Add docuentation for the new options and an option to manage the ecotag

cache size

doc/sphinx/source/optionsSet/inputformat.txt

@@ -3,6 +3,24 @@ Options to specify input format
 
 .. program:: obitools
 
+
+Restrict the analysis to a sub-part of the input file
+.....................................................
+
+.. cmdoption::  --skip <N>
+
+      The N first sequence records of the file are discarded from the analysis and 
+      not reported to the output file
+      
+
+.. cmdoption::  --only <N>
+
+      Only the N next sequence records of the file are analyzed. The following sequences
+      in the file are neither analyzed, neither reported to the output file.
+      This option can be used conjointly with the `--skip` option.
+      
+
+
 Sequence annotated format
 .........................
 

doc/sphinx/source/scripts/ecotag.rst

@@ -1,55 +1,70 @@
 .. automodule:: ecotag
-   
+
    :py:mod:`ecotag` specific options
    ---------------------------------
 
-   .. cmdoption::  -R <FILENAME>, --ref-database=<FILENAME>   
+   .. cmdoption::  -R <FILENAME>, --ref-database=<FILENAME>
-   
+
         <FILENAME> is the fasta file containing the reference sequences
 
    .. cmdoption::  -m FLOAT, --minimum-identity=FLOAT
+
+        When the best match with the reference database present an identity
+        level below FLOAT, the taxonomic assignment for the sequence record
+        is not computed. The sequence record is nevertheless included in the
+        output file. FLOAT is included in a [0,1] interval.
+
+   .. cmdoption::    --minimum-circle=FLOAT
    
-        When sequence identity is less than FLOAT, the taxonomic 
+        minimum identity considered for the assignment circle.
-        assignment for the sequence record is not indicated in ``ecotag``'s 
+        FLOAT is included in a [0,1] interval.
-        output. FLOAT is included in a [0,1] interval.
-        (This option doesn't seem to work).
 
    .. cmdoption::  -x RANK, --explain=RANK
-   
+
    .. cmdoption::  -u, --uniq
-   
+
-        When this option is specified, the program first dereplicates the sequence 
+        When this option is specified, the program first dereplicates the sequence
-        records to work on unique sequences only. This option greatly improves 
+        records to work on unique sequences only. This option greatly improves
         the program's speed, especially for highly redundant datasets.
 
    .. cmdoption::  --sort=<KEY>
-   
+
         The output is sorted based on the values of the relevant attribute.
 
    .. cmdoption::  -r, --reverse
-   
+
         The output is sorted in reverse order (should be used with the --sort option).
-        (Works even if the --sort option is not set, but could not find on what 
+        (Works even if the --sort option is not set, but could not find on what
         the output is sorted).
 
    .. cmdoption::  -E FLOAT, --errors=FLOAT
-   
+
-        FLOAT is the fraction of reference sequences that will 
+        FLOAT is the fraction of reference sequences that will
-        be ignored when looking for the most recent common ancestor. This 
+        be ignored when looking for the most recent common ancestor. This
-        option is useful when a non-negligible proportion of reference sequences 
+        option is useful when a non-negligible proportion of reference sequences
-        is expected to be assigned to the wrong taxon, for example because of 
+        is expected to be assigned to the wrong taxon, for example because of
         taxonomic misidentification. FLOAT is included in a [0,1] interval.
 
+   .. cmdoption::  --cache-size=INTEGER
+
+        A cache for computed similarities is maintained by `ecotag`. the default
+        size for this cache is 1,000,000 of scores. This option allows to change
+        the cache size.
+
    .. include:: ../optionsSet/taxonomyDB.txt
-   
+
+   .. include:: ../optionsSet/inputformat.txt
+
+   .. include:: ../optionsSet/outputformat.txt
+
    .. include:: ../optionsSet/defaultoptions.txt
-   
+
    :py:mod:`ecotag` added sequence attributes
    ------------------------------------------
-   
+
       .. hlist::
            :columns: 3
-           
+
            - :doc:`best_identity <../attributes/best_identity>`
            - :doc:`best_match <../attributes/best_match>`
            - :doc:`family <../attributes/family>`
@@ -65,4 +80,3 @@
            - :doc:`species_list <../attributes/species_list>`
            - :doc:`species_name <../attributes/species_name>`
            - :doc:`taxid <../attributes/taxid>`
-      

src/ecotag.py

@@ -148,6 +148,13 @@ def addSearchOptions(optionManager):
                              default=0.0,
                              help='Tolerated rate of wrong assignation')    
 
+    optionManager.add_option('--cache-size',
+                             action='store',dest='cache',
+                             type='int',
+                             metavar='<SIZE>',
+                             default=1000000,
+                             help='Cache size for the aligment score')    
+
 
 def count(data):
     rep = {}
@@ -203,6 +210,7 @@ def cachedLenLCS(s1,s2,minid,normalized,reference):
     global __LCSCache__
     global __INCache__
     global __OUTCache__
+    global __CACHE_SIZE__
     
     pair=frozenset((s1.id,s2.id))
     
@@ -217,7 +225,7 @@ def cachedLenLCS(s1,s2,minid,normalized,reference):
         
     __LCSCache__[pair]=rep
     
-    if len(__LCSCache__) > 1000000:
+    if len(__LCSCache__) > __CACHE_SIZE__:
         __LCSCache__.popitem(0)
     return rep
     
@@ -292,9 +300,15 @@ if __name__=='__main__':
     __INCache__=1.0
     __OUTCache__=1.0
     
+    
     optionParser = getOptionManager([addSearchOptions,addTaxonomyDBOptions,addInOutputOption],progdoc=__doc__)
     
     (options, entries) = optionParser()
+    
+    __CACHE_SIZE__=options.cache
+    
+    if __CACHE_SIZE__ < 10:
+        __CACHE_SIZE__=10
         
     taxonomy = loadTaxonomyDatabase(options)
     writer = sequenceWriterGenerator(options)
@@ -317,7 +331,7 @@ if __name__=='__main__':
     taxonlink = {}
 
     rankid = taxonomy.findRankByName(options.explain)
-    
+
     for seq in db:
         id = seq.id[0:46]
         seq.id=id
@@ -338,6 +352,8 @@ if __name__=='__main__':
 
     search = lcsIteratorSelf(entries,db,options)
                      
+    print >>sys.stderr,'\nCache size : %d\n'
+
                     
     for seq,best,match in search:
         try:
@@ -424,9 +440,9 @@ if __name__=='__main__':
             else:
                 seq['species_name']=None
                         
-        print >>sys.stderr,'\rCache size : %5.3f  ' % (__INCache__/__OUTCache__),
+        
         writer(seq)        
-                    
+    print >>sys.stderr,'\n%5.3f% of the alignments was cached' % (__INCache__/(__INCache__+__OUTCache__)*100)