--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/demultiplex.py	Fri Nov 09 05:37:11 2018 -0500
@@ -0,0 +1,187 @@
+import argparse
+import csv
+import logging
+import os
+import sys
+from collections import defaultdict
+from collections import namedtuple
+
+from Bio import SeqIO
+from Bio.Alphabet import generic_dna
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+def sniff_format(file_path):
+    """
+    Try to guess the file format (fastq/fasta) by looking at the first character of the first line.
+    Should be '@' for fastq and '>' for fasta.
+    """
+    with open(file_path, 'rU') as file_handle:
+        for line in file_handle:
+            if line.startswith("@"):
+                return "fastq"
+            if line.startswith(">"):
+                return "fasta"
+            break
+        return None
+        
+        
+def search_barcode_in_first_half(sequence, barcode):
+    if type(sequence) is Seq:
+        sequence = str(sequence)
+    elif type(sequence) is SeqRecord:
+        sequence = str(sequence.seq)
+    return sequence.find(barcode, 0, int(len(sequence) / 2))
+
+
+def search_barcode_in_second_half(sequence, barcode):
+    if type(sequence) is Seq:
+        sequence = str(sequence)
+    elif type(sequence) is SeqRecord:
+        sequence = str(sequence.seq)
+    return sequence.find(barcode, int(len(sequence) / 2))
+
+
+def search_barcodes_in_sequence(barcode_datas, sequence):
+    for barcode_data in barcode_datas:
+        barcode_search_position = search_barcode_in_first_half(sequence, barcode_data.barcode)
+        if barcode_search_position != -1:
+            return barcode_search_position, barcode_data, False
+        barcode_search_position = search_barcode_in_second_half(sequence, barcode_data.barcode_reverse)
+        if barcode_search_position != -1:
+            return barcode_search_position, barcode_data, True
+
+        barcode_search_position = search_barcode_in_first_half(sequence, barcode_data.barcode_reverse)
+        if barcode_search_position != -1:
+            return barcode_search_position, barcode_data, True
+
+        barcode_search_position = search_barcode_in_second_half(sequence, barcode_data.barcode)
+        if barcode_search_position != -1:
+            return barcode_search_position, barcode_data, False
+
+    return -1, None, None
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", "--input", help="The input file")
+    parser.add_argument("-f", "--format", help="The format of the input file (fastq/fasta)", default="auto", choices=["fasta", "fastq", "auto"])
+    parser.add_argument("-o", "--output-dir", help="The output dir")
+    parser.add_argument("-m", "--mapping-file", help="A tab seperated file containing two columns, ID and barcode (no header)")
+
+    args = parser.parse_args()
+
+    input_file_path = args.input
+    basename_input_file_path = os.path.basename(input_file_path)
+    input_basename_no_ext, input_extension = os.path.splitext(basename_input_file_path)
+
+    input_format = args.format
+
+    logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+
+    if input_format == "auto":
+        if input_extension in [".fasta", ".fa"]:
+            input_format = "fasta"
+        elif input_extension in [".fastq", ".fq"]:
+            input_format = "fastq"
+        else:
+            logging.info("Can't auto detect input format based on extension: {0}".format(input_extension))
+            logging.info("Sniffing format...")
