def getInput(self):
'''
Open a single .seq, .fasta, .fastq, .ztr, .scf, .ab1 file (or even a text file with a DNA sequence) and set variables accordingly.
'''
#read the input
if self.input_type in ['TXT', None
] and self.filename not in ['allseqs.txt']:
f = open(self.filepath, 'r')
input = f.read()
f.close()
self.setDNA(input.replace('\n', ''))
elif self.input_type in ['SEQ', 'SEQ.CLIPPED']:
output = fasta.parseFile(
self.filepath
) #parse the fasta file. File should contain ONE entry
for item in output:
id, seq = item
self.setDNA(seq)
elif self.input_type in ['AB1', 'ABI', 'ABIF']:
ab1 = ABIreader.Trace(self.filepath,
trimming=True) #optionally ', trimming=True'
self.setDNA(ab1.seq)
self.setQualVal(ab1.qual_val)
self.setTrace([
ab1.data['raw1'], ab1.data['raw2'], ab1.data['raw3'],
ab1.data['raw4']
]) #need to RC this too
# elif self.input_type == 'ZTR':
# print('Support for .ztr files has not yet been implemented')
# elif self.input_type == 'SCF':
# print('Support for .scf files has not yet been implemented')
elif self.input_type is 'FASTA':
id, seq = fasta.parseFile(
self.filepath
) #parse the fasta file. File should contain ONE entry
self.setDNA(seq)
elif self.input_type is 'FASTQ':
id, seq, id2, qual_val = fastq.parse(
self.filepath
) #parse the fastq file. File should contain ONE entry
self.setDNA(seq)
self.setQualVal(qual_val)
else:
print((
'"%s" is not a .txt, .seq, .scf, .fasta, .fastq, .abif, .ab1, .abi or .ztr file'
% self.filename))
def getInput(self):
'''
Open a single .seq, .fasta, .fastq, .ztr, .scf, .ab1 file (or even a text file with a DNA sequence) and set variables accordingly.
'''
#read the input
if self.input_type in ['TXT', 'SEQ', 'SEQ.CLIPPED', None] and self.filename not in ['allseqs.txt']:
f = open(self.filepath, 'r')
input = f.read()
f.close()
self.setDNA(input.replace('\n', ''))
elif self.input_type in ['AB1', 'ABI', 'ABIF']:
ab1 = ABIreader.Trace(self.filepath, trimming=True) #optionally ', trimming=True'
self.setDNA(ab1.seq)
self.setQualVal(ab1.qual_val)
self.setTrace([ab1.data['raw1'], ab1.data['raw2'], ab1.data['raw3'], ab1.data['raw4']]) #need to RC this too
# elif self.input_type == 'ZTR':
# print('Support for .ztr files has not yet been implemented')
# elif self.input_type == 'SCF':
# print('Support for .scf files has not yet been implemented')
elif self.input_type is 'FASTA':
id, seq = fasta.parseFile(self.filepath) #parse the fasta file. File should contain ONE entry
self.setDNA(seq)
elif self.input_type is 'FASTQ':
id, seq, id2, qual_val = fastq.parse(self.filepath) #parse the fastq file. File should contain ONE entry
self.setDNA(seq)
self.setQualVal(qual_val)
else:
print('"%s" is not a .txt, .seq, .scf, .fasta, .fastq, .abif, .ab1, .abi or .ztr file' % self.filename)
def getInput(self):
"""
Open a single .seq, .fasta, .fastq, .ztr, .scf, .ab1 file (or even a text file with a DNA sequence) and set variables accordingly.
"""
# read the input
if self.input_type in ["TXT", None] and self.filename not in ["allseqs.txt"]:
f = open(self.filepath, "r")
input = f.read()
f.close()
self.setDNA(input.replace("\n", ""))
elif self.input_type in ["SEQ", "SEQ.CLIPPED"]:
output = fasta.parseFile(self.filepath) # parse the fasta file. File should contain ONE entry
for item in output:
id, seq = item
self.setDNA(seq)
elif self.input_type in ["AB1", "ABI", "ABIF"]:
ab1 = ABIreader.Trace(self.filepath, trimming=True) # optionally ', trimming=True'
self.setDNA(ab1.seq)
self.setQualVal(ab1.qual_val)
self.setTrace(
[ab1.data["raw1"], ab1.data["raw2"], ab1.data["raw3"], ab1.data["raw4"]]
) # need to RC this too
# elif self.input_type == 'ZTR':
# print('Support for .ztr files has not yet been implemented')
# elif self.input_type == 'SCF':
# print('Support for .scf files has not yet been implemented')
elif self.input_type is "FASTA":
id, seq = fasta.parseFile(self.filepath) # parse the fasta file. File should contain ONE entry
self.setDNA(seq)
elif self.input_type is "FASTQ":
id, seq, id2, qual_val = fastq.parse(self.filepath) # parse the fastq file. File should contain ONE entry
self.setDNA(seq)
self.setQualVal(qual_val)
else:
print('"%s" is not a .txt, .seq, .scf, .fasta, .fastq, .abif, .ab1, .abi or .ztr file' % self.filename)
def make_codon_freq_table(file):
'''
Input is a file path.
Counts the usage of each codon in a FASTA file of DNA sequences.
Then converts that as codon usage per 1000 codons.
Good for generating codon tables.
Output is a dictionary of codon frequencies per 1000 codons and the total number in brackets.
'''
num_table = {'UUU': 0, 'UUC': 0, 'UUA': 0, 'UUG': 0, 'CUU': 0,
'CUC': 0, 'CUA': 0, 'CUG': 0, 'AUU': 0, 'AUC': 0,
'AUA': 0, 'AUG': 0, 'GUU': 0, 'GUC': 0, 'GUA': 0,
'GUG': 0, 'UAU': 0, 'UAC': 0, 'UAA': 0, 'UAG': 0,
'CAU': 0, 'CAC': 0, 'CAA': 0, 'CAG': 0, 'AAU': 0,
'AAC': 0, 'AAA': 0, 'AAG': 0, 'GAU': 0, 'GAC': 0,
'GAA': 0, 'GAG': 0, 'UCU': 0, 'UCC': 0, 'UCA': 0,
'UCG': 0, 'CCU': 0, 'CCC': 0, 'CCA': 0, 'CCG': 0,
'ACU': 0, 'ACC': 0, 'ACA': 0, 'ACG': 0, 'GCU': 0,
'GCC': 0, 'GCA': 0, 'GCG': 0, 'UGU': 0, 'UGC': 0,
'UGA': 0, 'UGG': 0, 'CGU': 0, 'CGC': 0, 'CGA': 0,
'CGG': 0, 'AGU': 0, 'AGC': 0, 'AGA': 0, 'AGG': 0,
'GGU': 0, 'GGC': 0, 'GGA': 0, 'GGG': 0}
records = fasta.parseFile(file)
for record in records:
cds = record[1]
codons = count_codons(cds)
for key in codons.keys():
num_table[key] += codons[key]
#sum codons
sum = 0.0
for key in num_table.keys():
sum += num_table[key]
#divide each by the sum and multiply by 1000
freq_table = {}
for key in num_table.keys():
freq_table[key] = '%s(%s)' % (1000*(num_table[key]/sum), num_table[key]) #ouput is following format: freq/thousand(number)
return freq_table
def make_codon_freq_table(file):
'''
Input is a file path.
Counts the usage of each codon in a FASTA file of DNA sequences.
Then converts that as codon usage per 1000 codons.
Good for generating codon tables.
Output is a dictionary of codon frequencies per 1000 codons and the total number in brackets.
'''
num_table = {'UUU': 0, 'UUC': 0, 'UUA': 0, 'UUG': 0, 'CUU': 0,
'CUC': 0, 'CUA': 0, 'CUG': 0, 'AUU': 0, 'AUC': 0,
'AUA': 0, 'AUG': 0, 'GUU': 0, 'GUC': 0, 'GUA': 0,
'GUG': 0, 'UAU': 0, 'UAC': 0, 'UAA': 0, 'UAG': 0,
'CAU': 0, 'CAC': 0, 'CAA': 0, 'CAG': 0, 'AAU': 0,
'AAC': 0, 'AAA': 0, 'AAG': 0, 'GAU': 0, 'GAC': 0,
'GAA': 0, 'GAG': 0, 'UCU': 0, 'UCC': 0, 'UCA': 0,
'UCG': 0, 'CCU': 0, 'CCC': 0, 'CCA': 0, 'CCG': 0,
'ACU': 0, 'ACC': 0, 'ACA': 0, 'ACG': 0, 'GCU': 0,
'GCC': 0, 'GCA': 0, 'GCG': 0, 'UGU': 0, 'UGC': 0,
'UGA': 0, 'UGG': 0, 'CGU': 0, 'CGC': 0, 'CGA': 0,
'CGG': 0, 'AGU': 0, 'AGC': 0, 'AGA': 0, 'AGG': 0,
'GGU': 0, 'GGC': 0, 'GGA': 0, 'GGG': 0}
records = fasta.parseFile(file)
for record in records:
cds = record[1]
codons = count_codons(cds)
for key in codons.keys():
num_table[key] += codons[key]
#sum codons
sum = 0.0
for key in num_table.keys():
sum += num_table[key]
#divide each by the sum and multiply by 1000
freq_table = {}
for key in num_table.keys():
freq_table[key] = '%s(%s)' % (1000*(num_table[key]/sum), num_table[key]) #ouput is following format: freq/thousand(number)
return freq_table
def getInput(self):
'''Open a single .seq, .fasta, .fastq, .ztr, .scf, .ab1 file (or even a text file with a DNA sequence) and set variables accordingly.'''
