index += 1
entry += line
elif line.find('ORIGIN') >= 0:
#found sequence start, set the flag on and parses the last entry
is_seq = True
genes.append(parse_entry(entry))
elif is_seq == True:
#if flag is true keep going, usually sequences are store at the end of the file
line = line.split()
sequence.append(line)
else:
#this is an entry so append line
entry += line
str_seq = ''
#make the sequence a string
for i in sequence:
str_seq += ''.join(i[1:]).upper()
for i in genes:
if len(i.gi_id) > 2:
print i.id, i.start, i.end
output = open(i.gi_id + '.DNA.fasta', 'w')
output.write('>' + i.gi_id + '\t' + i.id + '\n')
# if this is a complement, print both 5'-3' and reverse complement sequences
if i.complement == True:
output.write(fasta.format_output(fasta.invert(str_seq[int(i.start)-1:int(i.end)]), 80) + '\n')
else:
if not i.start.find('join') >= 0:
output.write(fasta.format_output(str_seq[int(i.start)-1:int(i.end)], 80))
proteins = []
index = 0
entry = ''
for line in gbfile:
if line.find(' gene ') >= 0:
if index >= 1:
#parses the CDS and appends to a list
proteins.append(parse_entry(entry))
entry = ''
index += 1
entry += line
elif line.find('ORIGIN') >= 0:
#found the DNA sequence, we can stop now
break
else:
entry += line
#parses the last entry after leaving the loop
proteins.append(parse_entry(entry))
#output
for i in proteins:
if len(i.gi) > 2:
print i.gi, i.id
output = open(i.gi + '.fasta', 'w')
output.write('>' + i.gi + '\t' + i.id + '\n')
i.sequence = i.sequence.replace('\"', '')
output.write(fasta.format_output(i.sequence, 80))
print i.id
proteins = []
index = 0
entry = ''
for line in gbfile:
if line.find(' gene ') >= 0:
if index >= 1:
#parses the CDS and appends to a list
proteins.append(parse_entry(entry))
entry = ''
index += 1
entry += line
elif line.find('ORIGIN') >= 0:
#found the DNA sequence, we can stop now
break
else:
entry += line
#parses the last entry after leaving the loop
proteins.append(parse_entry(entry))
#output
for i in proteins:
if len(i.gi) > 2:
print i.gi, i.id
output = open(i.gi + '.fasta', 'w')
output.write('>' + i.gi + '\t' + i.id + '\n')
i.sequence = i.sequence.replace('\"', '')
output.write(fasta.format_output(i.sequence, 80))
print i.id
genes.append(parse_entry(entry))
elif is_seq == True:
#if flag is true keep going, usually sequences are store at the end of the file
line = line.split()
sequence.append(line)
else:
#this is an entry so append line
entry += line
str_seq = ''
#make the sequence a string
for i in sequence:
str_seq += ''.join(i[1:]).upper()
for i in genes:
if len(i.gi_id) > 2:
print i.id, i.start, i.end
output = open(i.gi_id + '.DNA.fasta', 'w')
output.write('>' + i.gi_id + '\t' + i.id + '\n')
# if this is a complement, print both 5'-3' and reverse complement sequences
if i.complement == True:
output.write(
fasta.format_output(
fasta.invert(str_seq[int(i.start) - 1:int(i.end)]), 80) +
'\n')
else:
if not i.start.find('join') >= 0:
output.write(
fasta.format_output(str_seq[int(i.start) - 1:int(i.end)],
80))
#!/usr/bin/env python
#import two modules
import dnatranslate
import fasta
import sys
#read the fasta file in one line: open the file, read the contents
#and send it to the fasta reading function
dna = fasta.read_fasta(open(sys.argv[1], 'r').readlines())
for item in dna:
#translate the DNA
protein = dnatranslate.translate_dna(item.sequence)
print item.name
#format and print the protein
print fasta.format_output(protein, 60)
