Changeset 294

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Timestamp:
02/01/08 01:20:00 (10 months ago)
Author:
t
Message:

fixed batch export; commented out batch import.

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  • trunk/cartwheel-server/website/canal/motif/__init__.py

    r289 r294  
    11""" 
    22Per-leaf-folder motif handling. 
     3 
     4TODO: 
     5 
     6 - batch import 
     7 - explicit color, rgb from color wheel? 
     8 - add formats - clusterbuster?? 
     9   http://www.benoslab.pitt.edu/stamp/help.html#input 
     10 
     11to test: 
     12 
     13base 0 should not exist! 
     14display in rows vs display all together (checkbox for image display) 
     15notes!! on edit page 
     16allow choice of AT/GC for statistics 
     17test list o' sites / list o' short sequences 
     18palindromicize 
     19enter matrix by hand; formats clusterbuster? 
    320""" 
    421 
    …… 
    109126        notes = motif.notes.split("\n") 
    110127        for n in notes: 
    111             output.write('%% notes=%s' % (n,)) 
     128            output.write('%% notes=%s\n' % (n,)) 
    112129             
    113130        if motif.motif_type == 'IUPAC': 
    114131            output.write('%% IUPAC\n%% mismatches=%d\n' % (motif.mismatches,)) 
    115             output.write('%s' % (motif.motif,)) 
     132            output.write('%s\n' % (motif.motif,)) 
    116133 
    117134        elif motif.motif_type == 'PWM': 
    118             output.write('%% PWM from sites\n') 
     135            output.write('% PWM from sites\n') 
    119136            output.write('%% threshold=%g\n' % (motif.threshold,)) 
     137            output.write('%% palindromic=%s\n' % (motif.palindromic,)) 
    120138            output.write('%s\n' % (motif.source_motifs,)) 
     139             
     140        elif motif.motif_type == 'RawPWM': 
     141            output.write('% Imported PWM\n') 
     142            output.write('%% threshold=%g\n' % (motif.threshold,)) 
     143            output.write('%% format=%s\n' % (motif.format,)) 
     144            output.write('%s\n' % (motif.matrix,)) 
     145             
    121146        else: 
    122147            raise Exception("unknown motif type! %s" % (motif.motif_type,)) 

  • trunk/cartwheel-server/website/canal/motif/pages.ptl

    r289 r294  
    108108    """ 
    109109    <b>Other actions:</b> <ul> 
    110    <li> <a href="batch_export">export motifs to a text file</a> 
    111    <li> <a href="batch_import">import motifs from a text file</a> 
     110   <li> <a href="batch_export">export motif library to a text file</a> 
     111<!--   <li> <a href="batch_import">import motifs from a text file</a> --> 
    112112   <li> <a href="set_DNA_bias">set DNA bias (AT/GC content) for motif statistics calculations</a> 
    113113         </ul>