def extract_seqs_for_edlib(ref_seq, contig_seq, rstart, rend, qstart, qend): if (rend > rstart): nw_ref = ref_seq[(rstart-1):(rend+1-1)]; # +1 because the end base is inclusive, and -1 because it's 1-based. else: nw_ref = fastqparser.revcomp_seq(ref_seq[(rend-1):(rstart+1-1)]); if (qend > qstart): nw_contig = contig_seq[(qstart-1):(qend+1-1)]; # +1 because the end base is inclusive, and -1 because it's 1-based. else: nw_contig = fastqparser.revcomp_seq(contig_seq[(qend-1):(qstart+1-1)]); return [nw_ref, nw_contig];
def get_circular_score(ref_path, contig_path, temp_folder):
if (not os.path.exists(temp_folder)):
os.makedirs(temp_folder)
[headers_ref, seqs_ref, quals_ref] = fastqparser.read_fastq(ref_path)
circularized_fwd_path = '%s/circ-fwd.fa' % (temp_folder)
circularized_rev_path = '%s/circ-rev.fa' % (temp_folder)
fp_fwd = open(circularized_fwd_path, 'w')
fp_rev = open(circularized_rev_path, 'w')
for i in xrange(0, len(seqs_ref)):
rev_seq = fastqparser.revcomp_seq(seqs_ref[i])
rev_qual = quals_ref[i][::-1]
# if (len(quals_ref) > 0):
# fp_fwd.write('@%s\n%s%s\n+\n%s%s\n' % (headers_ref[i], seqs_ref[i], seqs_ref[i], quals_ref[i], quals_ref[i]));
# fp_rev.write('@%s\n%s%s\n+\n%s%s\n' % (headers_ref[i], rev_seq, rev_seq, rev_qual, rev_qual));
# else:
fp_fwd.write('>%s\n%s%s\n' %
(headers_ref[i], seqs_ref[i], seqs_ref[i]))
fp_rev.write('>%s\n%s%s\n' % (headers_ref[i], rev_seq, rev_seq))
fp_fwd.close()
fp_rev.close()
# sys.stdout.write('Aligning the fwd orientation...\n');
# command = '%s %s %s -m HW' % (EDLIB_PATH, contig_path, circularized_fwd_path);
# [rc_fwd, rstdout_fwd, rstderr_fwd] = execute_command_with_ret(DRY_RUN, command);
# scores_fwd = parse_edlib_scores(rstdout_fwd);
# for i in xrange(0, len(scores_fwd)):
# sys.stdout.write('[%d] %d %s\n' % (i, scores_fwd[i], 'fwd'));
# sys.stdout.write('\n');
sys.stdout.write('Aligning the rev orientation...\n')
command = '%s %s %s -m HW' % (EDLIB_PATH, contig_path,
circularized_rev_path)
[rc_rev, rstdout_rev,
rstderr_rev] = execute_command_with_ret(DRY_RUN, command)
scores_rev = parse_edlib_scores(rstdout_rev)
for i in xrange(0, len(scores_rev)):
sys.stdout.write('[%d] %d %s\n' % (i, scores_rev[i], 'rev'))
sys.stdout.write('\n')
def extract_seqs_for_edlib(temp_folder,
temp_suffix,
ref_path,
contig_path,
rstart,
rend,
qstart,
qend,
is_fwd,
rname,
qname,
generate_kmer_spectrum=False):
if (not os.path.exists(temp_folder)):
os.makedirs(temp_folder)
[headers_ref, seqs_ref, quals_ref] = fastqparser.read_fastq(ref_path)
[headers_contig, seqs_contig,
quals_contig] = fastqparser.read_fastq(contig_path)
ref_hash = hash_headers(headers_ref)
contig_hash = hash_headers(headers_contig)
print ref_hash
if ((rname in ref_hash) == False):
sys.stderr.write(
'ERROR: Reference name "%s" not found in file "%s"! Exiting.\n' %
(rname, ref_path))
exit(1)
if ((qname in contig_hash) == False):
sys.stderr.write(
'ERROR: Contig name "%s" not found in file "%s"! Exiting.\n' %
(qname, contig_path))
exit(1)
if (rend < rstart):
sys.stderr.write(
'ERROR: Reference end should come before reference start (it is expected that the ref is forward oriented), but ref_start = %d, ref_end = %d. Exiting.\n'
% (ref_start, ref_end))
exit(1)
rid = ref_hash[rname]
ref_header = headers_ref[rid]
ref_seq = seqs_ref[rid][(rstart - 1):(rend)]
