def print_dest(self):
# XXX: Muss in rcmd, rsync und search_for_output verwendet werden!
output = self.output
print(colored(output, '\nDestination: '
+ colored(output, self.name, attrs=['bold']),
on_color='on_green'), file=output)
self.print_dest = tunix
def diff(a, b, a_filename, out=stdout, diffpdf=tunix):
def diff_bin(diff_bin_func):
if a != b:
if a:
explanation = not_printable_diff_text
diff_bin_func()
else:
explanation = make_explanation('is empty')
out.write(filename_prepared_for_output + explanation)
def diff_bin_tunix():
diff_bin(tunix)
def diff_bin_pdf():
diff_bin(diffpdf)
filename_prepared_for_output = colored(out, a_filename,
on_color='on_yellow')
{'pdf': diff_bin_pdf,
'PDF': diff_bin_pdf,
'war': diff_bin_tunix, 'so': diff_bin_tunix,
}.get(splitext(a_filename)[1][1:], lambda:
out.write(''.join(map(lambda x: x + '\n',
unified_diff(a.splitlines(),
# \r must be stripped from windows files:
map(lambda x: x.rstrip('\r'), b.splitlines()),
filename_prepared_for_output))
))
)()
def do_file_list(self, out=stdout):
file_list_file_name = self.file_list_file_name()
if exists(file_list_file_name):
stored_file_list = file_content(file_list_file_name
).splitlines()
else:
stored_file_list = []
cease_to_be_managed = set(stored_file_list) - self.file_list
if cease_to_be_managed:
out.write(colored(out,
'These files cease to be managed by this system:',
on_color='on_red') + '\n'
+ '\n'.join(sorted(cease_to_be_managed)) + '\n')
from dna_toolkit import *
from utilities import colored
import random
random_dna = ''.join([random.choice(nucleotides) for nuc in range(50)])
dna_str = validate_seq(random_dna)
print('Test: ', count_nuc_freq(dna_str))
print('Test:', reverse_complement(dna_str))
print('Sequence: {}\n'.format(colored(dna_str)))
print('[1] + Sequence Length: {}\n'.format(len(dna_str)))
print(
colored('[2] + Nucleotide Frequence: {}\n'.format(
count_nuc_freq(dna_str))))
print('[3] + DNA/RNA transcription: {}\n'.format(transcription(dna_str)))
print('[4] + DNA string + reverse transcript:\n5\' {} 3\''.format(
colored(dna_str)))
print(' ' + ''.join('|' for i in range(len(dna_str))))
print(
colored('3\' {} 5\' [Complement]\n'.format(
reverse_complement(dna_str)[::-1])))
print(
colored('3\' {} 5\' [Rev. Complement]\n'.format(
reverse_complement(dna_str))))
print('[5] + GC content {}%\n'.format(gc_content(dna_str)))
print('[6] + GC content in subseq k=5: {}\n'.format(
gc_content_subsec(dna_str, k=5)))
print('[7] + Aminoacids sequence from DNA: {}\n'.format(
translate_seq(dna_str, 0)))
print('[8] + Codon Frequencyof (L): {}\n'.format(codon_usage(dna_str, 'L')))
from DNAToolkit import *
from utilities import colored
import random
randDNAStr = ''.join([random.choice(Nucleotidos) for nuc in range(50)])
DNAStr = validateSeq(randDNAStr)
print(f'\nSequence: {colored(DNAStr)}\n')
print(f'[1] + Sequence Lenght: {len(DNAStr)}\n')
print(colored(f'[2] + Nucleotide Frecuency: {countNucFrequency(DNAStr)}\n'))
print(f'[3] + DNA/RNA Transcription: {colored(transcription(DNAStr))}\n')
print(f"[4] + DNA String + Reverse Complement:\n5' {colored(DNAStr)} 3' ")
print(f" {''.join(['|' for c in range(len(DNAStr))])}")
print(f"3' {colored(reverse_complement(DNAStr)[::-1])} 5'[Complement]")
print(f"5' {colored(reverse_complement(DNAStr))} 3'[Rev.Complement]\n")
print(f'[5] + GC Content: {gc_content(DNAStr)}%\n')
print(
f'[6] + GC Content in Subsection k = 5: {gc_content_subsec(DNAStr, k=5)}\n'
)
print(f'[7] + Aminoacids Sequence from DNA: {translate_seq(DNAStr, 0)}\n')
print(f'[8] + Codon Frecuency (L): {codon_usage(DNAStr, "L")}\n')
print('[9] + Reading Frames: ')
for frame in gen_reading_frames(DNAStr):
print(frame)
from DNAToolkit import *
from utilities import colored
if __name__ == "__main__":
randStr = createRandDNA(50)
DNAStr = validateSeq(randStr)
print(f"\nSequence: {colored(DNAStr)}")
print(f"[1] + Sequence length: {len(DNAStr)}")
print(colored(f"[2] + Nucleotide Frequency {countNucFrequency(DNAStr)}"))
print(f"[3] + DNA/RNA Transcription: {colored(transcription(DNAStr))}")
print(f"[4] + DNA String + Reverese Complemet:\n")
print(f"3\' {colored(DNAStr)} 5\'")
print(f" " + ''.join(['|' for _ in range(len(DNAStr))]))
