def parse_CDS(file):
'''Function to parse the CDS numbers along with their accession numbers
input: read file, genbank
output: CDS description
'''
write_file= cg.cds_file
fm.wipe_file(write_file) #wipe write file
for rec in SeqIO.parse(file, "genbank"):# for every entry(rec) run though the following
if rec.features:
for feature in rec.features:
#gathering and cleaning accession
if feature.type=='CDS':
acc= cl.remove_version(rec.id)
fm.write_file("insert into CDS values ('"+ acc + "',", write_file)
#Accession numbers
cds_region= cl.clean_cds_region(feature.location)
fm.write_file("'"+cds_region+"',", write_file)
#CDS regions
try:
cds_seq=str(feature.location.extract(rec).seq)
fm.write_file("'"+cds_seq+"'); \n", write_file)
#CDS sequence
except:
fm.write_file("'CDS ERROR; FULL DNA SEQUENCE:"+str(rec.seq) +"');\n", write_file)
continue
def parse_CHROM8(file):
'''Function to parse the CDS numbers along with their accession numbers
input: read file, genbank
output: CDS description
'''
#write_file= cg.cds_file
#fm.wipe_file(write_file) #wipe write file
for rec in SeqIO.parse(file, "genbank"):# for every entry(rec) run though the following
if rec.features:
for feature in rec.features:
if feature.type=='CDS':
#Accession numbers
acc= cl.remove_version(rec.id)
print(acc)
#chromosomal location
try:
chroma_loc= feature.source["map"]
print(chroma_loc[0])
except:
print('chroma_loc not found')
def parse_acc():
'''Using Biopython to parse Accession numbers
input: empty, indirectly
output: Accession numbers
'''
fm.wipe_file(cg.acc_file)
for i in SeqIO.parse(cg.r_file, "genbank"):
acc= cl.remove_version(i.id)
fm.write_file(acc + '\n', cg.acc_file)
def parse_acc_dna(r_file):
'''This function captures Accession numbers and whole DNA sequences
from a variable database
input: read file, containing sequences
output: return captured DNA sequences
'''
write_file=cg.gene_file
fm.wipe_file(write_file)
for record in SeqIO.parse(cg.r_file, "genbank"):
acc= cl.remove_version(record.id)
fm.write_file("insert into GENE values ('"+ acc + "', '", write_file)
fm.write_file(str(record.seq) +"'); \n", write_file)
def parse_CDS(file):
'''Function to parse the CDS numbers along with their accession numbers
input: read file, genbank
output: CDS description
'''
fm.wipe_file(cg.cds_file)
for rec in SeqIO.parse(file, "genbank"):
if rec.features:
for feature in rec.features:
acc= cl.remove_version(rec.id)
fm.write_file("insert into CDS values ("+"'"+ acc + "' ,", cg.cds_file)
#gathering and cleaning accession
if feature.type == "CDS":
aa_seq=feature.qualifiers['translation']
fm.write_file("'"+aa_seq[0]+"')", cg.cds_file) #captures string inside the list []
else:
cds_region= cl.clean_cds_region(feature.location)
fm.write_file("'"+cds_region+"'", cg.cds_file) #Where the CDS regions are
fm.write_file("'"+feature.location.extract(rec).seq+"');", cg.cds_file) #CDS sequences