# 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!"