print(f"3\' {colored(reverseComplement(DNAStr))} 5\'\n")
def rcmd(self, cmd, output_catcher=None):
print(colored(stdout, cmd, 'red'))
from DNA_toolkit import *
import random
from utilities import colored
# Random_DNA = "aActgAGGTG"
Random_Num = random.randint(1, 50)
Random_DNA2 = ''.join([random.choice(Nucleotides) for i in range(Random_Num)])
# Nuc_Val(Random_DNA)
a = Nuc_Val(Random_DNA2)
print(colored(a) + "\n")
c = Nuc_Freq(a)
print(colored(f"{c}"))
d = Transcription(a)
e = RNA_Nuc_Freq(d)
print(colored(f"{e}"))
l = len(a)
r = Reverse_Complement(a)
print(colored(r))
g = gc_content(a)
g_s = gc_content_subsec(a, k=5)
#Conversion of dictionary to string to insert in the database as .txt
a = str(a)
c = str(c)
d = str(d)
e = str(e)
l = str(l)
r = str(r)
g = str(g)
g_s = str(g_s)
import dna_toolkit as dtlk
import random
from utilities import colored
#test_seq = "ACGTTAGTGATGTG"
rand_seq = ''.join([random.choice(dtlk.Nucleotides) for nuc in range(20)
]) # remember, list comprehension goes from right to left
print(colored(dtlk.validate_seq(rand_seq.lower())))
print(f"[1] Sequence length {len(rand_seq)}\n")
print(
colored(
f"[2] Nucloetide frequency {dtlk.count_nucleotide_freq(rand_seq)}\n"))
print(f"[3] DNA->RNA Transcription {colored(dtlk.transcription(rand_seq))}\n")
print(f"p[4] Reverse complement:\n5' {colored(rand_seq)} 3'")
print(f" {''.join(['|' for c in range(len(rand_seq))]) } ")
print(f"5' {colored(dtlk.reverse_complement(rand_seq))} 3' ")
print(f"[6] GC Content {dtlk.gc_content(rand_seq)}")
print(f"[7] GC Subsequence Content {dtlk.gc_content_subsec(rand_seq, 10)}")
#print(f"[8] Aminoacids sequence from DNA {dtlk.translate_seq(rand_seq)}")
print(dtlk.translate_seq("AAGGTCTC"))
from DNAToolkit import *
from utilities import colored
import random
# Main testing file
# Create random DNA sequence:
randDNAStr = ''.join([random.choice(Nucleotides) for nuc in range(100)])
DNAStr = validate_seq(randDNAStr)
print(f"\nSequence: {colored(DNAStr)}\n")
print(f"[1] + Sequence Length: {len(DNAStr)}\n")
print(colored(f'[2] + Nucleotide Frequency: {nucleotide_frequency(DNAStr)}\n'))
print(f"[3] + DNA/RNA Transcription: {colored(transcription(DNAStr))}\n")
print(f"[4] + DNA String + Complement:\n5' {colored(DNAStr)} 3' ")
print(f" {''.join(['|' for c in range(len(DNAStr))])}")
print(f"3' {colored(complement(DNAStr))} 5' [Complement]\n")
print(f"5' {colored(reverse_complement(DNAStr))} 3' [Rev. Complement]\n")
print(f"[5] + GC Content: {gc_content(DNAStr)}%\n")
print(
f"[6] + GC Content in Subsection k=5: {gc_content_subseq(DNAStr, k=5)}\n")
print(f'[7] + Amino acids Sequence from DNA: {translate_seq(DNAStr, 0)}\n')
print(f'[8] + Codon frequency (L): {codon_usage(DNAStr, "L")}\n')
print(f'[9] + Reading frames:')
for frame in gen_reading_frames(DNAStr):
from DNAToolkit import *
from utilities import colored
import random
randomStr = ''.join([random.choice(Nucleotides) for nuc in range(50)])
DNAStr = validateSequence(randomStr)
testDNAStr = "AThTCGT"
print(f'\nSequence: {colored(DNAStr)}\n')
print(f'[1] + Sequence Lenght: {len(DNAStr)}\n')
print(colored(f'[2] + Nucleotide Frequency {countNucFrequency(DNAStr)}\n'))
print(colored(f'[3] + DNA -> RNA Transcription {transcription(DNAStr)}\n'))
print(colored(f"[4] + DNA String + Complement + Reverse Complement: \n5' {DNAStr} 3'"))
print(f" {''.join(['|' for c in range(len(DNAStr))])}")
print(colored(f"3' {reverse_complement(DNAStr)} 5'\n"))
print(colored(f"5' {reverse_complement(DNAStr[::-1])} 3' [Rev Complement]"))
print(colored(f"[5] + GC Content: {gc_content(DNAStr)}%\n"))
print(f"[6] + GC Content in Subsection k=5: {gc_content_subsec(DNAStr, k=5)}\n")
print(f"[7] + Aminoacids Sequence from DNA: {translate_seq(DNAStr, 0)}\n")
print(f'[8] + Codon Frequency (L): {codon_usage(DNAStr, "L")}\n')
print(f'[9] + Reading_frames:')
for frame in gen_reading_frames(DNAStr):
print(frame)
test_rf_frame = ['L', 'M', 'T', 'A', 'L', 'V', 'V', 'L', 'S', 'R', 'R', 'G', 'S', '_', 'G', 'H']
print('\n[10] + All proteins in 6 open reading frames:')
for prot in all_proteins_from_open_reading_frames(DNAStr, 0, 0, True):
print(f'{prot}')