# HG changeset patch
# User iuc
# Date 1647161132 0
# Node ID 7e01297a3b4a0085cd02e596dcb22c89d1d8d97e

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"

diff -r 000000000000 -r 7e01297a3b4a coverage_table.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage_table.py	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+
+import argparse
+import gzip
+from functools import partial
+
+from Bio import SeqIO
+
+
+def generate_coverage_table(input_fasta, input_tabular, gzipped, output):
+    # Read input file into a dict and return everything
+    # in the table format required by CONCOCT.
+    gc_and_len_dict = get_gc_and_len_dict(input_fasta, gzipped)
+    assert(len(gc_and_len_dict) > 0)
+    bed_coverage_dict = get_bed_coverage_dict(input_tabular)
+
+    with open(output, 'w') as fh:
+        # Output the header.
+        fh.write("contig\tlength")
+        t = tuple(range(len(bed_coverage_dict)))
+        fh.write("\tcov_mean_sample_%d\n" % len(t))
+        # Output the content.
+        for acc in gc_and_len_dict:
+            # Fasta stats.
+            fh.write("%s\t%s" % (acc, gc_and_len_dict[acc]['length']))
+            # Mean
+            try:
+                # Coverage mean
+                fh.write("\t%f" % (bed_coverage_dict[acc]["cov_mean"]))
+            except KeyError:
+                # No reads mapped to this contig
+                fh.write("\t0")
+            fh.write("\n")
+
+
+def get_bed_coverage_dict(input_tabular):
+    # Ddetermine mean coverage and percentage covered
+    # for each contig, returning a dict with fasta id
+    # as key and percentage covered and cov_mean as keys
+    # for the inner dict.
+    out_dict = {}
+
+    with open(input_tabular, 'r') as fh:
+        for line in fh:
+            line = line.rstrip('\r\n')
+            cols = line.split('\t')
+            try:
+                d = out_dict[cols[0]]
+            except KeyError:
+                d = {}
+                out_dict[cols[0]] = d
+            if int(cols[1]) == 0:
+                d["percentage_covered"] = 100 - float(cols[4]) * 100.0
+            else:
+                d["cov_mean"] = d.get("cov_mean", 0) + int(cols[1]) * float(cols[4])
+    return out_dict
+
+
+def get_gc_and_len_dict(input_fasta, gzipped):
+    # Creates a dictionary with the fasta id as key
+    # and GC and length as keys for the inner dictionary.
+    if gzipped:
+        _open = partial(gzip.open, mode='rt')
+    else:
+        _open = open
+
+    out_dict = {}
+    with _open(input_fasta) as input_fh:
+        for rec in SeqIO.parse(input_fh, "fasta"):
+            out_dict[rec.id] = {}
+            out_dict[rec.id]["length"] = len(rec.seq)
+    return out_dict
+
+
+parser = argparse.ArgumentParser(description=__doc__)
+parser.add_argument('--input_tabular', action='store', dest='input_tabular', help='bedtools genomeCoverageBed bed file')
+parser.add_argument('--input_fasta', action='store', dest='input_fasta', help='Contigs fasta file')
+parser.add_argument("--gzipped", action="store_true", dest="gzipped", default=False, help="input_fasta is gzipped")
+parser.add_argument('--output', action='store', dest='output', help='Output file')
+
+args = parser.parse_args()
+
+generate_coverage_table(args.input_fasta, args.input_tabular, args.gzipped, args.output)
diff -r 000000000000 -r 7e01297a3b4a coverage_table.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage_table.xml	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,40 @@
+<tool id="concoct_coverage_table" name="CONCOCT coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/coverage_table.py'
+--input_fasta '$input_fasta'
+#if $input_fasta.is_of_type('fasta.gz'):
+    --gzipped
+#end if
+--input_tabular '$input_tabular'
+--output '$output'
+    ]]></command>
+    <inputs>
+        <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Contigs fasta file"/>
+        <param name="input_tabular" type="data" format="tabular" label="Tabular bedtools Genome Coverage histogram file" help="Set the bedtools Genome Coverage Output type to be Data suitable for Histogram"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="input_coverage_table.fasta.gz" ftype="fasta.gz"/>
+            <param name="input_tabular" value="input_coverage_table.tabular" ftype="tabular"/>
+            <output name="output" file="output_coverage_table.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
+file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
+CONCOCT metagenome binning tool.
