files.extend(glob.glob(root + "/*.xlsx"))
kinomes = []
for root, dirnames, filenames in os.walk(path):
kinomes.extend(glob.glob(root + "/*full*.tsv"))
peptide_files = sorted([i for i in files if (("peptide" in os.path.basename(i)) and ("overview" not in i) and ("Panther" not in i) and ("CytoPurA_CytoNoc" in i))])
protein_files = sorted([i for i in files if (("protein" in os.path.basename(i)) and ("overview" not in i) and ("Panther" not in i) and ("CytoPurA_CytoNoc" in i))])
kinome_files = sorted(kinomes)
#==============================================================================
# Start processing
#==============================================================================
FASTA_dic = cutils.get_fasta_dic(fasta_file)
phosphositeDB = cutils.read_phosphosite(path+"\\Phosphosite_data\\Phosphorylation_site_dataset")
reports = []
ratios_default = ["Heavy/Light"]
ratios_log = ['log10HL']
ratios_norm = ['norm_log10HL']
alpha = 0.05
columns = [u'# Proteins', 'Sequence', u'# Protein Groups', u'Protein Group Accessions',
u'Modifications', u'MH+ [Da]', u'phosphoRS Isoform Probability',
u'phosphoRS Site Probabilities', u'Area',
u'Heavy/Light Count', u'Heavy/Light Variability [%]',
u'Medium/Light Count',
u'Medium/Light Variability [%]', u'q-Value', u'PEP',
u'phosphoRS Binomial Peptide Score', u'# Missed Cleavages',
kinomes = []
for root, dirnames, filenames in os.walk(path):
kinomes.extend(glob.glob(root + "/*full*.tsv"))
peptide_files = sorted([i for i in files if (("peptide" in os.path.basename(i)) and ("overview" not in i) and ("Panther" not in i))])
protein_files = sorted([i for i in files if (("protein" in os.path.basename(i)) and ("overview" not in i) and ("Panther" not in i))])
kinome_files = sorted(kinomes)
#==============================================================================
# Start processing
#==============================================================================
FASTA_dic = cutils.get_fasta_dic(fasta_file)
#phosphositeDB = cutils.read_phosphosite("D:\\Sven\\Dropbox\\shared_folders\\nurhan\\VX data for Sven\\SVEN\\Phosphosite_data\\Phosphorylation_site_dataset")
phosphositeDB = cutils.read_phosphosite("/home/sven/Dropbox/shared_folders/nurhan/VX data for Sven/SVEN/Phosphosite_data/Phosphorylation_site_dataset")
reports = []
ratios_default = ["Heavy/Light"]
ratios_log = ['log2HL']
ratios_norm = ['norm_2HL']
alpha = 0.05
columns = [u'# Proteins', 'Sequence', u'# Protein Groups', u'Protein Group Accessions',
u'Modifications', u'MH+ [Da]', u'phosphoRS Isoform Probability',
u'phosphoRS Site Probabilities', u'Area',
u'Heavy/Light Count', u'Heavy/Light Variability [%]',
u'q-Value', u'PEP',
u'phosphoRS Binomial Peptide Score', u'# Missed Cleavages',
u'Heavy/Light']
