + print '## should do for tool_data_tables.xml' +if __name__=="__main__": + main()