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changeset 0:3e33310a7082 draft

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planemo upload for repository https://github.com/rplanel/galaxy-tools/tree/master/tools/sequence-splitter commit cba12d215a89e9685c7d1f55d067770d7ec0dea2
author rplanel
date Thu, 08 Aug 2019 11:18:30 -0400
parents
children 7b509a1801e4
files sequence-splitter.py sequence-splitter.xml test-data/sample-2-chunk-1.fasta test-data/sample-2-chunk-2.fasta test-data/sample-2-chunk-3.fasta test-data/sample-2-chunk-4.fasta test-data/sample-3-chunk-1.fastq test-data/sample-3-chunk-2.fastq test-data/sample-chunk-1.fasta test-data/sample-chunk-1.fastq test-data/sample-chunk-2.fasta test-data/sample-chunk-2.fastq test-data/sample-chunk-3.fastq test-data/sample-chunk-4.fastq test-data/sample-chunk-5.fastq test-data/sample.fasta test-data/sample.fastq
diffstat 17 files changed, 405 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequence-splitter.py	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,129 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+import argparse
+import logging
+import os
+from itertools import chain, islice, tee
+
+# BioPython
+from Bio import SeqIO
+
+logging.basicConfig(
+    level=logging.INFO, format="%(asctime)s : %(levelname)s : %(message)s"
+)
+logger = logging.getLogger()
+
+
+def main():
+    args = parse_arguments()
+    # extract the basename and the file extension
+    basename, file_extension = os.path.splitext(args.sequences)
+    # extract the filename (with no extension)
+    _, filename = os.path.split(basename)
+    chunk_size = args.chunk_size
+    # split the sequences in chunks
+    if chunk_size:
+        logger.info("%s = %s", "chunk size parameter", chunk_size)
+        sequences_record = gen_sequence_record(args.sequences, args.format)
+        chunks = gen_get_chunks_by_size(sequences_record, chunk_size)
+    else:
+        logger.info("%s = %s", "number of chunks parameter", args.nb_chunk)
+        chunks = gen_get_chunks(args.sequences, args.format, args.nb_chunk)
+
+    # Write the chunks in numbered files.
+    write_chunks(chunks, args.output, filename, file_extension, args.format)
+
+
+def gen_get_chunks(sequences_path, sequences_format, nb_chunk):
+    """[summary]
+
+    Arguments:
+        sequences_path {[type]} -- [description]
+        sequences_format {[type]} -- [description]
+        nb_chunk {[type]} -- [description]
+
+    Returns:
+        [type] -- [description]
+    """
+    # First record to count the sequences
+    sequences_record_to_count = gen_sequence_record(
+        sequences_path, sequences_format)
+    # Get the number of sequences
+    nb_sequences = get_nb_sequences(sequences_record_to_count)
+    logger.info("%s = %i", "Number of sequences per chunk", nb_sequences)
+    # Second record to that will be splitted
+    sequences_to_split = gen_sequence_record(sequences_path, sequences_format)
+
+    # Get the size of the chunks
+    chunk_size = int(nb_sequences / nb_chunk) if nb_sequences > nb_chunk else 1
+    return gen_get_chunks_by_size(sequences_to_split, chunk_size)
+
+
+def gen_get_chunks_by_size(iterable, size=10):
+    logger.info(
+        "%s = %i",
+        "chunk size got (could be different from parameter if more chunk asked \
+         than sequences in multifasta)",
+        size
+    )
+    iterator = iter(iterable)
+    for first in iterator:
+        yield chain([first], islice(iterator, size - 1))
+
+
+def gen_sequence_record(sequences_path, sequence_format):
+    return SeqIO.parse(sequences_path, sequence_format)
+
+
+def get_nb_sequences(sequences):
+    return sum(1 for _ in sequences)
+
+
+def write_chunks(iterable, dirname, filename, file_extension, sequence_format):
+    for idx, chunk in enumerate(iterable):
+        if not os.path.exists(dirname):
+            os.mkdir(dirname)
+        output_file = os.path.join(
+            dirname, filename + "-chunk-" + str(idx + 1) + file_extension
+        )
+        with open(output_file, mode="w") as output_handle:
+            count_seq, seq_to_write = tee(chunk, 2)
+            logger.info(
+                "%s : number of seuquences = %i", output_file, len(
+                    list(count_seq))
+            )
+            SeqIO.write(seq_to_write, output_handle, sequence_format)
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(description="Split fasta/fastq files")
+    parser.add_argument(
+        "-s", "--sequences", type=str, help="File that contains the sequences"
+    )
+
+    parser.add_argument("-f", "--format", type=str,
+                        help="File format (fastq, fasta)")
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument(
+        "-c", "--chunk-size",
+        type=int,
+        help="The number of sequences by chunks."