+            input_format = sniff_format(input_file_path)
+            if not input_format:
+                logging.error("Can't auto detect input format")
+                sys.exit(1)
+            logging.info("Sniffed '{0}' as format.".format(input_format))
+
+    output_dir = args.output_dir
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    with open(args.mapping_file, newline="") as handle:
+        ID_barcode_mapping = list(csv.DictReader(handle, fieldnames=['ID', 'barcode'], delimiter="\t"))
+
+    logging.info("Input:   {0}".format(input_file_path))
+    logging.info("Format:  {0}".format(input_format))
+    logging.info("Output:  {0}".format(output_dir))
+    logging.info("Mapping: {0} ({1} mappings)".format(args.mapping_file, len(ID_barcode_mapping)))
+
+    BarcodeData = namedtuple("BarcodeData", [
+        "ID",
+        "barcode",
+        "barcode_reverse",
+        "output_file_path",
+        "output_file_handle"
+    ])
+
+    barcode_data_dict = defaultdict(list)
+    ID_file_handle_dict = {}
+
+    for ID_barcode in ID_barcode_mapping:
+        ID = ID_barcode["ID"]
+        barcode = ID_barcode["barcode"]
+
+        output_file_path = os.path.join(
+            output_dir,
+            "{0}_{1}.{2}".format(input_basename_no_ext, ID, input_format)
+        )
+
+        if ID not in ID_file_handle_dict:
+            ID_file_handle = open(output_file_path, 'w')
+            ID_file_handle_dict[ID] = ID_file_handle
+
+        ID_file_handle = ID_file_handle_dict[ID]
+
+        barcode_data_dict[ID] += [BarcodeData(
+            ID=ID,
+            barcode=barcode,
+            barcode_reverse=str(Seq(barcode, generic_dna).reverse_complement()),
+            output_file_path=output_file_path,
+            output_file_handle=ID_file_handle
+        )]
+
+    discarded_output_file_path = os.path.join(
+        output_dir,
+        "{0}_{1}.{2}".format(basename_input_file_path, "discarded", input_format)
+    )
+
+    total_sequences = 0
+    sequences_assigned_by_id = defaultdict(int)
+
+    with open(input_file_path, 'rU') as input_file_handle, open(discarded_output_file_path, 'w') as discarded_output_handle:
+        for record in SeqIO.parse(input_file_handle, input_format):
+            total_sequences += 1
+            for ID, barcode_datas in barcode_data_dict.items():
+                barcode_position, barcode_data, reverse = search_barcodes_in_sequence(barcode_datas, record)
+                if barcode_position == -1:
+                    continue
+                barcode = barcode_data.barcode if not reverse else barcode_data.barcode_reverse
+                sequences_assigned_by_id[barcode_data.ID] += 1
+                logging.debug(str(record.seq))
+                logging.debug(" " * barcode_position + barcode)
+                SeqIO.write(record, ID_file_handle_dict[ID], input_format)
+                break
+            else:  # no match # TODO fuzzy match ?
+                SeqIO.write(record, discarded_output_handle, input_format)
+            if total_sequences % 10000 == 0:
+                assigned_sequences = sum(sequences_assigned_by_id.values())
+                logging.info("Processed {0} sequences, assigned {1} ({2}%)".format(
+                    total_sequences,
+                    assigned_sequences,
+                    round(assigned_sequences / total_sequences * 100)
+                ))
+
+    for file_handle in ID_file_handle_dict.values():
+        file_handle.close()
+
+    assigned_sequences = sum(sequences_assigned_by_id.values())
+    logging.info("Processed {0} sequences, assigned {1} ({2}%)".format(
+        total_sequences,
+        assigned_sequences,
+        round(assigned_sequences / total_sequences * 100)
+    ))
+
+
+if __name__ == "__main__":
+    main()
+ 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/demultiplex.xml	Fri Nov 09 05:37:11 2018 -0500
@@ -0,0 +1,46 @@
+<tool id="demultiplex-emc" name="Demultiplex" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="3.7.0">python</requirement>
+        <requirement type="package" version="1.7.2">biopython</requirement>
+    </requirements>
+    <description></description>
+    <command>
+        mkdir outputs;
+        python3 $__tool_directory__/demultiplex.py 
+        --input $input
+        --format auto
+        --output-dir ./outputs
+        --mapping-file $mapping
+    </command>
+    <inputs>
+        <param name="input" type="data" format='fasta,fastq' label="The input fasta/fastq"/>
+        <param name="mapping" type="data" format='tabular' label="The mapping file"/>
+    </inputs>
+    <outputs>
+        <data name="debug" format="txt" label="debug"/>
+        <collection name='demultiplex_out' format_source='input' type='list'>
+            <discover_datasets pattern="__name_and_ext__" directory="outputs" format_source='input'/>
+        </collection>
+    </outputs>
+    <tests>
+    <!--
+        <test>
+            <param name="input1" value="1.bed"/>
+            <param name="input2" value="2.bed"/>
+            <output name="out_file1" file="cat_wrapper_out1.bed"/>
+        </test>
+        TODO: if possible, enhance the underlying test code to handle this test
+            the problem is multiple params with the same name "input2"
+        <test>
+            <param name="input1" value="1.bed"/>
+            <param name="input2" value="2.bed"/>
+            <param name="input2" value="3.bed"/>
+            <output name="out_file1" file="cat_wrapper_out2.bed"/>
+        </test>
+    -->
+    </tests>
+    <help>
+There is no help
+    </help>
+</tool>
+