-"""
-
-def timenow():
- """return current time as a string
- """
- return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
-
-def getMissval(inped=''):
- """
- read some lines...ugly hack - try to guess missing value
- should be N or 0 but might be . or -
- """
- commonmissvals = {'N':'N','0':'0','n':'n','9':'9','-':'-','.':'.'}
- try:
- f = file(inped,'r')
- except:
- return None # signal no in file
- missval = None
- while missval == None: # doggedly continue until we solve the mystery
- try:
- l = f.readline()
- except:
- break
- ll = l.split()[6:] # ignore pedigree stuff
- for c in ll:
- if commonmissvals.get(c,None):
- missval = c
- f.close()
- return missval
- if not missval:
- missval = 'N' # punt
- close(f)
- return missval
-
-def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):
- """
- """
- pedf = '%s.ped' % inpedfilepath
- basename = os.path.split(inpedfilepath)[-1] # get basename
- outroot = os.path.join(outfilepath,basename)
- missval = getMissval(inped = pedf)
- if not missval:
- print '### lped_to_pbed_converter.py cannot identify missing value in %s' % pedf
- missval = '0'
- cl = '%s --noweb --file %s --make-bed --out %s --missing-genotype %s' % (plink,inpedfilepath,outroot,missval)
- p = subprocess.Popen(cl,shell=True,cwd=outfilepath)
- retval = p.wait() # run plink
-
-
-
-
-def main():
- """
- need to work with rgenetics composite datatypes
- so in and out are html files with data in extrafiles path
-
- """
- nparm = 4
- if len(sys.argv) < nparm:
- sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
- sys.exit(1)
- inpedfilepath = sys.argv[1]
- outhtmlname = sys.argv[2]
- outfilepath = sys.argv[3]
- try:
- os.makedirs(outfilepath)
- except:
- pass
- plink = sys.argv[4]
- rgConv(inpedfilepath,outhtmlname,outfilepath,plink)
- f = file(outhtmlname,'w')
- f.write(galhtmlprefix % prog)
- flist = os.listdir(outfilepath)
- s = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
- print s
- f.write('
")
- f.close()
-
-
-
-if __name__ == "__main__":
- main()
+# for rgenetics - lped to pbed
+# where to stop with converters
+# pbed might be central
+# eg lped/eigen/fbat/snpmatrix all to pbed
+# and pbed to lped/eigen/fbat/snpmatrix ?
+# that's a lot of converters
+import sys,os,time,subprocess
+
+
+prog = os.path.split(sys.argv[0])[-1]
+myversion = 'Oct 10 2009'
+
+galhtmlprefix = """
+
+
+
+
+"""
+
+def timenow():
+ """return current time as a string
+ """
+ return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+def getMissval(inped=''):
+ """
+ read some lines...ugly hack - try to guess missing value
+ should be N or 0 but might be . or -
+ """
+ commonmissvals = {'N':'N','0':'0','n':'n','9':'9','-':'-','.':'.'}
+ try:
+ f = file(inped,'r')
+ except:
+ return None # signal no in file
+ missval = None
+ while missval == None: # doggedly continue until we solve the mystery
+ try:
+ l = f.readline()
+ except:
+ break
+ ll = l.split()[6:] # ignore pedigree stuff
+ for c in ll:
+ if commonmissvals.get(c,None):
+ missval = c
+ f.close()
+ return missval
+ if not missval:
+ missval = 'N' # punt
+ close(f)
+ return missval
+
+def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):
+ """
+ """
+ pedf = '%s.ped' % inpedfilepath
+ basename = os.path.split(inpedfilepath)[-1] # get basename
+ outroot = os.path.join(outfilepath,basename)
+ missval = getMissval(inped = pedf)
+ if not missval:
+ print '### lped_to_pbed_converter.py cannot identify missing value in %s' % pedf
+ missval = '0'
+ cl = '%s --noweb --file %s --make-bed --out %s --missing-genotype %s' % (plink,inpedfilepath,outroot,missval)
+ p = subprocess.Popen(cl,shell=True,cwd=outfilepath)
+ retval = p.wait() # run plink
+
+
+
+
+def main():
+ """
+ need to work with rgenetics composite datatypes
+ so in and out are html files with data in extrafiles path
+
lped_to_pbed_converter.py '$input1/$input1.metadata.base_name'
+ '$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+
+ """
+ nparm = 4
+ if len(sys.argv) < nparm:
+ sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
+ sys.exit(1)
+ inpedfilepath = sys.argv[1]
+ outhtmlname = sys.argv[2]
+ outfilepath = sys.argv[3]
+ try:
+ os.makedirs(outfilepath)
+ except:
+ pass
+ plink = sys.argv[4]
+ rgConv(inpedfilepath,outhtmlname,outfilepath,plink)
+ f = file(outhtmlname,'w')
+ f.write(galhtmlprefix % prog)
+ flist = os.listdir(outfilepath)
+ s = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
+ print s
+ f.write('
%s\n
' % (s))
+ for i, data in enumerate( flist ):
+ f.write('- %s
\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
+ f.write("
")
+ f.close()
+
+
+
+if __name__ == "__main__":
+ main()
diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
index 8f96f618cb5..df62e347242 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
@@ -1,32 +1,32 @@
