Mercurial > repos > brenninc > data_manager_tagdust_architecture

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/tagdust_architecture_data_manager.py	Sun May 08 04:44:17 2016 -0400
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+
+import json
+import optparse
+import os.path
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+    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 get_param(name, params, default=None,  check_tab=True):
+    value = params.get(name)
+    print name, value
+    return check_param(name, value, default=default, check_tab=check_tab)
+
+
+def check_param(name, value, default=None,  check_tab=True):
+    if value in [ None, '', '?' ]:
+        if default:
+            print "Using {0} for {1} as no value provided".format( default, name )
+            value = default
+        else:
+            raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) )
+    if check_tab and "\t" in value:
+        raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) )
+    return value
+
+
+def createFileBasedOnHmm(hmms):
+    file_name = ""
+    bar_code = "no"
+    for hmm in hmms:
+        block = hmm["block"].strip()
+        if not (block[0] in ['R','O','G','B','F','S','P']):
+            raise Exception( "hmm block {0} is not a valid. It must start with one of  ['R','O','G','B','F','S','P'].".format( block ) )
+        if block[0] == 'B':
+            bar_code = "yes"
+        if block[1] != ':':
+            raise Exception( "hmm block {0} is not a valid. The second character must be ':'".format( block ) )
+        if "\t" in hmm:
+            raise Exception( "hmm block {0} is not a valid. It may not contain a tab, due to galaxy using tabs as seperators".format( block ) )
+        file_name = file_name + block + "_"
+    file_name = file_name[:-1] + ".txt"
+    return bar_code, file_name
+
+
+def get_path(galaxy_tool_dir, file_name):
+    file_path =  os.path.join(galaxy_tool_dir, "tagdust_architecture")
+    if os.path.exists(file_path):
+        if os.path.isfile(file_path):
+            raise Exception( "Found a file at {0}, but expecting a directory there".format( file_path ) )
+    else:
+        os.mkdir(file_path)
+    return os.path.join(file_path, file_name)
+
+
+def writeHmm(hmms, file_path):
+    with open( file_path, 'w' ) as output_file:
+        output_file.write("./tagdust")
+        for i, hmm in enumerate( hmms, 1 ):
+            output_file.write(" ")
+            output_file.write(str(-i))
+            output_file.write(" ")
+            output_file.write(hmm["block"])
+        output_file.write("\n")
+
+def main():
+
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '--data_table_name', action='store', type="string", default=None, help='path' )
+    parser.add_option( '--json_output_file', action='store', type="string", default=None, help='path' )
+    (options, args) = parser.parse_args()
+
+    data_table_name = check_param("data_table_name", options.data_table_name)
+    json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
+
+    param_dict = json.loads( open( json_output_file ).read() )
+    params = param_dict.get("param_dict")
+    print "input params:"
+    print params
+
+    hmms = get_param("hmms", params)
+    galaxy_tool_dir = get_param("GALAXY_DATA_INDEX_DIR", params)
+
+    data_table_entry = {}
+
+    data_table_entry["barcode"], file_name = createFileBasedOnHmm(hmms)
+    data_table_entry["path"] =  get_path(galaxy_tool_dir, file_name)
+    writeHmm(hmms, data_table_entry["path"])
+
+    basename = os.path.basename(data_table_entry["path"])
+    filename = os.path.splitext(basename)[0]
+    data_table_entry["name"] = get_param("name", params, default=filename)
+    data_table_entry["value"] = get_param("value", params, default=data_table_entry["name"])
+    data_table_entry["dbkey"] = get_param("dbkey", params, default=data_table_entry["value"])
+
+    data_manager_dict = {}
+    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+    print "output:"
+    print data_manager_dict
+    # save info to json file
+    with open( json_output_file, 'wb' ) as output_file:
+        output_file.write( json.dumps( data_manager_dict ) )
+        output_file.write( "\n" )
+
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/tagdust_architecture_data_manager.xml	Sun May 08 04:44:17 2016 -0400
@@ -0,0 +1,93 @@
+<tool id="tagdust_architecture_manager" name="tagdust architecture manager" tool_type="manage_data" version="0.0.1">
+    <description>architecture creator</description>
+    <command interpreter="python">
+        tagdust_architecture_data_manager.py
+            --data_table_name "tagdust_architecture"
+            --json_output_file "${json_output_file}"
+    </command>
+    <inputs>
+        <repeat name="hmms" title="HMM Building Blocks">
+            <param name="block" type="text" size="25" label="Next HMM Building block" />
+        </repeat>
+        <param name="name" type="text" value="" label="name field for the entry. Defaults to a contactenation of hmm values if left blank." />
+        <param name="value" type="text" value="" label="value field for the entry.  Defaults to name if left blank." />
+        <param name="dbkey" type="text" value="" label="dbkey field for the entry.  Defaults to value if left blank." />
+    </inputs>
+    <outputs>
+        <data name="json_output_file" format="data_manager_json"/>
+    </outputs>
+
+    <help>
+Adds a path to the tagdust references.
