code reorganization - created obsolet and legacy directories

--HG-- rename : AlignatorBenchmark.py => legacy/AlignatorBenchmark.py rename : GraphTree.py => legacy/GraphTree.py rename : NeighbourTools.py => legacy/NeighbourTools.py rename : PdbTools.py => legacy/PdbTools.py rename : Rsdb2Html.py => legacy/Rsdb2Html.py rename : Rsdb2Plot.py => legacy/Rsdb2Plot.py rename : ScopTester.py => legacy/ScopTester.py rename : Stats2Html.py => legacy/Stats2Html.py rename : gnuplot_data.py => legacy/gnuplot_data.py rename : gnuplot_histogram.py => legacy/gnuplot_histogram.py rename : pdb2filter_residues.py => legacy/pdb2filter_residues.py rename : pdb2sequence.py => legacy/pdb2sequence.py rename : pdb2superimpose.py => legacy/pdb2superimpose.py rename : pdb_annotate_structure.py => legacy/pdb_annotate_structure.py rename : pdb_domains2molscript.py => legacy/pdb_domains2molscript.py rename : pdb_filter_residues.py => legacy/pdb_filter_residues.py rename : pdb_renumber.py => legacy/pdb_renumber.py rename : pdb_superimpose.py => legacy/pdb_superimpose.py rename : renumber_pdb_file.py => legacy/renumber_pdb_file.py rename : renumber_pdb_files.py => legacy/renumber_pdb_files.py rename : zinba.py => obsolete/zinba.py
CGATOxford · Aug 22, 2012 · c35ce25 · c35ce25
1 parent e23ebc3
commit c35ce25
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Showing 64 changed files with 58 additions and 63 deletions.
diff --git a/Pipeline.py b/Pipeline.py
@@ -962,13 +962,14 @@ def peekParameters( workingdir, pipeline ):
     '''
 
     dirname = os.path.dirname( __file__ )
+    # special case: pipeline called in source directory
+    if dirname == "": dirname = os.path.abspath(".")
     pipeline = os.path.join( dirname, pipeline )
     assert os.path.exists( pipeline ), "can't find pipeline source %s" % pipeline
-    if workingdir == "":
-        return {}
+    if workingdir == "": workingdir = os.path.abspath(".")
 
     assert os.path.exists( workingdir ), "can't find working dir %s" % workingdir
-    
+
     process = subprocess.Popen(  "python %s -f -v 0 dump" % pipeline,
                                  cwd = workingdir, 
                                  shell = True,

diff --git a/SaryFasta.py b/SaryFasta.py
@@ -32,8 +32,6 @@
 
 import os, sys, array, string, re, types, optparse, time, struct, hashlib, base64, shutil, subprocess
 import glob, random
-import psyco
-psyco.full()
 
 ##------------------------------------------------------------
 def getHID ( sequence ):

diff --git a/Stats2Plot.py b/Stats2Plot.py
@@ -33,30 +33,26 @@
 ----
 
 '''
-from Pairsdb import *
-
 import sys
 import os
 import string
 import re
 
-from RSDB2PLOT import RSDB2PLOT
-import GraphXY
-import Plot
+from Rsdb2Plot import Rsdb2Plot
 
-class RSDB2PLOT_test( RSDB2PLOT):
+class Rsdb2Plot_test( Rsdb2Plot):
 
     def __init__( self, grap ):
-        RSDB2PLOT.__init__( self, graph )
+        Rsdb2Plot.__init__( self, graph )
 
     def ParseColumns( self, columns ):
         return columns
 
 
-class RSDB2PLOT_clustering ( RSDB2PLOT ):
+class Rsdb2Plot_clustering ( Rsdb2Plot ):
 
     def __init__( self, graph, columns ):
-        RSDB2PLOT.__init__( self, graph )
+        Rsdb2Plot.__init__( self, graph )
         self.mColumns = columns
 
     def ParseHeader( self, line ):

diff --git a/align_all_vs_all.py b/align_all_vs_all.py
@@ -63,8 +63,7 @@
 import Experiment
 
 import alignlib
-import Bio
-import Bio.Fasta
+import FastaIterator
 
 """ program $Id: align_all_vs_all.py 2782 2009-09-10 11:40:29Z andreas $
 """
@@ -88,8 +87,7 @@
     else:
         infile = sys.stdin
 
