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@@ -24,6 +24,8 @@ genomes_path = 'datasets/' # genome datasets raw data
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genomes_list_path = "datasets/genome.list" # genome list
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universal_primer_list_path = "resources/PATTERNS/UPL.list" # UPL list
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dna_codons_list_path = "resources/PATTERNS/DNAcodon.list" # DNA codon list
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+open_reading_frames_init_path = "resources/PATTERNS/ORF/ORF-init.list" # ORF init list
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+open_reading_frames_end_path = "resources/PATTERNS/ORF/ORF-end.list" # ORF end list
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genomes = {} # main sources dict: genome_name
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seeds_checked = [] # list used for random checked patterns
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repeats = {} # repetitions 'tmp' dict: genome_name:(repets,pattern)
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@@ -400,7 +402,7 @@ def extract_pattern_most_present_local(memory):
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for m in memory:
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total_patterns = total_patterns + 1 # counter used for known patterns
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max_size_pattern_name, less_size_pattern_name, biggest_pattern_name, biggest_pattern_size, smaller_pattern_name, smaller_pattern_size, total_patterns_all_genomes, most_present_patterns_by_len_list, less_present_patterns_by_len_list = extract_patterns_most_found_in_all_genomes(memory_dict)
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- print(" * Trying -[ "+str(total_patterns)+" ]- [PATTERNS LEARNED!] against -[ "+str(total_genomes)+ " ]- [DNA SECUENCES]:")
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+ print(" * Searching -[ "+str(total_patterns)+" ]- [PATTERNS LEARNED!] in -[ "+str(total_genomes)+ " ]- [DNA SECUENCES]:")
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if total_patterns_all_genomes:
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print("\n + Total [PATTERNS FOUND!]: [ "+str(total_patterns_all_genomes)+" ]")
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biggest_pattern_name_codon = None
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@@ -465,7 +467,7 @@ def extract_potential_primer_pairs(UPL, total_genomes, codons):
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pair_times = v.count(pair_name)
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total_primer_pairs_found += pair_times
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primer_pairs_found_list[pair_sec] = pair_name, total_primer_pairs_found
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- print(" * Trying -[ "+str(total_universal_primer_pairs)+" ]- [UNIVERSAL PRIMER PAIRS!] against -[ "+str(total_genomes)+ " ]- [DNA SECUENCES]:")
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+ print(" * Searching -[ "+str(total_universal_primer_pairs)+" ]- [UNIVERSAL PRIMER PAIRS!] in -[ "+str(total_genomes)+ " ]- [DNA SECUENCES]:")
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if total_primer_pairs_found:
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total_primer_pairs_found_list = 0
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for m, n in primer_pairs_found_list.items():
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@@ -482,19 +484,21 @@ def extract_potential_dna_codons(codons, total_genomes):
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total_codons_found = 0
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codons_found_list = {}
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codons_found_list_by_codon = {}
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+ index = 0
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for c in codons:
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total_codons = total_codons + 1
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for k, v in genomes.items():
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codon_name = c.split(":")[0].upper().replace("\n","")
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if str(codon_name) in str(v.upper()):
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+ index = index + 1
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codons_times = v.count(codon_name)
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total_codons_found += codons_times
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- codons_found_list[codons_times] = c.split(":")[0], str(c.split(":")[1]), k
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- print(" * Trying -[ "+str(total_codons)+" ]- [PATTERN CODONS!] against -[ "+str(total_genomes)+ " ]- [DNA SECUENCES]:")
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+ codons_found_list[index] = codons_times, c.split(":")[0], str(c.split(":")[1]), k
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+ print(" * Searching -[ "+str(total_codons)+" ]- [PATTERN CODONS!] in -[ "+str(total_genomes)+ " ]- [DNA SECUENCES]:")
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if total_codons_found:
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for m, n in codons_found_list.items():
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- codon_sec = str(n[0])
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- codon_name = str(n[1].replace("\n",""))
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+ codon_sec = str(n[1])
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+ codon_name = str(n[2].replace("\n",""))
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if not codon_sec in codons_found_list_by_codon.keys():
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codons_found_list_by_codon[codon_sec] = codon_name, m
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else:
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@@ -524,6 +528,72 @@ def extract_potential_dna_codons(codons, total_genomes):