-#!/usr/bin/env python
-#Dan Blankenberg
-
-import sys
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-import bx.align.maf
-from galaxy.tools.util import maf_utilities
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def __main__():
- output_name = sys.argv.pop(1)
- input_name = sys.argv.pop(1)
- out = open( output_name, 'w' )
- count = 0
- for count, block in enumerate( bx.align.maf.Reader( open( input_name, 'r' ) ) ):
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+import bx.align.maf
+from galaxy.tools.util import maf_utilities
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():
+ output_name = sys.argv.pop(1)
+ input_name = sys.argv.pop(1)
+ out = open( output_name, 'w' )
+ count = 0
+ for count, block in enumerate( bx.align.maf.Reader( open( input_name, 'r' ) ) ):
spec_counts = {}
- for c in block.components:
+ for c in block.components:
spec, chrom = maf_utilities.src_split( c.src )
if spec not in spec_counts:
spec_counts[ spec ] = 0
else:
- spec_counts[ spec ] += 1
- out.write( "%s\n" % maf_utilities.get_fasta_header( c, { 'block_index' : count, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, count, spec_counts[ spec ] ) ) )
- out.write( "%s\n" % c.text )
- out.write( "\n" )
- out.close()
- print "%i MAF blocks converted to FASTA." % ( count )
-
-
-if __name__ == "__main__": __main__()
+ spec_counts[ spec ] += 1
+ out.write( "%s\n" % maf_utilities.get_fasta_header( c, { 'block_index' : count, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, count, spec_counts[ spec ] ) ) )
+ out.write( "%s\n" % c.text )
+ out.write( "\n" )
+ out.close()
+ print "%i MAF blocks converted to FASTA." % ( count )
+
+
+if __name__ == "__main__": __main__()
diff --git a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py
index 036727b5f98..2ddb00cbe43 100644
--- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py
+++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py
@@ -1,32 +1,32 @@
-#!/usr/bin/env python
-#Dan Blankenberg
-
-import sys
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
import bx.align.maf
-from galaxy.tools.util import maf_utilities
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def __main__():
- output_name = sys.argv.pop(1)
- input_name = sys.argv.pop(1)
- species = sys.argv.pop(1)
- out = open(output_name,'w')
- count = 0
- #write interval header line
- out.write( "#chrom\tstart\tend\tstrand\n" )
- try:
- for block in bx.align.maf.Reader( open( input_name, 'r' ) ):
- for c in maf_utilities.iter_components_by_src_start( block, species ):
- if c is not None:
- out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) )
- count += 1
- except Exception, e:
- print >> sys.stderr, "There was a problem processing your input: %s" % e
- out.close()
- print "%i MAF blocks converted to Genomic Intervals for species %s." % ( count, species )
-
-
-if __name__ == "__main__": __main__()
+from galaxy.tools.util import maf_utilities
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():
+ output_name = sys.argv.pop(1)
+ input_name = sys.argv.pop(1)
+ species = sys.argv.pop(1)
+ out = open(output_name,'w')
+ count = 0
+ #write interval header line
+ out.write( "#chrom\tstart\tend\tstrand\n" )
+ try:
+ for block in bx.align.maf.Reader( open( input_name, 'r' ) ):
+ for c in maf_utilities.iter_components_by_src_start( block, species ):
+ if c is not None:
+ out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) )
+ count += 1
+ except Exception, e:
+ print >> sys.stderr, "There was a problem processing your input: %s" % e
+ out.close()
+ print "%i MAF blocks converted to Genomic Intervals for species %s." % ( count, species )
+
+
+if __name__ == "__main__": __main__()
diff --git a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
index 7fea37cb034..817fd9f7fd3 100644
--- a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
+++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
@@ -21,7 +21,7 @@ galhtmlprefix = """
"""
-plinke = 'plink'
+plinke = 'plink'
def timenow():
@@ -51,7 +51,7 @@ def pruneLD(plinktasks=[],cd='./',vclbase = []):
except:
alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl)))
return alog
-
+
def makeLDreduced(basename,infpath=None,outfpath=None,plinke='plink',forcerebuild=False,returnFname=False,
winsize="60", winmove="40", r2thresh="0.1" ):
@@ -79,11 +79,11 @@ def main():
need to work with rgenetics composite datatypes
so in and out are html files with data in extrafiles path
- .. raw:: xml
+ .. raw:: xml
- pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh'
- '$output1' '$output1.files_path' 'plink'
+ pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh'
+ '$output1' '$output1.files_path' 'plink'
"""
@@ -116,7 +116,7 @@ def main():
f.write('
%s\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
f.write("