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:
