def Main():
#Initializes the protein class which contains all main functions for manipulation and storage of protein data
P = Protein()
# Gets user input for the name of the desired output file. Output graphic displays in the subfolder of completed trees
name_of_run = nameOfRun()
P.run_name = name_of_run
# timer that determines how much pause is placed between calls to NCBI servers, reccomend 0.5 however 0 works when running NOT during peak hours
time = timer()
P.timer = time
#Set input/output paths
input_file_path = os.path.join('Input', 'ProteinInput')
output_file_path = os.path.join('Output')
#Clears previous CDS and genomic output from last run
clearPreviousOutput(output_file_path)
#Functions from the Protein class that use the input protein accession numbers to determine the corresponding protein ID, CDS, and genomic data
P.Entrez_Protein_ID_Fetch(input_file_path)
P.Entrez_Genome_Fetch()
# Writes the fasta seq for the genome corresponding the protein. Establishing a parallel list. Ouput file path: PhyloRewrite/Output/Genome
for i in range(len(P.gene)):
data_type = 'gene'
writeOutput(data_type, P.gene[i])
print 'Genomic Sequences written to Output File... '
P.Entrez_CDS_Fetch()
#Writes the fasta seq for the CDS corresponding the protein. Establishing a parallel list. Ouput file path: PhyloRewrite/Output/CDS
for i in range(len(P.retrieved_full_cds)):
data_type = 'CDS'
writeOutput(data_type, P.retrieved_full_cds[i])
print 'CDS Sequences written to Output File... '
#Checks as to whether the lists are in parallel, if they are not error will rise
print '\n Checking the output for errors... \n'
if len(P.gene) != len(P.retrieved_full_cds):
repair_script()
sys.exit()
print 'No errors found, continuing... \n'
#Function of the protein class that determines the intron phase and location of intron/exon boundry
P.intronCalculator()
#Contained within the lists is each
print 'Intron Phases: ' + str(P.intron_phase)
print 'Length of the Exons: ' + str(P.exon_lengths)
#Uses clustal X linux executible to format a multiple sequencing alignment for the input protein sequences. Files found in execs/tmp
P.multiple_sequencing_alignment()
#Takes the multiple sequencing alignment output from clustal X and inputs into fasttree to generate an unrooted tree, then piped into ete2 to root. Files found in execs/tmp
P.rootedTreeConstruction()
#Builds the tree graphic
P.renderingTreeImage()
#Code produces the Phylogenetic tree and intron mapping
P = Protein()
P.multiple_sequencing_alignment()
P.intronCalculator()
P.rootedTreeConstruction()
P.renderingTreeImage()
elif response == '3':
repair_script()
elif response == '4':
duplicate_management()
elif response == '5':
#Enter experimental code here:
P = Protein()
id_list = P.Entrez_Protein_ID_Fetch(
os.path.join('Input', 'ProteinInput'))
P.Genomic_Context(id_list)
elif response == '6':
file_merger()
elif response != '1' or '2' or '3' or '4' or '5' or '6':
print 'Sorry your response was not recognized! '
sys.exit()
