Commits

Faheem Mitha committed 83cee91

Replace datafile with gene.

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Files changed (2)

     cdf_cmd = "./cm-cdf"
     neglogpp_cmd = "./cm-neglogpp"
     neglogpptable_cmd = "./cm-neglogpptable"
-    datafiletable_cmd = "./cm-datafiletable"
+    genetable_cmd = "./cm-genetable"
 else:
     cdf_cmd = "cm-cdf"
     neglogpp_cmd = "cm-neglogpp"
     neglogpptable_cmd = "cm-neglogpptable"
-    datafiletable_cmd = "cm-datafiletable"
+    genetable_cmd = "cm-genetable"
 
 pdffig_tex = Split("MODEL.tex CDF.tex NEGLOGPPHUMAN.tex NEGLOGPPMOUSE.tex")
 pgffig_pdf = Split("Figure1-model.pdf Figure4-cdf.pdf Figure5-neglogpphuman.pdf Figure6-neglogppmouse.pdf")
-table_tex = Split("NEGLOGPPTABLEHUMAN.tex NEGLOGPPTABLEMOUSE.tex DATAFILETABLEHUMAN.tex DATAFILETABLEMOUSE.tex")
+table_tex = Split("NEGLOGPPTABLEHUMAN.tex NEGLOGPPTABLEMOUSE.tex GENETABLEHUMAN.tex GENETABLEMOUSE.tex")
 env = Environment()
 env.Append(PDFLATEXFLAGS=[ "-shell-escape"])
 
 env.Command("CDF.tex", source=None, action=cdf_cmd)
 env.Command(Split("NEGLOGPPHUMAN.tex NEGLOGPPMOUSE.tex"), source=None, action=neglogpp_cmd)
 env.Command(Split("NEGLOGPPTABLEHUMAN.tex NEGLOGPPTABLEMOUSE.tex"), source=None, action=neglogpptable_cmd)
-env.Command(Split("DATAFILETABLEHUMAN.tex DATAFILETABLEMOUSE.tex"), source=None, action=datafiletable_cmd)
+env.Command(Split("GENETABLEHUMAN.tex GENETABLEMOUSE.tex"), source=None, action=genetable_cmd)
 
 env.Depends("figures.pdf", pdffig_tex + table_tex)
 env.PDF(target=["figures.pdf"]+pgffig_pdf, source="figures.tex")
 def getfasta(dataset, dirpath):
     """
     Make multiple wget calls to download a fasta file corresponding to
-    the accession numbers in 'datafiles_info' corresponding to
+    the accession numbers in 'genes_info' corresponding to
     'dataset'. Each call downloads a fasta file. wgetcmd concatenates
     them together. NOTE: The hardwired 30 is the maximum number of
     accession numbers that ebi accepts in a single request.
     import os
     from corrmodel import utils
     conf = utils.get_conf()
-    datafiles_info = conf[dataset]["datafiles_info"]
-    accnumlst = list(set([d[0] for d in datafiles_info]))
+    genes_info = conf[dataset]["genes_info"]
+    accnumlst = list(set([d[0] for d in genes_info]))
     accnumlst.sort()
     lstlen = len(accnumlst)
     try: