--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_contigs_from_re_archive.py	Mon Oct 18 11:01:20 2021 +0000
@@ -0,0 +1,214 @@
+#!/usr/bin/env python
+'''
+parse .aln file - output from cap3 program. Output is fasta file and
+profile file
+'''
+import argparse
+import re
+import zipfile
+import tempfile
+import textwrap
+
+def parse_args():
+    '''Argument parsin'''
+    description = """
+    parsing cap3 assembly aln output
+    """
+
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument('-re',
+                        '--re_file',
+                        default=None,
+                        required=True,
+                        help="RepeatExlorer archive or directory",
+                        type=str,
+                        action='store')
+    parser.add_argument('-f',
+                        '--fasta',
+                        default=None,
+                        required=True,
+                        help="fasta output file name",
+                        type=str,
+                        action='store')
+    parser.add_argument('-m',
+                        '--min_coverage',
+                        default=5,
+                        required=False,
+                        help="minimum contig coverage",
+                        type=int,
+                        action="store")
+    parser.add_argument('-L',
+                        '--min_contig_length',
+                        default=50,
+                        required=False,
+                        help="minimum contig length",
+                        type=int,
+                        action="store")
+    return parser.parse_args()
+
+
+def get_header(f):
+    aln_header = "    .    :    .    :    .    :    .    :    .    :    .    :"
+    contig_lead = "******************"
+    aln_start = -1
+    while True:
+        line = f.readline()
+        if not line:
+            return None, None
+        if line[0:18] == contig_lead:
+            line2 = f.readline()
+        else:
+            continue
+        if aln_header in line2:
+            aln_start = line2.index(aln_header)
+            break
+    contig_name = line.split()[1] + line.split()[2]
+    return contig_name, aln_start
+
+
+def segment_start(f):
+    pos = f.tell()
+    line = f.readline()
+    # detect next contig or end of file
+    if "********" in line or line == "" or "Number of segment pairs = " in line:
+        segment = False
+    else:
+        segment = True
+    f.seek(pos)
+    return segment
+
+
+def get_segment(f, seq_start):
+    if not segment_start(f):
+        return None, None
+    aln = []
+    while True:
+        line = f.readline()
+        if ".    :    .    :" in line:
+            continue
+        if "__________" in line:
+            consensus = f.readline().rstrip('\n')[seq_start:]
+            f.readline()  # empty line
+            break
+        else:
+            aln.append(line.rstrip('\n')[seq_start:])
+    return aln, consensus
+
+
+def aln2coverage(aln):
+    coverage = [0] * len(aln[0])
+    for a in aln:
+        for i, c in enumerate(a):
+            if c not in " -":
+                coverage[i] += 1
+    return coverage
+
+
+def read_contig(f, seq_start):
+    contig = ""
+    coverage = []
+    while True:
+        aln, consensus = get_segment(f, seq_start)
+        if aln:
+            contig += consensus
+            coverage += aln2coverage(aln)
+        else:
+            break
+    return contig, coverage
+
+
+def remove_gaps(consensus, coverage):
+    if "-" not in consensus:
+        return consensus, coverage
+    new_coverage = [
+        cov for cons, cov in zip(consensus, coverage) if cons != "-"
+    ]
+    new_consensus = consensus.replace("-", "")
+    return new_consensus, new_coverage
+
+
+def extract_contigs_from_re_archive(archive, aln_output):
+    with zipfile.ZipFile(archive, 'r') as zip_object, open(aln_output,
+                                                           'w') as fout:
+        flist = zip_object.infolist()
+        for fn in flist:
+            if re.match('seqclust.+[.]aln$', fn.filename):
+                with zip_object.open(fn.filename) as aln:
+                    for l in aln:
+                        fout.write(l.decode('utf-8'))
+    return aln_output
+
+def read_tarean_fasta(fobj):
+    ids = []
+    s = []
+    for i in fobj:
+        ii = i.decode('utf-8')
+        if ii[0] == ">":
+            ids.append(ii)
+            s.append("")
+        else:
+            s[-1] = s[-1] + ii.strip()
+    return ids, s
+
+def extract_tarean_contigs_from_re_archive(archive):
+    with zipfile.ZipFile(archive, 'r') as zip_object:
+        flist = zip_object.infolist()
+        seqs_all = []
+        ids_all = []
+        for fn in flist:
+            if re.match("seqclust.+dir_CL[0-9]+[/]tarean_contigs.fasta", fn.filename):
+                print(fn.filename)
+                with zip_object.open(fn.filename) as fobj:
+                    ids, seqs = read_tarean_fasta(fobj)
+                    # wrap sequences
+                    seqs = ["\n".join(textwrap.wrap(s + s, 80)) for s in seqs]
+                    seqs_all += seqs
+                    ids_all += ids
+    return ids_all, seqs_all
+
+
+def extract_contigs_from_re_directory(dir, aln_output):
+    # TODO
+    pass
+
+
+def filter_contigs(consensus, coverage, min_coverage=5):
+    x = "".join([
+        s if cov >= min_coverage else " "
+        for s, cov in zip(consensus, coverage)
+    ]).strip()
+    consensus_N = "\n".join(textwrap.wrap(x.replace(" ", "N"),80))
+    return consensus_N
+
+
+def main():
+    args = parse_args()
+    # extract aln from archive
+    ids, seqs = extract_tarean_contigs_from_re_archive(args.re_file)
+    aln_file = extract_contigs_from_re_archive(
+        args.re_file,
+        tempfile.NamedTemporaryFile().name)
+    with open(aln_file, 'r') as f1, open(args.fasta, 'w') as ffasta:
+        while True:
+            contig_name, seq_start = get_header(f1)
+            if contig_name:
+                consensus, coverage = remove_gaps(*read_contig(f1, seq_start))
+                clean_consensus = filter_contigs(consensus, coverage,
+                                                 args.min_coverage)
+                if len(clean_consensus) >= args.min_contig_length:
+                    ffasta.write(">{}\n".format(contig_name))
+                    ffasta.write("{}\n".format(clean_consensus))
+            else:
+                break
+
+        # write tarean sequences:
+        for i, s in zip(ids, seqs):
+            ffasta.write(i)
+            ffasta.write(s + "\n")
+
+
+
+if __name__ == "__main__":
+
+    main()