-    parser = Bio.Fasta.RecordParser()
-    iterator = Bio.Fasta.Iterator( infile, parser)
+    parser = FastaIterator.FastaIterator( infile )
 
     sequences = []
     while 1:

diff --git a/analyze_logfiles.py b/analyze_logfiles.py
@@ -170,7 +170,7 @@ def getHeader(self):
                        choices = ("file", "node" ),
                        help="analysis mode [%default]." )
 
-    parser.add_option( "-r", "--recursive", action="store_true"
+    parser.add_option( "-r", "--recursive", action="store_true",
                        help="recursively look for logfiles from current directory [%default]." )
 
     parser.set_defaults(

diff --git a/annotator.py b/annotator.py
@@ -69,7 +69,6 @@
 
 import Experiment as E
 import GFF, GTF
-import rtree
 import numpy
 import Stats
 

diff --git a/get_sequences_from_www.py b/get_sequences_from_www.py
@@ -64,8 +64,8 @@
 import Experiment
 
 from Bio import SeqRecord
-from Bio.WWW import ExPASy
-from Bio.SwissProt import SProt
+import Bio.ExPASy as ExPASy
+import Bio.SwissProt as SProt
 from Bio import File
 
 parser = optparse.OptionParser( version = "%prog version: $Id: get_sequences_from_www.py 2782 2009-09-10 11:40:29Z andreas $")

diff --git a/AlignatorBenchmark.py → legacy/AlignatorBenchmark.py b/AlignatorBenchmark.py → legacy/AlignatorBenchmark.py
diff --git a/GraphTree.py → legacy/GraphTree.py b/GraphTree.py → legacy/GraphTree.py
diff --git a/NeighbourTools.py → legacy/NeighbourTools.py b/NeighbourTools.py → legacy/NeighbourTools.py
diff --git a/PdbTools.py → legacy/PdbTools.py b/PdbTools.py → legacy/PdbTools.py
diff --git a/Rsdb2Html.py → legacy/Rsdb2Html.py b/Rsdb2Html.py → legacy/Rsdb2Html.py
diff --git a/Rsdb2Plot.py → legacy/Rsdb2Plot.py b/Rsdb2Plot.py → legacy/Rsdb2Plot.py
diff --git a/ScopTester.py → legacy/ScopTester.py b/ScopTester.py → legacy/ScopTester.py
diff --git a/Stats2Html.py → legacy/Stats2Html.py b/Stats2Html.py → legacy/Stats2Html.py
diff --git a/gnuplot_data.py → legacy/gnuplot_data.py b/gnuplot_data.py → legacy/gnuplot_data.py
diff --git a/gnuplot_histogram.py → legacy/gnuplot_histogram.py b/gnuplot_histogram.py → legacy/gnuplot_histogram.py
diff --git a/pdb2filter_residues.py → legacy/pdb2filter_residues.py b/pdb2filter_residues.py → legacy/pdb2filter_residues.py
diff --git a/pdb2sequence.py → legacy/pdb2sequence.py b/pdb2sequence.py → legacy/pdb2sequence.py
diff --git a/pdb2superimpose.py → legacy/pdb2superimpose.py b/pdb2superimpose.py → legacy/pdb2superimpose.py
diff --git a/pdb_annotate_structure.py → legacy/pdb_annotate_structure.py b/pdb_annotate_structure.py → legacy/pdb_annotate_structure.py
diff --git a/pdb_domains2molscript.py → legacy/pdb_domains2molscript.py b/pdb_domains2molscript.py → legacy/pdb_domains2molscript.py
diff --git a/pdb_filter_residues.py → legacy/pdb_filter_residues.py b/pdb_filter_residues.py → legacy/pdb_filter_residues.py
diff --git a/pdb_renumber.py → legacy/pdb_renumber.py b/pdb_renumber.py → legacy/pdb_renumber.py
diff --git a/pdb_superimpose.py → legacy/pdb_superimpose.py b/pdb_superimpose.py → legacy/pdb_superimpose.py
diff --git a/renumber_pdb_file.py → legacy/renumber_pdb_file.py b/renumber_pdb_file.py → legacy/renumber_pdb_file.py
diff --git a/renumber_pdb_files.py → legacy/renumber_pdb_files.py b/renumber_pdb_files.py → legacy/renumber_pdb_files.py
diff --git a/nr2table.py b/nr2table.py
@@ -59,7 +59,8 @@
 
 
 import Experiment
-import Bio, Bio.Fasta
+import Bio
+import FastaIterator
 
 ##------------------------------------------------------------
 if __name__ == '__main__':
@@ -70,8 +71,7 @@
 