+    )
+    group.add_argument("-n", "--nb-chunk", help="Number of chunks", type=int)
+
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=str,
+        default="./",
+        help="The output directory where the chunks will be saved",
+    )
+
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    logger.info("START")
+    main()
+    logger.info("FINISHED")
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequence-splitter.xml	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,132 @@
+<tool id="sequence-splitter" name="Sequence Splitter" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="2.7.11">python</requirement>
+        <requirement type="package" version="1.73">biopython</requirement>
+    </requirements>
+    <edam_operations>
+        <edam_operation>operation_2409</edam_operation>
+        <edam_operation>operation_3359</edam_operation>
+    </edam_operations>
+    <edam_topics>
+        <edam_topic>topic_3307</edam_topic>
+        <edam_topic>topic_0080</edam_topic>
+    </edam_topics>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$sequences' ./sequences.${sequences.ext} &&
+        python 
+            '$__tool_directory__/sequence-splitter.py' 
+            -s ./sequences.$sequences.ext
+            #if $sequences.is_of_type("fasta") 
+                -f fasta
+            #else
+                -f fastq
+            #end if 
+            #if $split_mode.selector == 'chunk_size'
+                -c $split_mode.chunk_size
+            #else
+                -n $split_mode.nb_chunk
+            #end if
+            -o 'outputs'
+    ]]>    </command>
+    <inputs>
+        <param type="data" name="sequences" format="fasta,fastq"/>
+        <conditional name="split_mode">
+            <param name="selector" type="select" label="Split by:">
+                <option value="chunk_size">Number of sequence(s) by chunk</option>
+                <option value="nb_chunk">Number of chunk(s)</option>
+            </param>
+            <when value="chunk_size">
+                <param name="chunk_size" label="Chunk size" type="integer" min="1" value="100" help="How many sequences by chunk ?"/>
+            </when>
+            <when value="nb_chunk">
+                <param name="nb_chunk" label="Number of chunks" type="integer" min="1" value="10" help="How many chunks ?"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="split_output" type="list" label="splitted sequences">
+            <discover_datasets pattern="(?P&lt;designation&gt;\w+-chunk-\d+)\.(?P&lt;ext&gt;.+)" directory="outputs" />
+        </collection>
+        <data format="text" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="sequences" value="sample.fasta"/>
+            <conditional name="split_mode">
+                <param name="selector" value="chunk_size"/>
+                <param name="chunk_size" value="2"/>
+            </conditional>
+            <output_collection name="split_output" type="list" count="2">
+                <element name="sequences-chunk-1" file="sample-chunk-1.fasta" ftype="fasta"/>
+                <element name="sequences-chunk-2" file="sample-chunk-2.fasta" ftype="fasta"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="sequences" value="sample.fastq"/>
+            <conditional name="split_mode">
+                <param name="selector" value="chunk_size"/>
+                <param name="chunk_size" value="2"/>
+            </conditional>
+            <output_collection name="split_output" type="list" count="5">
+                <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger"/>
+                <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger"/>
