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 SixTeens.append(fasta[0]) break # If 16S is found in one contig break out and skip all the other contigs else: # If accession is a regular genome... fasta = get16sFasta(sequenceID, sequence) # Builds list fasta files. if fasta: No16s = False SixTeens.append(fasta[0]) if No16s: # If not 16S is found add genome to the no 16s found list. No16sGenomeInfo = [sequenceID, sequence.annotations["organism"]]
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( contigList) # Extract sequence record object for each contig. for contig in contigRecords: writeFile.write( contig.format("fasta") ) # Write each contig to the same file in fasta format. # If accession is a regular genome... else: writeFile.write( sequence.format("fasta")) # Write genome as fasta to file writeFile.close() except IOError: print("Failed to create " + outFile)
seqRecords = getSeqRecords(seqList) # Gets sequence record objects from NCBI using the sequence list as reference. for sequence in seqRecords: outFile = sequence.id + ".faa" outCSV = sequence.id + ".csv" try: # Attempted to create to output file. writeFile = open(outFile, "w") print "Writing " + outFile + " to file..." csvFile = open(outCSV, "w") CSVWriter = csv.writer(csvFile) print "Writing " + outCSV + " 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(contigList) # Extract sequence record object for each contig. for contig in contigRecords: fasta = getProtienAnnotationFasta(contig) # Builds list fasta files. csvRows = getProtienAnnotationCSV(contig) # Builds list of csv rows. for annotation in fasta: writeFile.write(annotation) for row in csvRows: CSVWriter.writerow(row) # If accession is a regular genome... else: OrganismGenomeLength = len(sequence.seq) # Gets Genome Length fasta = getProtienAnnotationFasta(sequence) # Builds list fasta files. csvRows = getProtienAnnotationCSV(sequence) # Builds list of csv rows. for annotation in fasta:
"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 SixTeens.append(fasta[0]) break # If 16S is found in one contig break out and skip all the other contigs else: # If accession is a regular genome... fasta = get16sFasta(sequenceID, sequence) # Builds list fasta files. if fasta: No16s = False SixTeens.append(fasta[0])