     (options, args) = Experiment.Start( parser )
 
-    parser = Bio.Fasta.RecordParser()
-    iterator = Bio.Fasta.Iterator( sys.stdin, parser)
+    iterator = FastaIterator.FastaIterator( sys.stdin )
 
     sequences = []
 

diff --git a/zinba.py → obsolete/zinba.py b/zinba.py → obsolete/zinba.py
diff --git a/pipeline_ancestral_repeats.py b/pipeline_ancestral_repeats.py
@@ -138,7 +138,7 @@
 ###################################################
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = { 

diff --git a/pipeline_annotations.py b/pipeline_annotations.py
@@ -193,7 +193,7 @@
 ## Pipeline configuration
 ###################################################
 PARAMS = P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 

diff --git a/pipeline_benchmark_rnaseqmappers.py b/pipeline_benchmark_rnaseqmappers.py
@@ -172,7 +172,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 PARAMS = P.PARAMS

diff --git a/pipeline_chains.py b/pipeline_chains.py
@@ -109,7 +109,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = { "maps" : "" } )

diff --git a/pipeline_cpg.py b/pipeline_cpg.py
@@ -162,7 +162,7 @@
 ## Pipeline configuration
 ###################################################
 import Pipeline as P
-P.getParameters(  ["%s/pipeline.ini" % __file__[:-len(".py")],  "../pipeline.ini", "pipeline.ini" ] )
+P.getParameters(  ["%s/pipeline.ini" % os.path.splitext(__file__)[0],  "../pipeline.ini", "pipeline.ini" ] )
 PARAMS = P.PARAMS
 PARAMS_ANNOTATIONS = P.peekParameters( PARAMS["annotations_dir"],"pipeline_annotations.py" )
 

diff --git a/pipeline_cufflinks_optimization.py b/pipeline_cufflinks_optimization.py
@@ -158,7 +158,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = {

diff --git a/pipeline_docs/pipeline_mapping/trackers/Status.py b/pipeline_docs/pipeline_mapping/trackers/Status.py
@@ -53,6 +53,9 @@ def testSplicedAlignments( self, track ):
 
         '''
 
+        if not self.hasTable( 'exon_validation'):
+            return "NA", 0
+
         value = self.getValue( "SELECT spliced/CAST(input AS FLOAT) from exon_validation WHERE track = '%(track)s'" )
         if value >= 0.15: status= "PASS"
         elif value >= 0.05: status= "WARNING"

diff --git a/pipeline_exome.py b/pipeline_exome.py
@@ -145,7 +145,7 @@
 #########################################################################
 #########################################################################
 # load options from the config file
-P.getParameters( ["%s/pipeline.ini" % __file__[:-len(".py")], "../exome.ini", "exome.ini" ] )
+P.getParameters( ["%s/pipeline.ini" % os.path.splitext(__file__)[0], "../exome.ini", "exome.ini" ] )
 PARAMS = P.PARAMS
 
 #########################################################################

diff --git a/pipeline_fastqToBigWig.py b/pipeline_fastqToBigWig.py
@@ -156,7 +156,7 @@
 USECLUSTER = True
 
 import Pipeline as P
-P.getParameters(  ["%s.ini" % __file__[:-len(".py")],  "pipeline.ini" ] )
+P.getParameters(  ["%s.ini" % os.path.splitext(__file__)[0],  "pipeline.ini" ] )
 PARAMS = P.PARAMS
 
 ###################################################################

diff --git a/pipeline_fusion.py b/pipeline_fusion.py
@@ -165,7 +165,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 

diff --git a/pipeline_intervals.py b/pipeline_intervals.py
@@ -205,7 +205,7 @@
 ###################################################
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = {

diff --git a/pipeline_kamilah.py b/pipeline_kamilah.py
@@ -68,7 +68,8 @@
 else:
     EXPERIMENTAL_TRACKS = []
 
-PARAMS = P.getParameters()
+PARAMS = P.getParameters(
+    defaults = { 'ancestral_repeats_filename': None } )
 
 PARAMS.update( {
     "annotation" : "regions.gff",

diff --git a/pipeline_liftover.py b/pipeline_liftover.py
@@ -112,7 +112,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 PARAMS = P.PARAMS

diff --git a/pipeline_mappability.py b/pipeline_mappability.py
@@ -35,7 +35,7 @@
 from ruffus import *
 import Pipeline as P
 