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print ("")
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else:
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print("\n + Total [PATTERN CODONS FOUND!]: [ 0 ]\n")
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+ if codons_found_list:
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+ extract_open_reading_frames(total_genomes)
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+
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+def extract_open_reading_frames(total_genomes):
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+ try:
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+ f=open(open_reading_frames_init_path, 'r')
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+ frames_init = f.readlines()
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+ f.close()
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+ except:
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+ pass
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+ try:
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+ e=open(open_reading_frames_end_path, 'r')
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+ frames_end = e.readlines()
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+ e.close()
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+ except:
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+ pass
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+ if frames_init and frames_end:
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+ print(" * Searching for [OPEN READING FRAMES!] in -[ "+str(total_genomes)+ " ]- [DNA SECUENCES]:")
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+ total_opr_found = 0
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+ r_found_by_pattern = 0
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+ opr_found_list = {}
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+ index = 0
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+ for k, v in genomes.items():
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+ for opr_i in frames_init:
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+ opr_init_name = opr_i.replace("\n","")
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+ if str(opr_init_name) in str(v.upper()): # open reading INIT frame found!
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+ for opr_e in frames_end:
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+ opr_end_name = opr_e.replace("\n","")
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+ if str(opr_end_name) in str(v.upper()): # open reading END frame found!
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+ regex_opr = str(opr_init_name) +"(.+?)"+str(opr_end_name) # regex magics! - extract secuence between ocr_i and ocr_e
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+ pattern_record = re.compile(regex_opr)
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+ record = re.findall(pattern_record, str(v.upper()))
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+ for r in record: # now extract each field
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+ total_opr_found = total_opr_found + 1
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+ r_found_by_pattern = v.count(opr_init_name+r+opr_end_name)
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+ index = index + 1
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+ opr_found_list[index] = k, r_found_by_pattern, opr_init_name, r, opr_end_name # [index]: genome, num_times, opr_i, pattern, opr_e
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+ if total_opr_found > 0:
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+ print("\n + Total [OPEN READING FRAMES FOUND!]: [ "+str(total_opr_found)+" ]\n")
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+ most_present_opr_found = max(opr_found_list, key=opr_found_list.get)
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+ largest_pattern = 0
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+ largest_pattern_found = None
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+ for m, n in opr_found_list.items():
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+ opr_found_init = str(n[2])
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+ opr_found_pattern = str(n[3])
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+ opr_found_end = str(n[4])
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+ opr_found_times = str(n[1])
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+ opr_found_genome = str(n[0])
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+ opr_found_pattern_len = len(opr_found_pattern)
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+ if opr_found_pattern_len > largest_pattern:
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+ largest_pattern = opr_found_pattern_len
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+ largest_pattern_found = opr_found_init, opr_found_pattern, opr_found_end, opr_found_genome
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+ if m == most_present_opr_found:
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+ most_present_opr_found_init = str(n[2])
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+ most_present_opr_found_pattern = str(n[3])
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+ most_present_opr_found_end = str(n[4])
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+ most_present_opr_found_times = str(n[1])
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+ most_present_opr_found_genome = str(n[0])
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+ print(" - [MOST-PRESENT!]: [ "+str(most_present_opr_found_times)+" ] time(s) found in [ "+str(most_present_opr_found_genome)+" ] is -> [ "+str(most_present_opr_found_init)+"-{?}-"+str(most_present_opr_found_end)+" ]:\n")
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+ print(str(" * "+str(most_present_opr_found_init+most_present_opr_found_pattern+most_present_opr_found_end)))
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+ print("\n - [LARGEST]: [ "+str(len(largest_pattern_found[1]))+" bp linear RNA ] found in [ "+str(largest_pattern_found[3])+" ] is -> [ "+str(largest_pattern_found[0])+"-{?}-"+str(largest_pattern_found[2])+" ]:\n")
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+ print(str(" * "+str(largest_pattern_found[0]+largest_pattern_found[1]+largest_pattern_found[2])+"\n"))
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+ else:
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+ print("\n + Total [OPEN READING FRAMES FOUND!]: [ 0 ]\n")
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+ else:
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+ print("\n + Total [OPEN READING FRAMES FOUND!]: [ 0 ]\n")
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def extract_patterns_most_found_in_all_genomes(memory_dict):
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present_patterns = []
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@@ -659,6 +729,12 @@ def list_genomes_on_database():
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codons = f.readlines()
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f.close()
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print("-"*15 + "\n")
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+ f=open(open_reading_frames_init_path, 'r')
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+ frames_init = f.readlines()
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+ f.close()
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+ f=open(open_reading_frames_end_path, 'r')
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+ frames_end = f.readlines()
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+ f.close()
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f=open(genomes_list_path, 'w')
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for k, v in genomes.items():
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print ("* "+str(k))
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@@ -674,8 +750,8 @@ def list_genomes_on_database():
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f.write(str(" - [C] Cytosine : " + str(v.count("C"))+"\n"))
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f.write(str(" - [T] Thymine : " + str(v.count("T"))+"\n"))
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if v.count("N") > 0:
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- print (" + [N] *ANY* :", str(v.count("N")))
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- f.write(str(" + [N] *ANY* : "+ str(v.count("N"))+"\n"))
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+ print (" - [N] *ANY* :", str(v.count("N")))
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+ f.write(str(" - [N] *ANY* : "+ str(v.count("N"))+"\n"))
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total_codons = 0
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for c in codons:
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codon_counter = v.count(str(c.split(":")[0]))
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@@ -688,6 +764,30 @@ def list_genomes_on_database():
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codon_counter = str(v.count(str(c.split(":")[0])))
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print (" - ["+codon_sec+"] "+codon_name+" :", codon_counter)
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f.write(str(" - ["+codon_sec+"] "+codon_name+" : "+ codon_counter)+"\n")
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+ if frames_init and frames_end:
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+ total_opr_found = 0
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+ r_found_by_pattern = 0
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+ opr_found_list = {}
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+ index = 0
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+ for opr_i in frames_init:
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+ opr_init_name = opr_i.replace("\n","")
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+ if str(opr_init_name) in str(v.upper()): # open reading INIT frame found!
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+ for opr_e in frames_end:
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+ opr_end_name = opr_e.replace("\n","")
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+ if str(opr_end_name) in str(v.upper()): # open reading END frame found!
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+ regex_opr = str(opr_init_name) +"(.+?)"+str(opr_end_name) # regex magics! - extract secuence between ocr_i and ocr_e
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+ pattern_record = re.compile(regex_opr)
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+ record = re.findall(pattern_record, str(v.upper()))
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+ for r in record: # now extract each field
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+ total_opr_found = total_opr_found + 1
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+ r_found_by_pattern = v.count(opr_init_name+r+opr_end_name)
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+ index = index + 1
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+ opr_found_list[index] = k, r_found_by_pattern, opr_init_name, r, opr_end_name # [index]: genome, num_times, opr_i, pattern, opr_e
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+ print ("\n + Total [OPEN READING FRAMES!]: [ "+str(total_opr_found)+" ] \n")
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+ f.write(str("\n + Total [OPEN READING FRAMES!]: [ "+str(total_opr_found)+" ] \n"))
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+ for m, n in opr_found_list.items():
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+ print(" - ["+str(n[2])+str(n[3])+str(n[4])+"] : [ "+str(n[1])+" ] time(s)")
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+ f.write(str(" - ["+str(n[2])+str(n[3])+str(n[4])+"] : "+ str(n[1]))+"\n")
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print ("")
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f.write("\n")
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print("-"*15 + "\n")
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