# Coordinates are 1-based.
qid = contig_hash[qname]
contig_header = headers_contig[qid]
contig_seq = ''
if (is_fwd):
if (qend >= qstart):
contig_seq = seqs_contig[qid][(qstart - 1):(qend)]
else:
contig_seq = seqs_contig[qid][(qstart -
1):] + seqs_contig[qid][0:(qend)]
else:
if (qend > qstart):
contig_seq = seqs_contig[qid][(qend -
1):] + seqs_contig[qid][0:(qstart)]
else:
contig_seq = seqs_contig[qid][(qend - 1):(qstart)]
contig_seq = fastqparser.revcomp_seq(contig_seq)
nw_ref_path = '%s/nw-ref%s.fasta' % (temp_folder, temp_suffix)
nw_contig_path = '%s/nw-contig%s.fasta' % (temp_folder, temp_suffix)
nw_kmer_comp_path = '%s/nw-kmers%s.spect' % (temp_folder, temp_suffix)
fp_nw_ref = open(nw_ref_path, 'w')
fp_nw_contig = open(nw_contig_path, 'w')
fp_nw_ref.write('>%s\n%s\n' % (ref_header, ref_seq))
fp_nw_contig.write('>%s\n%s\n' % (contig_header, contig_seq))
fp_nw_ref.close()
fp_nw_contig.close()
sys.stderr.write('Running Edlib to determine the edit distance...\n')
command = '%s %s %s -m NW' % (EDLIB_PATH, nw_contig_path, nw_ref_path)
[rc, rstdout, rstderr] = execute_command_with_ret(DRY_RUN, command)
# execute_command(command, None, False);
scores = parse_edlib_scores(rstdout)
unaligned_len = len(seqs_ref[rid]) - len(ref_seq)
if (len(scores) == 0):
sys.stderr.write(
'ERROR: len(scores) == 0!\nreturn code: %d\nrstdout:\n%s\n' %
(rc, rstdout))
sys.stderr.write(
'Final edit distance: %d, aligned edit distance: %d, unaligned ref len: %d, aligned ref len: %d, aligned contig len: %d\n'
% ((scores[0] + unaligned_len), scores[0], unaligned_len, len(ref_seq),
len(contig_seq)))
# for i in xrange(0, len(scores)):
# sys.stdout.write('[%d] edit dist: %d\tunaligned len: %d\n' % (i, scores[i], unaligned_len));
sys.stdout.write('\n')
if (generate_kmer_spectrum == True):
sys.stderr.write('Generating the kmer spectrum.\n')
command = '%s -o %s %s %s' % (KMERCOMP_PATH, nw_kmer_comp_path,
nw_contig_path, nw_ref_path)
[rc, rstdout, rstderr] = execute_command_with_ret(DRY_RUN, command)
sys.stderr.write('Stdout:\n%s\nStderr:\n%s\n' % (rstdout, rstderr))
sys.stderr.write('Done generating the kmer spectrum!\n')
# In this case, something weird happened. Most likely the header got messed up. # Another option is that someone changed the reads file. In any case, if the original read # cannot be found, we will call this alignment unmapped. seq = '*'; flag = 4; qual = '*'; if (len(read_quals) > 0): try: qual = read_quals[read_header_hash[qseqid]]; except: qual = '*'; sam_start = (int(sstart) - 1) if (sstrand == 'plus') else (int(send) - 1); sam_end = (int(send) - 1) if (sstrand == 'plus') else (int(sstart) - 1); sam_seq = (seq) if (sstrand == 'plus' or seq == '*') else (fastqparser.revcomp_seq(seq)); # Reverse the seq field if necessary. sam_qual = (qual) if (sstrand == 'plus' or qual == '*') else (qual[::-1]); # Reverse the quality values if necessary. num_clip_front = int(qstart) - 1; num_clip_back = int(qlen) - (int(qend)); sam_cigar = convert_btop_to_cigar(btop, num_clip_front, num_clip_back, sstrand); sam_line = ''; sam_line += '%s\t' % (qseqid); # 1. qname sam_line += '%d\t' % (flag); # 2. flag sam_line += '%s\t' % (sseqid); # 3. rname sam_line += '%d\t' % (sam_start + 1); # 4. pos sam_line += '255\t'; # 5. mapq sam_line += '%s\t' % (sam_cigar); # 6. CIGAR sam_line += '*\t'; # 7. rnext sam_line += '0\t'; # 8. pnext sam_line += '0\t'; # 9. tlen