parts = self.filepath.split('/')
filename = parts.pop() #get filename
path = '/'.join(parts)+'/' #path to file
#establish type of input file
if '.' in filename:
self.input_type = filename.split('.')[-1].upper()
print('type', self.input_type)
else:
self.input_type = None
#read the input
if self.input_type in ['TXT', 'SEQ', None] and filename not in ['allseqs.txt']:
#establish orientation of DNA
if filename.split('.')[0][-2:].upper() == 'FW':
self.setOrientation('fw')
elif filename.split('.')[0][-2:].upper() == 'RV':
self.setOrientation('rv')
else:
raise TypeError, 'The last two characters of the filename (before the .) must specify whether the sequence is fw or rv. Pleace rename file %s accordingly' % filename
self.setName(filename)
f = open(self.filepath, 'r')
input = f.read()
f.close()
if self.getOrientation() == 'fw':
self.setDNA(input.replace('\n', ''))
elif self.getOrientation() == 'rv':
self.setDNA(DNA.RC(input.replace('\n', '')))
self.setRC(True)
elif self.input_type in ['AB1', 'ABI', 'ABIF']:
#establish orientation of DNA
if filename.split('.')[0][-2:].upper() == 'FW':
self.setOrientation('fw')
elif filename.split('.')[0][-2:].upper() == 'RV':
self.setOrientation('rv')
else:
raise TypeError, 'The last two characters of the filename (before the .) must specify whether the sequence is fw or rv. Pleace rename file %s accordingly' % filename
self.setName(filename)
ab1 = ABIreader.Trace(self.filepath, trimming=True) #optionally ', trimming=True'
if self.getOrientation() == 'fw':
self.setDNA(ab1.seq)
self.setQualVal(ab1.qual_val) #need to RC this too
self.setTrace([ab1.data['raw1'], ab1.data['raw2'], ab1.data['raw3'], ab1.data['raw4']]) #need to RC this too
#abi=dict(baseorder=ab1.data['baseorder'], qual_val=ab1.qual_val, G=str(AB1Trace.data['raw1']), A=str(AB1Trace.data['raw2']), T=str(AB1Trace.data['raw3']), C=str(AB1Trace.data['raw4']))
elif self.getOrientation() == 'rv':
self.setDNA(DNA.RC(ab1.seq))
self.setQualVal(ab1.qual_val) #need to RC this too
self.setTrace([ab1.data['raw1'], ab1.data['raw2'], ab1.data['raw3'], ab1.data['raw4']]) #need to RC this too
#abi=dict(baseorder=ab1.data['baseorder'], qual_val=ab1.qual_val, G=str(AB1Trace.data['raw1']), A=str(AB1Trace.data['raw2']), T=str(AB1Trace.data['raw3']), C=str(AB1Trace.data['raw4']))
self.setRC(True)
# elif self.input_type == 'ZTR':
# print('Support for .ztr files has not yet been implemented')
# elif self.input_type == 'SCF':
# print('Support for .scf files has not yet been implemented')
elif fnmatch.fnmatch(filename, '*.fasta'):
self.setName(filename)
id, dna = fasta.parseFile(self.filepath) #parse the fasta file. File should contain ONE entry
self.setDNA(dna)
#establish orientation of DNA
if filename.split('.')[0][-2:].upper() == 'FW':
self.setOrientation('fw')
elif filename.split('.')[0][-2:].upper() == 'RV':
self.setOrientation('rv')
else:
raise TypeError, 'The last two characters of the filename (before the .) must specify whether the sequence is fw or rv. Pleace rename file %s accordingly' % filename
elif fnmatch.fnmatch(filename, '*.fastq'):
self.setName(filename)
id, dna, id2, qual_val = fastq.parse(self.filepath) #parse the fastq file. File should contain ONE entry
self.setDNA(dna)
self.setQualVal(qual_val)
#establish orientation of DNA
if filename.split('.')[0][-2:].upper() == 'FW':
self.setOrientation('fw')
elif filename.split('.')[0][-2:].upper() == 'RV':
self.setOrientation('rv')
else:
raise TypeError, 'The last two characters of the filename (before the .) must specify whether the sequence is fw or rv. Pleace rename file %s accordingly' % filename
else:
pass
print('"%s" is not a .txt, .seq, .scf, .fasta, .fastq, .abif, .ab1, .abi or .ztr file' % filename)