+                <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger"/>
+                <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger"/>
+                <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger"/>
+            </output_collection>
+        </test>
+
+        <test>
+            <param name="sequences" value="sample.fastq"/>
+            <conditional name="split_mode">
+                <param name="selector" value="nb_chunk" />
+                <param name="nb_chunk" value="2"/>
+            </conditional>
+            <output_collection name="split_output" type="list" count="2">
+                <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger"/>
+                <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="sequences" value="sample.fasta"/>
+            <conditional name="split_mode">
+                <param name="selector" value="nb_chunk" />
+                <param name="nb_chunk" value="10"/>
+            </conditional>
+            <output_collection name="split_output" type="list" count="4">
+                <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta"/>
+                <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta"/>
+                <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta"/>
+                <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta"/>
+            </output_collection>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+Usage:
+
+    sequence-splitter.py [-h] [-s SEQUENCES] [-f FORMAT] (-c CHUNK_SIZE | -n NB_CHUNK) [-o OUTPUT]
+
+Split fasta/fastq files
+
+optional arguments:
+-h, --help            show this help message and exit
+
+-s SEQUENCES, --sequences SEQUENCES
+                    File that contains the sequences
+
+-f FORMAT, --format FORMAT
+                    File format (fastq, fasta)
+
+-c CHUNK_SIZE, --chunk-size CHUNK_SIZE
+                    The number of sequences by chunks
+
+-n NB_CHUNK, --nb-chunk NB_CHUNK
+                    Number of chunks
+
+-o OUTPUT, --output OUTPUT
+                    The output directory where the chunks will be saved
+
+
+    ]]>    </help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-2-chunk-1.fasta	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,2 @@
+>derice
+ACTGACTAGCTAGCTAACTG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-2-chunk-2.fasta	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,2 @@
+>sanka
+GCATCGTAGCTAGCTACGAT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-2-chunk-3.fasta	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,2 @@
+>junior
+CATCGATCGTACGTACGTAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-2-chunk-4.fasta	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,2 @@
+>yul
+ATCGATCGATCGTACGATCG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-3-chunk-1.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,20 @@
+@cluster_2:UMI_ATTCCG
+TTTCCGGGGCACATAATCTTCAGCCGGGCGC
++
+9C;=;=<9@4868>9:67AA<9>65<=>591
+@cluster_8:UMI_CTTTGA
+TATCCTTGCAATACTCTCCGAACGGGAGAGC
++
+1/04.72,(003,-2-22+00-12./.-.4-
+@cluster_12:UMI_GGTCAA
+GCAGTTTAAGATCATTTTATTGAAGAGCAAG
++
+?7?AEEC@>=1?A?EEEB9ECB?==:B.A?A
+@cluster_21:UMI_AGAACA
+GGCATTGCAAAATTTATTACACCCCCAGATC
++
+>=2.660/?:36AD;0<14703640334-//
+@cluster_29:UMI_GCAGGA
+CCCCCTTAAATAGCTGTTTATTTGGCCCCAG
++
+8;;;>DC@DAC=B?C@9?B?CDCB@><<??A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-3-chunk-2.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,20 @@
+@cluster_34:UMI_AGCTCA
+TCTTGCAAAAACTCCTAGATCGGAAGAGCAC
++
+-/CA:+<599803./2065?6=<>90;?150
