def test_referenceset():
refstatsfile = get_testfile('cm-500pgun-ref-stats')
refphylfile = get_testfile('cm-ref-phyl')
r = Reference(['Acidobacterium capsulatum ATCC 51196', 'Acidobacterium capsulatum', 'Acidobacterium', 'Acidobacteriaceae', 'Acidobacteriales', 'Acidobacteriia', 'Acidobacteria', 'Fibrobacteres/Acidobacteria group', 'Bacteria', 'cellular organisms'])
assert(r.phyl["life"] == "cellular organisms")
refs = ReferenceSet(refphylfile, refstatsfile)
# There are 59 references, all indexable by id, fasta name or strain name
assert(len(refs) == 59)
assert(len(refs.refs) == 177)
# Every reference's full phylogeny is in the phyl dictionary attribute
assert(refs.get("Acidobacterium capsulatum ATCC 51196").phyl["life"] == "cellular organisms")
# The LCA of Shewanella baltica strains should be on the species level
sh1 = refs.get("Shewanella_baltica_OS185")
sh2 = refs.get("Shewanella_baltica_OS223,")
assert(sh1.get_lca(sh1) == ('strain', 'Shewanella baltica OS185'))
assert(sh1.get_lca(sh2) == ('species', 'Shewanella baltica'))
# LCA of an Archaea and a Bacteria should be life
ar = refs.get("Archaeoglobus_fulgidus_DSM_4304")
th = refs.get("gi|222528057|ref|NC_012034.1|")
assert(ar.get_lca(th) == ('life', 'cellular organisms'))
# Highest LCA of Bacteria and Archaea is Life
assert(ar.get_highest_lca([th, sh1, sh2]) == ('life', 'cellular organisms'))
# Highest LCA of given bacteria is domain or superkingdom in NCBI naming
assert(th.get_highest_lca([sh1, sh2]) == ('superkingdom', 'Bacteria'))
assert(sh1.get_highest_lca([sh1]) == ('strain', 'Shewanella baltica OS185'))
def test_read_contig_mappings():
bamasm = get_testfile('cm-500pgun-asm-b2mv31-bam')
contigfa = get_testfile('cm-500pgun-asm-b2mv31-fa')
bamref = get_testfile('cm-500pgun-ref-bam')
refstatsfile = get_testfile('cm-500pgun-ref-stats')
refphylfile = get_testfile('cm-ref-phyl')
refs = ReferenceSet(refphylfile, refstatsfile)
reads, contigs = get_read_contig_mappings(bamref, bamasm, refs, contigfa)
def test_assemblyvalidation():
bamasm = get_testfile('cm-500pgun-asm-b2mv31-bam')
contigfa = get_testfile('cm-500pgun-asm-b2mv31-fa')
bamref = get_testfile('cm-500pgun-ref-bam')
refstatsfile = get_testfile('cm-500pgun-ref-stats')
refphylfile = get_testfile('cm-ref-phyl')
nucmercoords = get_testfile('cm-500pgun-val-nucmer')
val = AssemblyValidation(bamref, bamasm, refphylfile, refstatsfile, contigfa, nucmercoords)
assert(len(val.contigs) == int(get_shell_output("grep -c '^>' " + contigfa)[0]))
make_dir(get_outdir() + "masm")
val.write_contig_purity(get_outdir() + "masm" + "/contig-purity.tsv")
val.write_general_stats(get_outdir() + "masm" + "/asm-stats.tsv")
val.write_genome_contig_cov(get_outdir() + "masm" + "/genome-contig-coverage.tsv")