# HG changeset patch
# User iracooke
# Date 1432100379 14400
# Node ID d1ea609e57d45cfd75ba20c6580688200970edbe
# Parent 29c43b953c1c5d360bce8efabed05538f3e20fe3
Make splib a composite datatype
diff -r 29c43b953c1c -r d1ea609e57d4 README.rst
--- a/README.rst Sun May 17 23:43:24 2015 -0400
+++ b/README.rst Wed May 20 01:39:39 2015 -0400
@@ -36,7 +36,7 @@
TandemXML_ tandem False XTandem output
RAW raw False Raw Mass Spec Data
Msp_ msp True Spectral Library
-SPLib_ splib True Spectral Library
+SPLib_ splib True Spectral Library
Ms2 ms2 False MS/MS Spectra
XHunterAslFormat hlf False Spectral Library
================ ===================== ======= ====================================
diff -r 29c43b953c1c -r d1ea609e57d4 proteomics.py
--- a/proteomics.py Sun May 17 23:43:24 2015 -0400
+++ b/proteomics.py Wed May 20 01:39:39 2015 -0400
@@ -289,6 +289,35 @@
class SPLib( Msp ):
"""SpectraST Spectral Library. Closely related to msp format"""
file_ext = "splib"
+ composite_type = 'auto_primary_file'
+
+ def __init__(self, **kwd):
+ Msp.__init__(self, **kwd)
+ self.add_composite_file( 'library.splib',
+ description = 'Spectral Library. Contains actual library spectra',
+ is_binary = False )
+ self.add_composite_file( 'library.spidx',
+ description = 'Spectrum index', is_binary = False )
+ self.add_composite_file( 'library.pepidx',
+ description = 'Peptide index', is_binary = False)
+
+
+ def generate_primary_file( self, dataset = None ):
+ rval = ['<html><head><title>Spectral Library Composite Dataset </title></head><p/>']
+ rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+ for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
+ fn = composite_name
+ opt_text = ''
+ if composite_file.optional:
+ opt_text = ' (optional)'
+ if composite_file.get('description'):
+ rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
+ else:
+ rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
+ rval.append( '</ul></div></html>' )
+ return "\n".join( rval )
+
+
def set_peek( self, dataset, is_multi_byte=False ):
"""Set the peek and blurb text"""
@@ -307,7 +336,6 @@
return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "LibID:")
-
class Ms2(Text):
file_ext = "ms2"