+@cluster_36:UMI_AACAGA
+TCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+5?:5;<02:@977=:<0=9>@5>7>;>*3,-
+@cluster_37:UMI_GAGGAG
+GTCTTTGTACAAAATTTTATTAAAGGTCTTT
++
+?B?DEC@A=?ADDAEEEC?EC@D6A@@>DE4
+@cluster_39:UMI_GAACCG
+CCTTCCATCACCAGATCGGAAAAACACACGC
++
+00>7;8@5<192?/8;0;;>=3=/3239713
+@cluster_43:UMI_GGATTG
+GAGTTATAATCCAATCTTTATTTAAAAATCT
++
+>=AEC?C@;??0A>?0DEB9EEB@DDC1?=6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-chunk-1.fasta	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,4 @@
+>derice
+ACTGACTAGCTAGCTAACTG
+>sanka
+GCATCGTAGCTAGCTACGAT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-chunk-1.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,8 @@
+@cluster_2:UMI_ATTCCG
+TTTCCGGGGCACATAATCTTCAGCCGGGCGC
++
+9C;=;=<9@4868>9:67AA<9>65<=>591
+@cluster_8:UMI_CTTTGA
+TATCCTTGCAATACTCTCCGAACGGGAGAGC
++
+1/04.72,(003,-2-22+00-12./.-.4-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-chunk-2.fasta	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,4 @@
+>junior
+CATCGATCGTACGTACGTAG
+>yul
+ATCGATCGATCGTACGATCG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-chunk-2.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,8 @@
+@cluster_12:UMI_GGTCAA
+GCAGTTTAAGATCATTTTATTGAAGAGCAAG
++
+?7?AEEC@>=1?A?EEEB9ECB?==:B.A?A
+@cluster_21:UMI_AGAACA
+GGCATTGCAAAATTTATTACACCCCCAGATC
++
+>=2.660/?:36AD;0<14703640334-//
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-chunk-3.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,8 @@
+@cluster_29:UMI_GCAGGA
+CCCCCTTAAATAGCTGTTTATTTGGCCCCAG
++
+8;;;>DC@DAC=B?C@9?B?CDCB@><<??A
+@cluster_34:UMI_AGCTCA
+TCTTGCAAAAACTCCTAGATCGGAAGAGCAC
++
+-/CA:+<599803./2065?6=<>90;?150
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-chunk-4.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,8 @@
+@cluster_36:UMI_AACAGA
+TCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+5?:5;<02:@977=:<0=9>@5>7>;>*3,-
+@cluster_37:UMI_GAGGAG
+GTCTTTGTACAAAATTTTATTAAAGGTCTTT
++
+?B?DEC@A=?ADDAEEEC?EC@D6A@@>DE4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-chunk-5.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,8 @@
+@cluster_39:UMI_GAACCG
+CCTTCCATCACCAGATCGGAAAAACACACGC
++
+00>7;8@5<192?/8;0;;>=3=/3239713
+@cluster_43:UMI_GGATTG
+GAGTTATAATCCAATCTTTATTTAAAAATCT
++
+>=AEC?C@;??0A>?0DEB9EEB@DDC1?=6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.fasta	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,8 @@
+>derice
+ACTGACTAGCTAGCTAACTG
+>sanka
+GCATCGTAGCTAGCTACGAT
+>junior
+CATCGATCGTACGTACGTAG
+>yul
+ATCGATCGATCGTACGATCG
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.fastq	Thu Aug 08 11:18:30 2019 -0400
@@ -0,0 +1,40 @@
+@cluster_2:UMI_ATTCCG
+TTTCCGGGGCACATAATCTTCAGCCGGGCGC
++
+9C;=;=<9@4868>9:67AA<9>65<=>591
+@cluster_8:UMI_CTTTGA
+TATCCTTGCAATACTCTCCGAACGGGAGAGC
++
+1/04.72,(003,-2-22+00-12./.-.4-
+@cluster_12:UMI_GGTCAA
+GCAGTTTAAGATCATTTTATTGAAGAGCAAG
++
+?7?AEEC@>=1?A?EEEB9ECB?==:B.A?A
+@cluster_21:UMI_AGAACA
+GGCATTGCAAAATTTATTACACCCCCAGATC
++
+>=2.660/?:36AD;0<14703640334-//
+@cluster_29:UMI_GCAGGA
+CCCCCTTAAATAGCTGTTTATTTGGCCCCAG
++
+8;;;>DC@DAC=B?C@9?B?CDCB@><<??A
+@cluster_34:UMI_AGCTCA
+TCTTGCAAAAACTCCTAGATCGGAAGAGCAC
++
+-/CA:+<599803./2065?6=<>90;?150
+@cluster_36:UMI_AACAGA
+TCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+5?:5;<02:@977=:<0=9>@5>7>;>*3,-
+@cluster_37:UMI_GAGGAG
+GTCTTTGTACAAAATTTTATTAAAGGTCTTT
++
+?B?DEC@A=?ADDAEEEC?EC@D6A@@>DE4
+@cluster_39:UMI_GAACCG
+CCTTCCATCACCAGATCGGAAAAACACACGC
++
+00>7;8@5<192?/8;0;;>=3=/3239713
+@cluster_43:UMI_GGATTG
+GAGTTATAATCCAATCTTTATTTAAAAATCT
++
+>=AEC?C@;??0A>?0DEB9EEB@DDC1?=6
\ No newline at end of file