ann = response.split('''FT METAL ''' +
str(annotation) + '''
FT /note="''')[1].split(' ')[0].strip()
ann = re.compile('[^a-zA-Z]').sub('', ann).replace('FT',
"").replace(
'"', '')
if annotation not in annotation_dict[ann]:
annotation_dict[ann].append(annotation)
except:
with open(SEQ_DIR + "error.txt", "a") as f:
print("error: " + uniprot_id + "\n")
sequence = response.strip()
sequence = sequence[(sequence.rindex(';') + 1):(-2)].strip().replace(
' ', '')
sequences = ''
for key, value in annotation_dict.items():
print(key)
with open(SEQ_DIR + "sequences/" + key + ".fasta", "a") as file_handle:
sequence = sequence.replace("\n", '')
sequences = aa.insert_annotations(sequence, value, '#')
sequences = textwrap.fill(sequences, 60)
if len(sequences) > 0:
print('>' + uniprot_id + "\n")
print(sequences + "\n")
# file_handle.write('>'+uniprot_id +"\n")
# file_handle.write(sequences+"\n")
except IndexError:
print("nothing")
if ('SEQRES') in records[i]:
sequences += records[i]
aa_acid = aa.sort_aa_dict(annotations)
seq_rec = sequences.split('\n')
for keys, values in aa_acid.items():
chain = keys.split('_')
print(pdb_id+'_'+chain[1]+':')
seq = ""
for line in seq_rec:
seq_info = line.split()
if len(seq_info) > 0:
if seq_info[2] == chain[1].strip():
seq = seq+(aa.aa_residue_list(' '.join(seq_info[4:]).strip()))
if len(seq) > 0:
seq = textwrap.fill(seq,60)
position = [int(x.split('_')[2]) for x in values]
position.sort()
if not os.path.exists(SEQ_DIR):
os.mkdir(SEQ_DIR)
with open("../data/sequences/"+chain[0]+'.fasta',"a") as filehandle:
seq = aa.insert_annotations(seq, position,'#')
filehandle.write(pdb_id+'_'+chain[0]+'_'+chain[1]+':'+'\n'+seq+'\n')
print((values))