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']