# HG changeset patch
# User greg
# Date 1634155968 0
# Node ID 787f1ca9045a017e8debc1c55c9adfac670af353
# Parent d69ebf52c233dfc980f857c34b389bf96173c493
Uploaded
diff -r d69ebf52c233 -r 787f1ca9045a data_manager/malt_index_builder.py
--- a/data_manager/malt_index_builder.py Tue Oct 12 14:15:35 2021 +0000
+++ b/data_manager/malt_index_builder.py Wed Oct 13 20:12:48 2021 +0000
@@ -6,8 +6,6 @@
import subprocess
import sys
-DEFAULT_DATA_TABLE_NAME = "malt_indices"
-
def get_id_name(params, dbkey, fasta_description=None):
sequence_id = params['param_dict']['sequence_id']
@@ -22,29 +20,40 @@
return sequence_id, sequence_name
-def build_malt_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, sequence_type, shapes, max_hits_per_seed, protein_reduct, data_table_name=DEFAULT_DATA_TABLE_NAME):
+def build_malt_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, sequence_type, shapes, max_hits_per_seed, protein_reduct):
+ # The malt-build program produces a directory of files,
+ # so the data table path entry will be a directory and
+ # not an index file.
fasta_base_name = os.path.split(fasta_filename)[-1]
sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
os.symlink(fasta_filename, sym_linked_fasta_filename)
- args = ['malt-build', '--input', sym_linked_fasta_filename, '--sequenceType', sequence_type, '--index', 'index']
+ args = ['malt-build', '--input', sym_linked_fasta_filename, '--sequenceType', sequence_type, '--index', target_directory]
threads = os.environ.get('GALAXY_SLOTS')
if threads:
args.extend(['--threads', threads])
if shapes is not None:
- args.extend('--shapes', shapes)
+ args.extend(['--shapes', shapes])
if max_hits_per_seed is not None:
- args.extend('--maxHitsPerSeed', max_hits_per_seed)
+ args.extend(['--maxHitsPerSeed', max_hits_per_seed])
if protein_reduct is not None:
- args.extend('--proteinReduct', protein_reduct)
+ args.extend(['--proteinReduct', protein_reduct])
proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
return_code = proc.wait()
if return_code:
sys.exit('Error building index, return_code: %d' % return_code)
- data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
- _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+ # Remove unwanted files from the output directory.
+ os.remove(sym_linked_fasta_filename)
+ # The path entry here is the directory
+ # where the index files will be located,
+ # not a single index file (malt-build
+ # produces a directory if files, which
+ # is considered an index..
+ data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=None)
+ _add_data_table_entry(data_manager_dict, data_table_entry)
-def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+def _add_data_table_entry(data_manager_dict, data_table_entry):
+ data_table_name = "malt_indices"
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)
@@ -58,7 +67,7 @@
parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta description')
parser.add_option('-e', '--sequence_type', dest='sequence_type', action='store', type="string", help='DNA or Protein sequences')
parser.add_option('-p', '--shapes', dest='shapes', action='store', type="string", default=None, help='Comma-separated list of seed shapes')
- parser.add_option('-m', '--max_hits_per_seed', dest='max_hits_per_seed', action='store', type="int", default=None, help='Maximum number of hits per seed')
+ parser.add_option('-m', '--max_hits_per_seed', dest='max_hits_per_seed', action='store', type="string", default=None, help='Maximum number of hits per seed')
parser.add_option('-r', '--protein_reduct', dest='protein_reduct', action='store', type="string", default=None, help='Name or definition of protein alphabet reduction')
(options, args) = parser.parse_args()
@@ -78,7 +87,7 @@
sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
# Build the index.
- build_malt_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.sequence_type, options.shapes, options.max_hits_per_seed, options.protein_reduct, data_table_name=DEFAULT_DATA_TABLE_NAME)
+ build_malt_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.sequence_type, options.shapes, options.max_hits_per_seed, options.protein_reduct)
# Save info to json file.
with open(filename, 'w') as fh:
diff -r d69ebf52c233 -r 787f1ca9045a data_manager/malt_index_builder.xml
--- a/data_manager/malt_index_builder.xml Tue Oct 12 14:15:35 2021 +0000
+++ b/data_manager/malt_index_builder.xml Wed Oct 13 20:12:48 2021 +0000
@@ -10,40 +10,32 @@
--fasta_dbkey '${all_fasta_source.fields.dbkey}'
--fasta_description '${all_fasta_source.fields.name}'
--sequence_type '${sequence_type}'
+#if str($protein_reduct_setting_cond.protein_reduct_setting) == 'yes':
+ --protein_reduct '${protein_reduct_setting_cond.protein_reduct}'
+#end if
#if str($seed_setting_cond.seed_setting) == 'yes':
--shapes '${seed_setting_cond.shapes}'
- --max_hits_per_seed $seed_setting_cond.max_hits_per_seed
- --protein_reduct '${seed_setting_cond.protein_reduct}'
+ ## malt-build requires a string here.
+ --max_hits_per_seed '${seed_setting_cond.max_hits_per_seed}'
#end if
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.. class:: infomark
-**Notice:** Values for name, description, and id will be generated automatically if left blank.
+**Notice:** Values for Name and ID of sequence will be generated automatically if left blank.
**What it does**
diff -r d69ebf52c233 -r 787f1ca9045a data_manager_conf.xml
--- a/data_manager_conf.xml Tue Oct 12 14:15:35 2021 +0000
+++ b/data_manager_conf.xml Wed Oct 13 20:12:48 2021 +0000
@@ -1,16 +1,15 @@
-
+
diff -r d69ebf52c233 -r 787f1ca9045a test-data/malt_index_builder.json
--- a/test-data/malt_index_builder.json Tue Oct 12 14:15:35 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"data_tables": {"malt_indices": [{"dbkey": "phiX174", "name": "phiX174", "path": "phiX174.fasta", "value": "phiX174"}]}}
\ No newline at end of file
diff -r d69ebf52c233 -r 787f1ca9045a test-data/malt_index_builder1.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/malt_index_builder1.json Wed Oct 13 20:12:48 2021 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"malt_indices": [{"dbkey": "phiX174", "name": "Pretty name for phiX174", "path": null, "value": "phiX174-1"}]}}
\ No newline at end of file
diff -r d69ebf52c233 -r 787f1ca9045a test-data/malt_index_builder2.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/malt_index_builder2.json Wed Oct 13 20:12:48 2021 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"malt_indices": [{"dbkey": "phiX174", "name": "Pretty name for phiX174", "path": null, "value": "phiX174-2"}]}}
\ No newline at end of file
diff -r d69ebf52c233 -r 787f1ca9045a tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Tue Oct 12 14:15:35 2021 +0000
+++ b/tool_data_table_conf.xml.sample Wed Oct 13 20:12:48 2021 +0000
@@ -1,7 +1,7 @@
- value, name, path, description
+ value, dbkey, name, path