def analyse_contigs(contig_file, read1, read2, outputdir, fasta_ref_files=[], verbose=False): #first prepare blast files for analysis renamedContigs = reNameContigs(contig_file, outputdir) blast_files = [] for reference in fasta_ref_files: blast_files.append( run_blast(reference, renamedContigs, outputdir, verbose)) #now align reads to contigs samfile = align_w_subread(read1, read2, renamedContigs, outputdir, verbose) #now convert to bam bamfile = convert_to_bam_create_index(renamedContigs, samfile, verbose) # bamfile="notused" #now compute analytics outfile = generate_summary(bamfile, outputdir, renamedContigs, blast_files) return outfile
def analyse_contigs(contig_file, read1, read2, outputdir , fasta_ref_files=[], verbose=False): #first prepare blast files for analysis renamedContigs = reNameContigs(contig_file, outputdir) blast_files = [] for reference in fasta_ref_files: blast_files.append(run_blast(reference, renamedContigs, outputdir , verbose)) #now align reads to contigs samfile = align_w_subread(read1, read2, renamedContigs, outputdir, verbose) #now convert to bam bamfile = convert_to_bam_create_index(renamedContigs, samfile, verbose) # bamfile="notused" #now compute analytics outfile = generate_summary(bamfile, outputdir , renamedContigs, blast_files) return outfile
raise pass curr_dir = os.getcwd() os.chdir(outputdir) # print thrd.getScriptPath() read1, read2 = thrd.trim_galore(options.read1, options.read2, outputdir , options.verbose) if options.reference: alignment = thrd.align_w_subread(read1, read2, options.reference, outputdir , options.verbose, options.ref_index) bamfile = thrd.convert_to_bam_create_index(options.reference, alignment , options.verbose) single_reads, paired_reads = thrd.extract_possible_var_reads(bamfile , outputdir, options.var_files, options.verbose) else: single_reads, paired_reads = thrd.combine_paired(read1, read2, outputdir , options.verbose) if options.read2 != None: if options.pear: single_reads, paired_reads = thrd.merge_with_pear(single_reads , paired_reads, outputdir, options.verbose) #now digital normalisation on the single_reads and paired reads seperately if options.norm:
pass curr_dir = os.getcwd() os.chdir(outputdir) # print thrd.getScriptPath() read1, read2 = thrd.trim_galore(options.read1, options.read2, outputdir, options.verbose) if options.reference: alignment = thrd.align_w_subread(read1, read2, options.reference, outputdir, options.verbose, options.ref_index) bamfile = thrd.convert_to_bam_create_index(options.reference, alignment, options.verbose) single_reads, paired_reads = thrd.extract_possible_var_reads( bamfile, outputdir, options.var_files, options.verbose) else: single_reads, paired_reads = thrd.combine_paired( read1, read2, outputdir, options.verbose) if options.read2 != None: if options.pear: single_reads, paired_reads = thrd.merge_with_pear( single_reads, paired_reads, outputdir, options.verbose) #now digital normalisation on the single_reads and paired reads seperately if options.norm: