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_")
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_')
def test_mascot_to_protxml():
tppit.other_binary_dirs.append('/usr/local/tpp/bin')
mascots = ['example/mascot/F02204{}.dat'.format(i) for i in [3, 5]]
fasta_db = 'example/mascot/HUMAN.fasta'
pepxmls = [tppit.change_ext(m, '.pep.xml') for m in mascots]
for mascot, pepxml in zip(mascots, pepxmls):
tppit.mascot2pepxml(mascot, fasta_db, pepxml)
tppit.resolve_proteins(pepxmls, 'example/mascot/interact.prot.xml')
def test_mascot_to_protxml():
tppit.other_binary_dirs.append("/usr/local/tpp/bin")
mascots = ["example/mascot/F02204{}.dat".format(i) for i in [3, 5]]
fasta_db = "../db/HUMAN.fasta"
pepxmls = [tppit.change_ext(m, ".pep.xml") for m in mascots]
for mascot, pepxml in zip(mascots, pepxmls):
tppit.mascot2pepxml(mascot, fasta_db, pepxml)
tppit.resolve_proteins(pepxmls, "example/mascot/interact.prot.xml")
def test_mascot_to_protxml():
tppit.other_binary_dirs.append('/usr/local/tpp/bin')
mascots = ['example/mascot/F02204{}.dat'.format(i) for i in [3, 5]]
fasta_db = 'example/mascot/HUMAN.fasta'
pepxmls = [tppit.change_ext(m, '.pep.xml') for m in mascots]
for mascot, pepxml in zip(mascots, pepxmls):
tppit.mascot2pepxml(mascot, fasta_db, pepxml)
tppit.resolve_proteins(pepxmls, 'example/mascot/interact.prot.xml')
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_')
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_")
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_')