-P.getParameters(  ["%s.ini" % __file__[:-len(".py")],  "pipeline.ini" ] )
+P.getParameters(  ["%s.ini" % os.path.splitext(__file__)[0],  "pipeline.ini" ] )
 PARAMS = P.PARAMS
 USECLUSTER = True
 

diff --git a/pipeline_mapping.py b/pipeline_mapping.py
@@ -240,7 +240,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = {

diff --git a/pipeline_mapping_benchmark.py b/pipeline_mapping_benchmark.py
@@ -92,7 +92,7 @@
 ## Pipeline configuration
 ###################################################
 import Pipeline as P
-P.getParameters(  ["%s/pipeline.ini" % __file__[:-len(".py")],  "../pipeline.ini", "pipeline.ini" ] )
+P.getParameters(  ["%s/pipeline.ini" % os.path.splitext(__file__)[0],  "../pipeline.ini", "pipeline.ini" ] )
 PARAMS = P.PARAMS
 
 bowtie_options = {'n0m1':"-n 0 -a --best --strata -m 1 -3 1",'n1m1':"-n 1 -a --best --strata -m 1 -3 1",'n2m1':"-n 2 -a --best --strata -m 1 -3 1",'n3m1':"-n 3 -a --best --strata -m 1 -3 1",

diff --git a/pipeline_medip.py b/pipeline_medip.py
@@ -170,7 +170,7 @@
 #########################################################################
 #########################################################################
 # load options from the config file
-P.getParameters( ["%s/pipeline.ini" % __file__[:-len(".py")], 
+P.getParameters( ["%s/pipeline.ini" % os.path.splitext(__file__)[0], 
                   "../pipeline.ini", 
                   "pipeline.ini" ] )
 

diff --git a/pipeline_peakcalling.py b/pipeline_peakcalling.py
@@ -239,7 +239,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = {

diff --git a/pipeline_polyphen.py b/pipeline_polyphen.py
@@ -68,7 +68,8 @@
 ###################################################################
 ###################################################################
 ## read global options from configuration file
-P.getParameters()
+P.getParameters( 
+    defaults = { 'polyphen_modes' : "" } )
 
 P.PARAMS.update( 
     { "transcripts" :"transcripts.gtf.gz",

diff --git a/pipeline_promotors.py b/pipeline_promotors.py
@@ -122,7 +122,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 

diff --git a/pipeline_readqc.py b/pipeline_readqc.py
@@ -175,7 +175,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 PARAMS = P.PARAMS

diff --git a/pipeline_rmaa.py b/pipeline_rmaa.py
@@ -144,7 +144,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 PARAMS = P.PARAMS

diff --git a/pipeline_rnaseq.py b/pipeline_rnaseq.py
@@ -454,7 +454,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = {

diff --git a/pipeline_rnaseqdiffexpression.py b/pipeline_rnaseqdiffexpression.py
@@ -314,7 +314,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 

diff --git a/pipeline_rnaseqtranscripts.py b/pipeline_rnaseqtranscripts.py
@@ -293,7 +293,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ],
     defaults = {

diff --git a/pipeline_snps.py b/pipeline_snps.py
@@ -78,7 +78,7 @@
 ###################################################################
 ## read global options from configuration file
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 

diff --git a/pipeline_species_conservation.py b/pipeline_species_conservation.py
@@ -124,7 +124,7 @@
 ## Pipeline configuration
 ###################################################
 import Pipeline as P
-P.getParameters(  ["%s.ini" % __file__[:-len(".py")],  "../pipeline.ini", "pipeline.ini" ] )
+P.getParameters(  ["%s.ini" % os.path.splitext(__file__)[0],  "../pipeline.ini", "pipeline.ini" ] )
 PARAMS = P.PARAMS
 #PARAMS_ANNOTATIONS = P.peekParameters( PARAMS["annotations_dir"],"pipeline_annotations.py" )
 

diff --git a/pipeline_template.py b/pipeline_template.py
@@ -117,7 +117,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )
 

diff --git a/pipeline_testing.py b/pipeline_testing.py
@@ -152,7 +152,7 @@
 # load options from the config file
 import Pipeline as P
 P.getParameters( 
-    ["%s/pipeline.ini" % __file__[:-len(".py")],
+    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
      "../pipeline.ini",
      "pipeline.ini" ] )