# 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()
except IOError:
print("Failed to open " + inFile)
sys.exit(1)
seqList = sequences.splitlines() # Splits string into a list. Each element is a single line from the string.
print()
"You have listed", len(seqList), "sequences. They are:"
print(sequences + "\n")
seqRecords = getSeqRecords(
seqList) # Acquires list of sequence record objects from NCBI using the sequence list as reference.
No16sGenomes = []
SixTeens = []
for sequence in seqRecords:
sequenceID = sequence.id
No16s = True
if "plasmid" in sequence.description.lower(): # If sequence is from a plasmid skip the iteration.
continue
if isSSProject(sequence): # If accession is a WGSS project...
contigList = extractContigs(sequence.id) # Extract all contig accessions.
contigRecords = getSeqRecords(contigList) # Extract sequence record object for each contig.
for contig in contigRecords:
fasta = get16sFasta(sequenceID, contig) # Builds list fasta files.
if fasta: # If 16S is found.
No16s = False
# 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:
print("Failed to open " + inFile)
sys.exit(1)
seqList = sequences.splitlines() # Splits string into a list. Each element is a single line from the string.
print("You have listed", len(seqList), "sequences. They are:")
print(sequences + "\n\n")
seqRecords = getSeqRecords(seqList, database_type="protein") # Gets sequence record objects from NCBI using the sequence list as reference.
outFile = inFile + ".faa"
try:
# Attempted to create to output file.
writeFile = open(outFile, "w")
print("Writing " + outFile + " to file...")
for sequence in seqRecords:
writeFile.write(sequence.format("fasta")) # Write genome as fasta to file.
writeFile.close()
except IOError:
print("Failed to create " + outFile)
sys.exit(1)
print("Done!")
try:
with open(inFile, "r") as newFile:
sequences = newFile.read()
newFile.close()
except IOError:
print("Failed to open " + inFile)
sys.exit(1)
seqList = sequences.splitlines(
) # Splits string into a list. Each element is a single line from the string.
print("You have listed", len(seqList), "sequences. They are:")
print(sequences + "\n\n")
seqRecords = getSeqRecords(
seqList
) # Gets sequence record objects from NCBI using the sequence list as reference.
for sequence in seqRecords:
outFile = sequence.id + ".fna"
try:
# Attempted to create to output file.
writeFile = open(outFile, "w")
print("Writing " + outFile + " to file...")
# Checks if the accession leads to a WGSS project.
# If accession is a WGSS project...
if isSSProject(sequence):
contigList = extractContigs(
sequence.id) # Extract all contig accessions.
contigRecords = getSeqRecords(
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:
print "Failed to open " + inFile
sys.exit(1)
seqList = sequences.splitlines() # Splits string into a list. Each element is a single line from the string.
print "You have listed", len(seqList), "sequences. They are:"
print sequences + "\n\n"
seqRecords = getSeqRecords(seqList) # Gets sequence record objects from NCBI using the sequence list as reference.
outFile = inFile + ".faa"
try:
# Attempted to create to output file.
writeFile = open(outFile, "w")
print "Writing " + outFile + " to file..."
for sequence in seqRecords:
writeFile.write(sequence.format("fasta")) # Write genome as fasta to file.
writeFile.close()
except IOError:
print "Failed to create " + outFile
sys.exit(1)
print "Done!"
