changeset 10:0bffd4183326 draft

Uploaded

--- a/cmbuild.xml	Sat Sep 07 16:14:02 2013 -0400
+++ b/cmbuild.xml	Sun Sep 08 05:08:20 2013 -0400
@@ -85,7 +85,6 @@
                     <option value="--wnone">no sequence weighting (--wnone)</option>
                     <option value="--wgiven">Sequence weight from given in input file (--wgiven)</option>
                     <option value="--wblosum">BLOSUM filtering algorithm (--wblosum)</option>
-                    <option value="--wid">BLOSUM filtering algorithm (--wblosum)</option>
                 </param>
                 <when value="--wpb"/>
                 <when value="--wgsc"/>

--- a/cmsearch.xml	Sat Sep 07 16:14:02 2013 -0400
+++ b/cmsearch.xml	Sun Sep 08 05:08:20 2013 -0400
@@ -63,6 +63,7 @@
         <inputs>
 
             <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
+
             <conditional name="cm_opts">
                 <param name="cm_opts_selector" type="select" label="Subject covariance models">
                   <option value="db" selected="True">Locally installed covariance models</option>

--- a/datatypes_conf.xml	Sat Sep 07 16:14:02 2013 -0400
+++ b/datatypes_conf.xml	Sun Sep 08 05:08:20 2013 -0400
@@ -6,10 +6,8 @@
    <registration>
         <!--INFERNAL1.1 Datatypes -->
         <datatype extension="cm" type="galaxy.datatypes.infernal:Infernal_CM_1_1" display_in_upload="False" />
-        <datatype extension="stockholm" type="galaxy.datatypes.infernal:Stockholm_1_0" display_in_upload="False" />
    </registration>
    <sniffers>
         <sniffer type="galaxy.datatypes.infernal:Infernal_CM_1_1"/>
-        <sniffer type="galaxy.datatypes.infernal:Stockholm_1_0"/>
    </sniffers>
 </datatypes>

--- a/infernal.py	Sat Sep 07 16:14:02 2013 -0400
+++ b/infernal.py	Sun Sep 08 05:08:20 2013 -0400
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-from galaxy.datatypes import data
+from galaxy.datatypes.data import Text
 from galaxy.datatypes.sniff import get_headers, get_test_fname
 from galaxy.datatypes.data import get_file_peek
 import subprocess
@@ -41,90 +41,7 @@
     return 0
 
 
-class Stockholm_1_0( data.text ):
-    file_ext = "stockholm"
-
-    MetadataElement( name="number_of_alignments", default=0, desc="Number of multiple alignments", readonly=True, visible=True, optional=True, no_value=0 )
-
-    def set_peek( self, dataset, is_multi_byte=False ):
-        if not dataset.dataset.purged:
-            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-            if (dataset.metadata.number_of_models == 1):
-                dataset.blurb = "1 alignment"
-            else:
-                dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
-            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
-
-    def sniff( self, filename ):
-        if count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', filename) > 0:
-            return True
-        else:
-            return False
-
-    def set_meta( self, dataset, **kwd ):
-        """
-
-        Set the number of models in dataset.
-        """
-        dataset.metadata.number_of_models = count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', dataset.file_name)
-
-    def split( cls, input_datasets, subdir_generator_function, split_params):
-        """
-
-        Split the input files by model records.
-        """
-        if split_params is None:
-            return None
-
-        if len(input_datasets) > 1:
-            raise Exception("STOCKHOLM-file splitting does not support multiple files")
-        input_files = [ds.file_name for ds in input_datasets]
-
-        chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
-            raise Exception('Split mode "%s" is currently not implemented for STOCKHOLM-files.' % split_params['split_mode'])
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
-        else:
-            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
-
-        def _read_stockholm_records( filename ):
-            lines = []
-            with open(filename) as handle:
-                for line in handle:
-                    lines.append( line )
-                    if line.strip() == '//':
-                        yield lines
-                        lines = []
-
-        def _write_part_stockholm_file( accumulated_lines ):
-            part_dir = subdir_generator_function()
-            part_path = os.path.join( part_dir, os.path.basename( input_files[0] ) )
-            part_file = open( part_path, 'w' )
-            part_file.writelines( accumulated_lines )
-            part_file.close()
-
-        try:
-
-            stockholm_records = _read_stockholm_records( input_files[0] )
-            stockholm_lines_accumulated = []
-            for counter, stockholm_record in enumerate( stockholm_records, start = 1):
-                stockholm_lines_accumulated.extend( stockholm_record )
-                if counter % chunk_size == 0:
-                    _write_part_stockholm_file( stockholm_lines_accumulated )
-                    stockholm_lines_accumulated = []
-            if stockholm_lines_accumulated:
-                _write_part_stockholm_file( stockholm_lines_accumulated )
-        except Exception,  e:
-            log.error('Unable to split files: %s' % str(e))
-            raise
-    split = classmethod(split)
-
-
-class Infernal_CM_1_1( data.text ):
+class Infernal_CM_1_1( Text ):
     file_ext = "cm"
 
     MetadataElement( name="number_of_models", default=0, desc="Number of covariance models", readonly=True, visible=True, optional=True, no_value=0 )
@@ -205,3 +122,7 @@
             raise
     split = classmethod(split)
 
+if __name__ == '__main__':
+    Infernal_CM_1_1()
+    Stockholm_1_0()
+

--- a/readme.rst	Sat Sep 07 16:14:02 2013 -0400
+++ b/readme.rst	Sun Sep 08 05:08:20 2013 -0400
@@ -32,16 +32,14 @@
 Miscellaneous
 =============
 
-Included in that repository is a CM datatype for INFERNAL 1.1. If you need that datatype in an additionl package,
-I can source it out as separate package. Please contact me in that case.
+Included in that repository is a CM datatype for INFERNAL 1.1 and TOCKHOLM .
+If you need that datatype in an additionl package, I can source it out as separate package. Please contact me in that case.
 
 
 =======
 History
 =======
 
-interproscan:
-
  - v1.1.0: Initial public release
 
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Sun Sep 08 05:08:20 2013 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="This requires the datatype definitions for Multiple Sequence Alignment (MSA) formats (e.g. STOCKHOLM, SELEX, ClustalW).">
+    <repository changeset_revision="ba3eba35a79d" name="msa_datatypes" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>