features = record.features
for feature in features:
if feature.type == "rRNA":
if "16S" in feature.qualifiers["product"][0]:
fasta = extract16sFasta(organismID, feature, record)
if 1000 < len(fasta) < 2000: # Removes partial sequences and really large sequence do to genbank.
FASTAS.append(fasta)
return FASTAS
# ===========================================================================================================
# Main program code:
# House keeping...
argsCheck(3) # Checks if the number of arguments are correct.
entrezEmail(sys.argv[2]) # Sets up arguments email require for genbank file extraction.
# Stores file one for input checking.
print()
">> Opening sequence list..."
inFile = sys.argv[1]
# File extension check
if not inFile.endswith(".txt"):
print("[Warning] " + inFile + " may not be a txt file!")
# Reads sequence file list and stores it as a string object. Safely closes file.try:
try:
with open(inFile, "r") as newFile:
sequences = newFile.read()
newFile.close()
"Entrez User Requirements. If the NCBI finds you are abusing their systems, they can"
)
print(
"and will ban your access! Use the optional email parameter so the NCBI can contact"
)
print("you if there is a problem.")
sys.exit(
1) # Aborts program. (exit(1) indicates that an error occurred)
# ===========================================================================================================
# Main program code:
# House keeping...
argsCheck(3) # Checks if the number of arguments are correct.
entrezEmail(sys.argv[2]
) # Sets up arguments email require for genbank file extraction.
# Stores file one for input checking.
print(">> Opening sequence list...")
inFile = sys.argv[1]
# File extension check
if not inFile.endswith(".txt"):
print("[Warning] " + inFile + " may not be a txt file!")
# Reads sequence file list and stores it as a string object. Safely closes file:
try:
with open(inFile, "r") as newFile:
sequences = newFile.read()
newFile.close()
except IOError: