[hg] galaxy 2870: symlinks are not very useful

13 Oct 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/1a0bb7d6897c
changeset: 2870:1a0bb7d6897c
user:      Ross Lazarus <ross.lazarus@gmail.com>
date:      Sun Oct 11 15:07:11 2009 -0400
description:
symlinks are not very useful

6 file(s) affected in this change:

lib/galaxy/datatypes/converters/lped_to_fped_converter.py
lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml

diffs (383 lines):

diff -r 639c6b5e0073 -r 1a0bb7d6897c lib/galaxy/datatypes/converters/lped_to_fped_converter.py

--- a/lib/galaxy/datatypes/converters/lped_to_fped_converter.py	Sun Oct 11 15:00:40 2009 -0400
+++ b/lib/galaxy/datatypes/converters/lped_to_fped_converter.py	Sun Oct 11 15:07:11 2009 -0400
@@ -1,1 +1,110 @@
-/opt/galaxy/tools/rgenetics/converters/lped_to_fped_converter.py
\ No newline at end of file
+# for rgenetics - lped to fbat
+# recode to numeric fbat version
+# much slower so best to always
+# use numeric alleles internally
+
+import sys,os,time
+
+
+prog = os.path.split(sys.argv[0])[-1]
+myversion = 'Oct 10 2009'
+
+galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+"""
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+
+def rgConv(inpedfilepath,outhtmlname,outfilepath):
+  """convert linkage ped/map to fbat"""  
+  recode={'A':'1','C':'2','G':'3','T':'4','N':'0','0':'0','1':'1','2':'2','3':'3','4':'4'}
+  basename = os.path.split(inpedfilepath)[-1] # get basename
+  inmap = '%s.map' % inpedfilepath
+  inped = '%s.ped' % inpedfilepath
+  outf = '%s.ped' % basename # note the fbat exe insists that this is the extension for the ped data
+  outfpath = os.path.join(outfilepath,outf) # where to write the fbat format file to
+  try:
+    mf = file(inmap,'r')
+  except:
+    sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog,inmap))
+    sys.exit(1)
+  try:
+    rsl = [x.split()[1] for x in mf]
+  except:
+      sys.stderr.write('## cannot parse %s' % inmap)
+      sys.exit(1)
+  try:
+      os.makedirs(outfilepath)
+  except:
+      pass # already exists
+  head = ' '.join(rsl) # list of rs numbers
+  # TODO add anno to rs but fbat will prolly barf?
+  pedf = file(inped,'r')
+  o = file(outfpath,'w',2**20)
+  o.write(head)
+  o.write('\n')
+  for i,row in enumerate(pedf):
+    if i == 0:
+       lrow = row.split()
+       try:
+          x = [int(x) for x in lrow[10:50]] # look for non numeric codes
+       except:
+          dorecode = 1
+    if dorecode:
+        lrow = row.strip().split()
+        p = lrow[:6]
+        g = lrow[6:]
+        gc = [recode.get(x,'0') for x in g]
+        lrow = p+gc
+        row = '%s\n' % ' '.join(lrow)
+    o.write(row)
+  o.close()
+
+
+def main():
+    """call fbater
+    need to work with rgenetics composite datatypes
+    so in and out are html files with data in extrafiles path
+    <command interpreter="python">rg_convert_lped_fped.py '$input1/$input1.metadata.base_name'
+    '$output1' '$output1.extra_files_path'
+    </command>
+    """
+    nparm = 3
+    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
+    rgConv(inpedfilepath,outhtmlname,outfilepath)
+    f = file(outhtmlname,'w')
+    f.write(galhtmlprefix % prog)
+    flist = os.listdir(outfilepath)
+    print '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
+    f.write('<div>## Rgenetics: http://rgenetics.org Galaxy Tools %s %s\n<ol>' % (prog,timenow()))
+    for i, data in enumerate( flist ):
+        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
+    f.write("</div></body></html>")
+    f.close()
+
+  
+
+if __name__ == "__main__":
+   main()
diff -r 639c6b5e0073 -r 1a0bb7d6897c lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
--- a/lib/galaxy/datatypes/converters/lped_to_fped_converter.xml	Sun Oct 11 15:00:40 2009 -0400
+++ b/lib/galaxy/datatypes/converters/lped_to_fped_converter.xml	Sun Oct 11 15:07:11 2009 -0400
@@ -1,1 +1,15 @@
-/opt/galaxy/tools/rgenetics/converters/lped_to_fped_converter.xml
\ No newline at end of file
+<tool id="lped2fpedconvert" name="Convert lped to fped" version="0.01">
+  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <!-- Used on the metadata edit page. -->
+  <command interpreter="python">
