parsedFilePath = os.path.realpath(
os.path.join(homeDir, "dn-trinity", "blast-dn-parsed.csv"))
summaryFile1 = os.path.join(homeDir, "blast", "blast-up-parsed_summary.csv")
summaryFile2 = os.path.join(homeDir, "blast", 'blast-dm-parsed_summary.csv')
summaryFile3 = os.path.join(homeDir, "blast", 'blast-dp-parsed_summary.csv')
bm = BlastMapper()
## load the gene and isoform maps
bmapSP = bm.load_summary(summaryFile1, trinityGene=False, best=True)
bmapDM = bm.load_summary(summaryFile2, trinityGene=False, best=True)
bmapDP = bm.load_summary(summaryFile3, trinityGene=False, best=True)
print("-----------")
print("SwissProt - isoforms")
bm.print_summary(bmapSP)
print("D. melanogaster - isoforms")
bm.print_summary(bmapDM)
print("Danaus plexippus - isoforms")
bm.print_summary(bmapDP)
bm.make_taxa_pie_chart_and_table(
bmapSP,
removeStrain=True,
figName="dn-trinity-blast-pie-isoforms.png",
csvName="dn-trinity-blast-species-isoforms.csv")
#bm.make_taxa_pie_chart_and_table(bmapInsects,removeStrain=True,
# figName="dn-trinity-blast-pie-insects.png",
# csvName="dn-trinity-blast-species-insects.csv")
summaryFile2 = os.path.join(homeDir, sourceDir, "blast-xt-parsed_summary.csv")
bm = BlastMapper()
## load the gene and isoform maps
bmapIsoforms = bm.load_summary(summaryFile1, trinityGene=False, best=True)
bmapFrog = bm.load_summary(summaryFile1,
trinityGene=False,
best=True,
taxaList=['8355', '8364'])
bmapXT = bm.load_summary(summaryFile2, trinityGene=False, best=True)
print("-----------")
print("SwissProt - isoforms")
bm.print_summary(bmapIsoforms)
print("SwissProt [8355,8364] - isoforms")
bm.print_summary(bmapFrog)
print("X. tropicalis - isoforms")
bm.print_summary(bmapXT)
bm.make_taxa_pie_chart_and_table(
bmapIsoforms,
removeStrain=True,
figName="%s-trinity-blast-pie-isoforms.png" % (source),
csvName="%s-trinity-blast-species-isoforms.csv" % (source))
bm.make_taxa_pie_chart_and_table(
bmapFrog,
removeStrain=True,
figName="%s-trinity-blast-pie-frog.png" % (source),
csvName="%s-trinity-blast-species-frog.csv" % (source))
