changeset 0:a4d4da89aae1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,2 @@
+# data_manager_fetch_tx2gene
+Load entries in tx2gene table with transcript to gene tables or GTF/GFF file.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_tx2gene.py	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,307 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+import os
+import tempfile
+import shutil
+import optparse
+from ftplib import FTP
+import tarfile
+import zipfile
+import gzip
+import bz2
+try:
+    # For Python 3.0 and later
+    from urllib.request import urlopen
+    from io import BytesIO as StringIO
+    from io import UnsupportedOperation
+except ImportError:
+    # Fall back to Python 2's urllib2
+    from urllib2 import urlopen
+    from StringIO import StringIO
+    UnsupportedOperation = AttributeError
+from json import loads, dumps
+
+
+CHUNK_SIZE = 2**20  # 1mb
+
+DATA_TABLE_NAME = 'tx2gene'
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+
+
+def get_dbkey_dbname_id_name( params, dbkey_description=None ):
+#    dbkey = params['param_dict']['dbkey_source']['dbkey']
+    #TODO: ensure sequence_id is unique and does not already appear in location file
+    sequence_id = params['param_dict']['sequence_id']
+    if not sequence_id:
+        sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead?
+    
+#    if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new':
+#        dbkey_name = params['param_dict']['dbkey_source']['dbkey_name']
+#        if not dbkey_name:
+#            dbkey_name = dbkey
+#    else:
+#        dbkey_name = None
+    dbkey = params['param_dict']['dbkey'] 
+    dbkey_name = dbkey_description
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = dbkey_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return dbkey, dbkey_name, sequence_id, sequence_name
+
+
+def _get_files_in_ftp_path( ftp, path ):
+    path_contents = []
+    ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
+    return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
+
+
+def _get_stream_readers_for_tar( fh, tmp_dir ):
+    fasta_tar = tarfile.open( fileobj=fh, mode='r:*' )
+    return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x]
+
+
+def _get_stream_readers_for_zip( fh, tmp_dir ):
+    """
+    Unpacks all archived files in a zip file.
+    Individual files will be concatenated (in _stream_fasta_to_file)
+    """
+    fasta_zip = zipfile.ZipFile( fh, 'r' )
+    rval = []
+    for member in fasta_zip.namelist():
+        fasta_zip.extract( member, tmp_dir )
+        rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
+    return rval
+
+
+def _get_stream_readers_for_gzip( fh, tmp_dir ):
+    return [ gzip.GzipFile( fileobj=fh, mode='rb') ]
+
+
+def _get_stream_readers_for_bz2( fh, tmp_dir ):
+    return [ bz2.BZ2File( fh.name, 'rb') ]
+
+
+def convert_tx2gene( fasta_filename, file_type, params ):
+    if file_type is 'tx2gene':
+        return   #no need to extract tx2gene table
+    #If the file is actually a GFF/GTF file then extract the tx2gene
+    gff_temp_filename = tempfile.NamedTemporaryFile().name
+    shutil.move(fasta_filename, gff_temp_filename)
+    args= ['Rscript']
+    args.append(RSCRIPT_GFF_TO_TX2GENE)
+    args.append(gff_temp_filename)
+    args.append(fasta_filename)
+
+    #assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
+    #return SORTING_METHODS[ sort_method ]( fasta_filename, params )
+    
+def _download_file(start, fh):
+    tmp = tempfile.NamedTemporaryFile()
+    tmp.write(start)
+    tmp.write(fh.read())
+    tmp.flush()
+    tmp.seek(0)
+    return tmp
+
+
+def get_stream_reader(fh, tmp_dir):
+    """
+    Check if file is compressed and return correct stream reader.
+    If file has to be downloaded, do it now.
+    """
+    magic_dict = {
+        b"\x1f\x8b\x08": _get_stream_readers_for_gzip,
+        b"\x42\x5a\x68": _get_stream_readers_for_bz2,
+        b"\x50\x4b\x03\x04": _get_stream_readers_for_zip,
+    }
+    start_of_file = fh.read(CHUNK_SIZE)
+    try:
+        fh.seek(0)
+    except UnsupportedOperation:  # This is if fh has been created by urlopen
+        fh = _download_file(start_of_file, fh)
+    for k,v in magic_dict.items():
+        if start_of_file.startswith(k):
+            return v(fh, tmp_dir)
+    try:  # Check if file is tar file
+        if tarfile.open(fileobj=StringIO(start_of_file)):
+            return _get_stream_readers_for_tar(fh, tmp_dir)
+    except tarfile.ReadError:
+        pass
+    return fh
+
+
+
+def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params):
+    for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
+        if data_table_entry:
+            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
+
+
+def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
+    urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
+    fasta_readers = [ get_stream_reader(urlopen( url ), tmp_dir) for url in urls ]
+    add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params)
+
+
+def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
+    #TODO: allow multiple FASTA input files
+    input_filename = params['param_dict']['reference_source']['input_fasta']
+    if isinstance( input_filename, list ):
+        fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
+    else:
+        fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
+    add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
+
+
+def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
+    input_filename = params['param_dict']['reference_source']['fasta_filename']
+    create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
+    if create_symlink:
+        data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
+    else:
+        if isinstance( input_filename, list ):
+            fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
+        else:
+            fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
+        data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
+    for data_table_name, data_table_entry in data_table_entries:
+        if data_table_entry:
+            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
+
+
+def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( DATA_TABLE_NAME, [] )
+    data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
+    return data_manager_dict
+
+
+def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
+    fasta_base_filename = "%s_tx2gene.tab" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    with open( fasta_filename, 'wb+' ) as fasta_writer:
+
+        if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
+            fasta_stream = fasta_stream[0]
+
+        if isinstance( fasta_stream, list ):
+            last_char = None
+            for fh in fasta_stream:
+                if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]:
