Python split_natural_sequences Beispiele

Beispiel #1

Datei: calculate_natural_distribution_files_ordered.py Projekt: clauswilke/protein_design_and_site_variability

    RSAValues = []	
    RSA = seq_data[1]
    print "RSA Length from dssp script: " + str(len(RSA))
    index = 0

    #Open the files you just created with the gapless sequences
    fp_natural = open(natural_pdb_file_title) 
    natural_data_arr = fp_natural.readlines()
    fp_natural.close()

    #filepointer for the partial result
    fpW_natural = open("results_array_natural_" + pdb_id + "_" + chain_id + ".csv","w")

    #write the RSA values:
    fpW_natural.write(af.dump_csv_line(RSA))
    [natural_sample1, natural_sample2] = af.split_natural_sequences(natural_data_arr) #Samples  

    #filepointer for the partial result
    fpW_natural_sample1 = open("results_array_natural_sample1_" + pdb_id + "_" + chain_id + ".csv","w")
    fpW_natural_sample2 = open("results_array_natural_sample2_" + pdb_id + "_" + chain_id + ".csv","w")

    #write the RSA values:
    fpW_natural_sample1.write(af.dump_csv_line(RSA))
    fpW_natural_sample2.write(af.dump_csv_line(RSA))

    if(len(RSA) != len(natural_data_arr[0].strip())):
        print "Error !!!!!!!!!"
        #print data_arr[0].strip()
        bad_list.append(natural_pdb_file_title)

    if(len(RSA) != len(natural_data_arr[0].strip())):

Beispiel #2

    print len(RSA)
    index = 0

    #Open the files you just created with the gapless sequences
    fp_natural = open(natural_pdb_file_title)
    natural_data_arr = fp_natural.readlines()
    fp_natural.close()

    #filepointer for the partial result
    fpW_natural = open(
        "results_array_natural_" + pdb_id + "_" + chain_id + ".csv", "w")

    #write the RSA values:
    fpW_natural.write(af.dump_csv_line(RSA))

    [natural_sample1, natural_sample2] = af.split_natural_sequences(
        natural_data_arr)  #Splits the sequences into two samples
    #filepointer for the partial result
    fpW_natural_sample1 = open(
        "results_array_natural_sample1_" + pdb_id + "_" + chain_id + ".csv",
        "w")
    fpW_natural_sample2 = open(
        "results_array_natural_sample2_" + pdb_id + "_" + chain_id + ".csv",
        "w")

    #write the RSA values:
    fpW_natural_sample1.write(af.dump_csv_line(RSA))
    fpW_natural_sample2.write(af.dump_csv_line(RSA))

    if (len(RSA) != len(natural_data_arr[0].strip())):
        print "Error !!!!!!!!!"
        #print data_arr[0].strip()

Beispiel #3

Datei: calculate_natural_distribution_files.py Projekt: clauswilke/protein_design_and_site_variability

    RSA = seq_data[1]
    print len(RSA)
    index = 0

    #Open the files you just created with the gapless sequences
    fp_natural = open(natural_pdb_file_title) 
    natural_data_arr = fp_natural.readlines()
    fp_natural.close()

    #filepointer for the partial result
    fpW_natural = open("results_array_natural_" + pdb_id + "_" + chain_id + ".csv","w")

    #write the RSA values:
    fpW_natural.write(af.dump_csv_line(RSA))

    [natural_sample1, natural_sample2] = af.split_natural_sequences(natural_data_arr) #Splits the sequences into two samples
    #filepointer for the partial result
    fpW_natural_sample1 = open("results_array_natural_sample1_" + pdb_id + "_" + chain_id + ".csv","w")
    fpW_natural_sample2 = open("results_array_natural_sample2_" + pdb_id + "_" + chain_id + ".csv","w")


    #write the RSA values:
    fpW_natural_sample1.write(af.dump_csv_line(RSA))
    fpW_natural_sample2.write(af.dump_csv_line(RSA))


    if(len(RSA) != len(natural_data_arr[0].strip())):
        print "Error !!!!!!!!!"
        #print data_arr[0].strip()
        bad_list.append(natural_pdb_file_title)