+
+@HELP_OVERVIEW@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 7e01297a3b4a cut_up_fasta.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cut_up_fasta.py	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import argparse
+import gzip
+from functools import partial
+
+from Bio import SeqIO
+
+
+def cut_up_fasta(input_fasta, chunk_size, overlap, merge_last, output_fasta, output_bed, gzipped):
+    if gzipped:
+        _open = partial(gzip.open, mode='rt')
+    else:
+        _open = open
+
+    fasta_fh = open(output_fasta, 'w')
+
+    if output_bed is not None:
+        bed_fh = open(output_bed, 'w')
+
+    with _open(input_fasta) as input_fh:
+        for record in SeqIO.parse(input_fh, "fasta"):
+            if (not merge_last and len(record.seq) > chunk_size) or (merge_last and len(record.seq) >= 2 * chunk_size):
+                for index, split_seq in enumerate(chunks(record.seq, chunk_size, overlap, merge_last)):
+                    fasta_fh.write(f">{record.id}.concoct_part_{index}\n{split_seq}\n")
+                    if output_bed is not None:
+                        bed_fh.write(f"{record.id}\t{chunk_size * index}\t{chunk_size * index + len(split_seq)}\t{record.id}.concoct_part_{index}\n")
+            else:
+                fasta_fh.write(f">{record.id}.concoct_part_0\n{record.seq}\n")
+                if output_bed is not None:
+                    bed_fh.write(f"{record.id}\t0\t{len(record.seq)}\t{record.id}.concoct_part_0\n")
+    if output_bed is not None:
+        bed_fh.close()
+
+
+def chunks(seq, chunk_size, overlap_size, merge_last):
+    # Yield successive chunk_size-sized chunks from seq
+    # with given overlap overlap_size between the chunks.
+    assert chunk_size > overlap_size
+    if merge_last:
+        for i in range(0, len(seq) - chunk_size + 1, chunk_size - overlap_size):
+            yield seq[i:i + chunk_size] if i + chunk_size + chunk_size - overlap_size <= len(seq) else seq[i:]
+    else:
+        for i in range(0, len(seq), chunk_size - overlap_size):
+            yield seq[i:i + chunk_size]
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Fasta files with contigs")
+parser.add_argument("--gzipped", action="store_true", dest="gzipped", help="Input file is gzipped")
+parser.add_argument("--chunk_size", action="store", dest="chunk_size", type=int, help="Chunk size\n")
+parser.add_argument("--overlap_size", action="store", dest="overlap_size", type=int, help="Overlap size\n")
+parser.add_argument("--merge_last", default=False, action="store_true", dest="merge_last", help="Concatenate final part to last contig\n")
+parser.add_argument("--output_bed", action="store", dest="output_bed", default=None, help="BED file to be created with exact regions of the original contigs corresponding to the newly created contigs")
+parser.add_argument("--output_fasta", action="store", dest="output_fasta", help="Output fasta file with cut contigs")
+
+args = parser.parse_args()
+cut_up_fasta(args.input_fasta, args.chunk_size, args.overlap_size, args.merge_last, args.output_fasta, args.output_bed, args.gzipped)
diff -r 000000000000 -r 7e01297a3b4a extract_fasta_bins.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_fasta_bins.py	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+import argparse
+import gzip
+import os
+import sys
+from collections import defaultdict
+from functools import partial
+
+import pandas as pd
+from Bio import SeqIO
+
+parser = argparse.ArgumentParser(description=__doc__)
+
+parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped')
+parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Input Fasta file")
+parser.add_argument("--input_cluster", action="store", dest="input_cluster", help="Concoct output cluster file")
+parser.add_argument("--output_path", help="Output directory")
+
+args = parser.parse_args()
+
+all_seqs = {}
+if args.gzipped:
+    _open = partial(gzip.open, mode='rt')
+else:
+    _open = open
+
+with _open(args.input_fasta) as fh:
+    for seq in SeqIO.parse(fh, "fasta"):
+        all_seqs[seq.id] = seq
+
+# Make sure we're reading the file as tabular!
+df = pd.read_csv(args.input_cluster, sep='\t')
+try:
+    assert df.columns[0] == 'contig_id'
+    assert df.columns[1] == 'cluster_id'
+except AssertionError:
+    sys.stderr.write("ERROR! Header line was not 'contig_id, cluster_id', please adjust your input file. Exiting!\n")
+    sys.exit(-1)
+
+cluster_to_contigs = defaultdict(list)
+for i, row in df.iterrows():
+    cluster_to_contigs[row['cluster_id']].append(row['contig_id'])
+
+for cluster_id, contig_ids in cluster_to_contigs.items():
+    output_file = os.path.join(args.output_path, "{0}.fa".format(cluster_id))
+    seqs = [all_seqs[contig_id] for contig_id in contig_ids]
+    with open(output_file, 'w') as ofh:
+        SeqIO.write(seqs, ofh, 'fasta')
diff -r 000000000000 -r 7e01297a3b4a macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,26 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.79">biopython</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">concoct</requirement>
+            <requirement type="package" version="0.19.2">pandas</requirement>
+        </requirements>
+    </xml>
+    <token name="@HELP_OVERVIEW@">
+
+The intended use of the CONCOCT tools is shown in the following image.
+
+.. image:: pipeline.png
+
+More information may be found on the CONCOCT homepage:: https://github.com/BinPro/CONCOCT
+
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nmeth.3103</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 7e01297a3b4a merge_cut_up_clustering.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_cut_up_clustering.py	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+import argparse
+import re
+import sys
+from collections import Counter
+from collections import defaultdict
+
+
+CONTIG_PART_EXPR = re.compile(r'(.*)\.concoct_part_([0-9]*)')
+
+
+def original_contig_name_special(contig_id):
+    try:
+        original_id, part_index = CONTIG_PART_EXPR.match(contig_id).group(1, 2)
+        return original_id, part_index
+    except AttributeError:
+        # No matches for concoct_part regex.
+        return contig_id, 0
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input", action="store", dest="input", help="Tabular file with cut up clusters")
+parser.add_argument("--output", action="store", dest="output", help="Output file with merged clusters")
+
+args = parser.parse_args()
+
+# Get cut up clusters
+all_seqs = {}
+all_originals = defaultdict(dict)
+with open(args.input, 'r') as ifh:
+    for i, line in enumerate(ifh):
+        if i == 0:
+            if 'contig_id' not in line:
+                sys.stderr.write("ERROR nvalid clustering file, 'contig_id' is not found in the header.")
+                sys.exit(-1)
+            # Skip header.
+            continue
+        line = line.rstrip('\r\n')
+        contig_id, cluster_id = line.split('\t')
+        original_contig_name, part_id = original_contig_name_special(contig_id)
+        all_originals[original_contig_name][part_id] = cluster_id
+
+# Merge cut up clusters.
+with open(args.output, 'w') as ofh:
+    ofh.write("contig_id\tcluster_id\n")
+    for original_contig_id, part_ids_d in all_originals.items():
+        if len(part_ids_d) > 1:
+            c = Counter(part_ids_d.values())
+            cluster_id = c.most_common(1)[0][0]
+            c_string = [(a, b) for a, b in c.items()]
+            # Here if len(c.values()) > 1,
+            # then no cluster for contig.
+        else:
+            cluster_id = list(part_ids_d.values())[0]
+        ofh.write(f"{original_contig_id}\t{cluster_id}\n")
diff -r 000000000000 -r 7e01297a3b4a static/images/pipeline.png
Binary file static/images/pipeline.png has changed
diff -r 000000000000 -r 7e01297a3b4a test-data/input.fasta.gz
Binary file test-data/input.fasta.gz has changed
diff -r 000000000000 -r 7e01297a3b4a test-data/input1.fa.gz
Binary file test-data/input1.fa.gz has changed
diff -r 000000000000 -r 7e01297a3b4a test-data/input1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.tabular	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,417 @@
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diff -r 000000000000 -r 7e01297a3b4a test-data/input_coverage_table.fasta.gz
Binary file test-data/input_coverage_table.fasta.gz has changed
diff -r 000000000000 -r 7e01297a3b4a test-data/input_coverage_table.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_coverage_table.tabular	Sun Mar 13 08:45:32 2022 +0000
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diff -r 000000000000 -r 7e01297a3b4a test-data/input_merge_clusters.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_merge_clusters.tabular	Sun Mar 13 08:45:32 2022 +0000
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diff -r 000000000000 -r 7e01297a3b4a test-data/inputcluster1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcluster1.tabular	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 7e01297a3b4a test-data/output_coverage_table.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_coverage_table.tabular	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,447 @@
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diff -r 000000000000 -r 7e01297a3b4a test-data/output_merge_clusters.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_merge_clusters.tabular	Sun Mar 13 08:45:32 2022 +0000
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diff -r 000000000000 -r 7e01297a3b4a test-data/process_log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/process_log.txt	Sun Mar 13 08:45:32 2022 +0000
@@ -0,0 +1,10 @@
+Results created at
+Successfully loaded composition data.
+Successfully loaded coverage data.
+Performed PCA, resulted in 154 dimensions
+Wrote PCA transformed file.
+Wrote PCA components file.
+PCA transformed data.
+Will call vbgmm with parameters: outdir/, 400, 1000, 1
+Wrote assign file.
+CONCOCT Finished