+                    fasta_writer.write( b'\n' )
+                while True:
+                    data = fh.read( CHUNK_SIZE )
+                    if data:
+                        fasta_writer.write( data )
+                        last_char = data[-1]
+                    else:
+                        break
+                if close_stream:
+                    fh.close()
+        else:
+            while True:
+                data = fasta_stream.read( CHUNK_SIZE )
+                if data:
+                    fasta_writer.write( data )
+                else:
+                    break
+            if close_stream:
+                fasta_stream.close()
+
+    convert_to_tx2gene( fasta_filename, params['param_dict']['file_type'], params )
+    return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
+
+
+def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
+
+    infile = fasta_file
+    out = open( out_file, 'w')
+
+    fasta_title = ''
+    seq_len = 0
+
+    first_entry = True
+
+    for line in open( infile ):
+        line = line.strip()
+        if not line or line.startswith( '#' ):
+            continue
+        if line[0] == '>':
+            if first_entry == False:
+                if keep_first_word:
+                    fasta_title = fasta_title.split()[0]
+                out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
+            else:
+                first_entry = False
+            fasta_title = line
+            seq_len = 0
+        else:
+            seq_len += len(line)
+
+    # last fasta-entry
+    if keep_first_word:
+        fasta_title = fasta_title.split()[0]
+    out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
+    out.close()
+
+
+def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
+    fasta_base_filename = "%s.fa" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    os.symlink( input_filename, fasta_filename )
+    return [  ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
+
+
+REFERENCE_SOURCE_TO_DOWNLOAD = dict( url=download_from_url, history=download_from_history, directory=copy_from_directory )
+
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
+    parser.add_option( '-t', '--type', dest='file_type', action='store', type='string', default=None, help='file_type')
+    (options, args) = parser.parse_args()
+    
+    filename = args[0]
+    #global DATA_TABLE_NAME
+    global RSCRIPT_GFF_TO_TX2GENE= os.path.join( options.base_dir, 'tximport.r')
+
+
+    if options.file_type == 'gff_gtf':
+        #DATA_TABLE_NAME= 'representative_gff'
+    else:   #file_type='tx2gene'
+        
+    params = loads( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+    
+    dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description ) 
+    
+    if dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+
+    # Create a tmp_dir, in case a zip file needs to be uncompressed
+    tmp_dir = tempfile.mkdtemp()
+    #Fetch the input file
+    try:
+        REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir)
+    finally:
+        cleanup_before_exit(tmp_dir)
+    #save info to json file
+    open( filename, 'wb' ).write( dumps( data_manager_dict ).encode() )
+        
+if __name__ == "__main__":
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_tx2gene.xml	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,68 @@
+<tool id="data_manager_fetch_gff" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data">
+    <description>fetching</description>
+    <command><![CDATA[
+       python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}"
+       --type $file_type
+       --dbkey_description ${ dbkey.get_display_text() }
+       --base_dir $__tool_directory__
+        
+    ]]></command>
+    <inputs>
+ 
+        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
+        <param type="text" name="sequence_name" value="" label="Name of sequence" />
+        <param type="text" name="sequence_id" value="" label="ID for sequence" />
+ 
+        <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)">
+                <option value="gff_gtf">GFF/GTF file</option>
+                <option value="tx2gene">tx2gene</option>
+            </param>
+	<conditional name="reference_source">
+	    <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+		<option value="url">URL</option>
+		<option value="history">History</option>
+		<option value="directory">Directory on Server</option>
+	    </param>
+	    <when value="url">
+		<param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
+	    </when>
+	    <when value="history">
+		<param name="input_fasta" type="data" label="File from History" multiple="False" optional="False" />
+	    </when>
+	    <when value="directory">
+		<param type="text" name="filename" value="" label="Full path to File on disk" optional="False" />
+		<param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
+	    </when>
+	</conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <!-- TODO: need some way to test that new entry was added to data table -->
+        <test>
+            <param name="dbkey" value="anoGam1"/>
+            <param name="sequence_name" value=""/>
+            <param name="sequence_desc" value=""/>
+            <param name="sequence_id" value=""/>
+            <param name="reference_source_selector" value="history"/>
+            <param name="input_fasta" value="phiX174.fasta"/>
+            <param name="sort_selector" value="as_is"/>
+            <output name="out_file" file="phiX174.data_manager_json"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table.
+
+------
+
+
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<data_managers>
+<data_manager tool_file="data_manager/data_manager_fetch_tx2gene.xml" id="data_manager_fetch_tx2gene">
+      <data_table name="all_gff">
+            <output>
+                <column name="value" />
+                <column name="dbkey" />
+                <column name="name" />
+                <column name="path" output_ref="out_file">
+                    <move type="file">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/tx2gene/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/tx2gene/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_gff.loc.sample	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,3 @@
+#The all_gff.loc file has this format:
+#
+#<unique_build_id>	<dbkey>	<display_name>	<path_to_gff_file>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/representative_gff.loc.sample	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,3 @@
+#The representative_gff.loc file has this format:
+#
+#<unique_build_id>	<dbkey>	<display_name>	<path_to_gff_file>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<tables>
+	<table name="tx2gene_table" comment_char="#" allow_duplicate_entries="False"><columns>value, dbkey, name, path</columns><file path="tool-data/tx2gene.loc" /></table>
+</tables>