def search(self,start,end):
ncbi_dict = GenBank.NCBIDictionary()
j=1
if start<1:
start =1
if end >len(self.accs) or end == 0:
end = len(self.accs)
for k in range(start-1,end):
sys.stderr.write("No " + repr(j) + ": " + self.accs[k] +'\n')
j=j+1
gi_list = GenBank.search_for(self.accs[k],database='protein')
for i in range(0,len(gi_list)):
try:
gb_record = ncbi_dict[gi_list[i]]
sys.stdout.write('>'+self.accs[k]+'\n')
sys.stdout.write( gb_record)
except:
sys.stderr.write( self.accs[k] + " fetching error \n")
body = '\n'.join(textwrap.wrap(rec.seq.data, width=80))
return head, body
if __name__ == '__main__':
mode = sys.argv[1]
text = sys.argv[2]
output_file = sys.argv[3]
print 'Searching for %s <br>' % text
# check if inputs are all numbers
try:
gi_list = text.split()
tmp = map(int, gi_list)
except ValueError:
gi_list = GenBank.search_for(text, max_ids=10)
fp = open(output_file, 'wt')
record_parser = GenBank.FeatureParser()
ncbi_dict = GenBank.NCBIDictionary(mode, 'genbank', parser = record_parser)
for gid in gi_list:
res = ncbi_dict[gid]
head, body = make_fasta(res)
fp.write(head+body+'\n')
print head
fp.close()
org = rec.annotations.get('organism', '')
date = rec.annotations.get('date', '')
head = '>gi:%s, id:%s, org:%s, date:%s\n' % (gi, rec.id, org, date)
body = '\n'.join(textwrap.wrap(rec.seq.data, width=80))
return head, body
if __name__ == '__main__':
mode = sys.argv[1]
text = sys.argv[2]
output_file = sys.argv[3]
print('Searching for %s <br>' % text)
# check if inputs are all numbers
try:
gi_list = text.split()
[int(_) for _ in gi_list]
except ValueError:
gi_list = GenBank.search_for(text, max_ids=10)
fp = open(output_file, 'wt')
record_parser = GenBank.FeatureParser()
ncbi_dict = GenBank.NCBIDictionary(mode, 'genbank', parser=record_parser)
for gid in gi_list:
res = ncbi_dict[gid]
head, body = make_fasta(res)
fp.write(head + body + '\n')
print(head)
fp.close()