+
+The tool will check the path exists but NOT check that it holds the expected data type.
+
+If name is not provided a concatenation of hmm values is used.
+
+If value is not provided, the name will be used (or its default)
+
+If dbkey is not provided, the value will be used (or its default)
+
+====
+
+Taken from The TagDust2 Manual http://tagdust.sourceforge.net (part of Version 2_31 download)
+
+Raw sequences produced by next generation sequencing (NGS) machines can contain adapter, linker,
+barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences
+to be mapped in downstream pipelines.
+TagDust allows users to specify the expected architecture of a read and converts it into a hidden
+Markov model. The latter can assign sequences to a particular barcode (or index) even in the presence
+of sequencing errors. Sequences not matching the architecture (primer dimers, contaminants etc.) are
+automatically discarded
+
+TagDust requires an input file containing sequences and a user defined HMM architecture used to ex-
+tract the reads. The architecture is composed of a selection of pre-defined building blocks representing
+indices, barcodes, spacers and other sequences one might encounter in the raw output of a sequenced
+sample.
+
+HMM Building Blocks
+
+TagDust comes with a set of pre-defined HMM building blocks. Each includes a silent state at the
+beginning and end used to link blocks together. Each block is specified by a unique letter following
+by a colon and some information about the sequence.
+
+Read
+Segment modeling the read.
+Code: R:N
+
+Optional
+Segment modeling an optional single or short stretch of nucleotides.
+Code: O:N
+
+G addition
+Segment modeling the occasional addition of guanines to the reads.
+(89.3% chance of a single G , 19.5% chance of 2 Gs..).
+Code: G:G
+
+Barcode or Index
+Segment modeling a set of barcode sequences. For each sequence a separate HMM is created. The
+barcode sequences must be given as a comma separated list. A null model of the same length as the
+barcode is automatically added and initialized to the background nucleotide frequencies.
+Code: B:GTA,AAC
+
+Fingerprint or Unique Molecular Identifier - UMI
+Segment modeling a fingerprint (or unique molecular identifiers). Insertions and deletions are by
+default not allowed within a fingerprint segment.
+Code: F:NNN
+
+Spacer
+Segment modeling a pre-defined sequence.
+Code: S:GTA
+
+Partial
+This segment is used to model sequences that may only be partially present at the 5‘ or 3‘ end of
+the read. The transition probabilities (orange and blue) are set automatically based on the length
+distribution of exactly matching adapters.
+Code: P:CCTTAA
+
+
+    </help>
+    <citations>
+    </citations>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Sun May 08 04:44:17 2016 -0400
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/tagdust_architecture_data_manager.xml" id="tagdust_architecture_manager" version="0.0.1">
+        <data_table name="tagdust_architecture">
+            <output>
+                <column name="value" />
+                <column name="dbkey" />
+                <column name="name" />
+                <column name="barcode" />
+                <column name="path" />
+            </output>
+        </data_table>
+    </data_manager>
+
+</data_managers>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tagdust_architecture.loc.sample	Sun May 08 04:44:17 2016 -0400
@@ -0,0 +1,15 @@
+#This is a location file for tagdust reference fasta files
+
+#See tagdust reference manual for architecture recommendatons
+
+#If the architecure file include a barcode HMM (B:) set the nacode field to yes
+#Otherwise leave is as no
+
+#Planemo does not handle commas in value field well so avoid these if including the file in testing.
+
+#file has this format (white space characters are TAB characters):
+#
+#value	dbkey	name	barcode	path
+#
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Sun May 08 04:44:17 2016 -0400
@@ -0,0 +1,7 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <table name="tagdust_architecture" comment_char="#">
+        <columns>value, dbkey, name, barcode, path</columns>
+        <file path="tool-data/tagdust_architecture.loc" />
+    </table>
+ </tables>