Ejemplo n.º 1
0
def test_big_protxml():
    kl4_dir = "../proteome/data/kl4/TandemXML/"
    fasta = kl4_dir + "../HUMAN_May13.fasta"
    decoy_fasta = tppit.change_ext(fasta, ".decoy.fasta")
    tppit.make_decoy_fasta(fasta, decoy_fasta, "DECOY_")
    mzxmls = [kl4_dir + "WMPY1-KLK4-1-0{}.mzXML".format(i) for i in [1, 2]]
    for mzxml in mzxmls:
        tppit.xtandem_match_spectra(mzxml, decoy_fasta)
    pepxmls = [kl4_dir + "WMPY1-KLK4-1-0{}.tandem.pep.xml".format(i) for i in [1, 2]]
    tppit.resolve_proteins(pepxmls, "example/kl4/interact.prot.xml", decoy_prefix="DECOY_")
Ejemplo n.º 2
0
def test_mzxml_to_protxml():
  tppit.other_binary_dirs.append('/usr/local/tpp/bin')
  fasta = 'example/xtandem/orf_trans.fasta'
  decoy_fasta = tppit.change_ext(fasta, '.decoy.fasta')
  tppit.make_decoy_fasta(fasta, decoy_fasta, 'DECOY_')
  mzxmls = ['example/xtandem/Seq2328{}_E1O1.mzXML'.format(i) for i in [2,3,4]]
  for mzxml in mzxmls:
    tppit.xtandem_match_spectra(mzxml, decoy_fasta)
  tandems = [tppit.change_ext(m, '.tandem') for m in mzxmls]
  pepxmls = [t + '.pep.xml' for t in tandems]
  for tandem, pepxml in zip(tandems, pepxmls):
    tppit.tandem2pepxml(tandem, pepxml)
  tppit.resolve_proteins(pepxmls, 'example/xtandem/interact.prot.xml', decoy_prefix='DECOY_')
Ejemplo n.º 3
0
def test_big_protxml():
    kl4_dir = '../proteome/data/kl4/TandemXML/'
    fasta = kl4_dir + '../HUMAN_May13.fasta'
    decoy_fasta = tppit.change_ext(fasta, '.decoy.fasta')
    tppit.make_decoy_fasta(fasta, decoy_fasta, 'DECOY_')
    mzxmls = [kl4_dir + 'WMPY1-KLK4-1-0{}.mzXML'.format(i) for i in [1, 2]]
    for mzxml in mzxmls:
        tppit.xtandem_match_spectra(mzxml, decoy_fasta)
    pepxmls = [
        kl4_dir + 'WMPY1-KLK4-1-0{}.tandem.pep.xml'.format(i) for i in [1, 2]
    ]
    tppit.resolve_proteins(pepxmls,
                           'example/kl4/interact.prot.xml',
                           decoy_prefix='DECOY_')
Ejemplo n.º 4
0
def test_mzxml_to_protxml():
    tppit.other_binary_dirs.append('/usr/local/tpp/bin')
    fasta = 'example/xtandem/orf_trans.fasta'
    decoy_fasta = tppit.change_ext(fasta, '.decoy.fasta')
    tppit.make_decoy_fasta(fasta, decoy_fasta, 'DECOY_')
    mzxmls = [
        'example/xtandem/Seq2328{}_E1O1.mzXML'.format(i) for i in [2, 3, 4]
    ]
    for mzxml in mzxmls:
        tppit.xtandem_match_spectra(mzxml, decoy_fasta)
    tandems = [tppit.change_ext(m, '.tandem') for m in mzxmls]
    pepxmls = [t + '.pep.xml' for t in tandems]
    for tandem, pepxml in zip(tandems, pepxmls):
        tppit.tandem2pepxml(tandem, pepxml)
    tppit.resolve_proteins(pepxmls,
                           'example/xtandem/interact.prot.xml',
                           decoy_prefix='DECOY_')