+   lped_to_fped_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$output1' '$output1.extra_files_path'
+  </command>
+  <inputs>
+    <param format="lped" name="input1" type="data" label="Choose linkage pedigree file"/>
+  </inputs>
+  <outputs>
+    <data format="fped" name="output1" metadata_source="input1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>
diff -r 639c6b5e0073 -r 1a0bb7d6897c lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
--- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py	Sun Oct 11 15:00:40 2009 -0400
+++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py	Sun Oct 11 15:07:11 2009 -0400
@@ -1,1 +1,110 @@
-/opt/galaxy/tools/rgenetics/converters/lped_to_pbed_converter.py
\ No newline at end of file
+# 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 = """<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+"""
+
+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
+    <command interpreter="python">lped_to_pbed_converter.py '$input1/$input1.metadata.base_name'
+    '$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+    </command>
+    """
+    nparm = 4
+    if len(sys.argv) < nparm:
+        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
+        sys.exit(1)
+    inpedfilepath = sys.argv[1]
+    outhtmlname = sys.argv[2]
+    outfilepath = sys.argv[3]
+    try:
+        os.makedirs(outfilepath)
+    except:
+        pass
+    plink = sys.argv[4]
+    rgConv(inpedfilepath,outhtmlname,outfilepath,plink)
+    f = file(outhtmlname,'w')
+    f.write(galhtmlprefix % prog)
+    flist = os.listdir(outfilepath)
+    s = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
+    print s
+    f.write('<div>%s\n<ol>' % (s))
+    for i, data in enumerate( flist ):
+        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
+    f.write("</div></body></html>")
+    f.close()
+
+  
+
+if __name__ == "__main__":
+   main()
diff -r 639c6b5e0073 -r 1a0bb7d6897c lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
--- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml	Sun Oct 11 15:00:40 2009 -0400
+++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml	Sun Oct 11 15:07:11 2009 -0400
@@ -1,1 +1,16 @@
-/opt/galaxy/tools/rgenetics/converters/lped_to_pbed_converter.xml
\ No newline at end of file
+<tool id="lped2pbedconvert" name="Convert lped to plink pbed" version="0.01">
+  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <!-- Used on the metadata edit page. -->
+  <command interpreter="python">
+   lped_to_pbed_converter.py '$input1.extra_files_path/$input1.metadata.base_name'
+   '$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+  </command>
+  <inputs>
+    <param format="lped" name="input1" type="data" label="Choose linkage pedigree file"/>
+  </inputs>
+  <outputs>
+    <data format="pbed" name="output1" metadata_source="input1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>
diff -r 639c6b5e0073 -r 1a0bb7d6897c lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
--- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py	Sun Oct 11 15:00:40 2009 -0400
+++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py	Sun Oct 11 15:07:11 2009 -0400
@@ -1,1 +1,80 @@
-/opt/galaxy/tools/rgenetics/converters/pbed_to_lped_converter.py
\ No newline at end of file
+# 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 = """<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+"""
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+   
+def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):
+    """
+    """
+    
+    basename = os.path.split(inpedfilepath)[-1] # get basename
+    outroot = os.path.join(outfilepath,basename)
+    cl = '%s --noweb --bfile %s --recode --out %s ' % (plink,inpedfilepath,outroot)
+    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
+    <command interpreter="python">pbed_to_lped_converter.py '$input1/$input1.metadata.base_name'
+    '$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+    </command>
+    """
+    nparm = 4
+    if len(sys.argv) < nparm:
+        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (myname,sys.argv,nparm))
+        sys.exit(1)
+    inpedfilepath = sys.argv[1]
+    outhtmlname = sys.argv[2]
+    outfilepath = sys.argv[3]
+    try:
+        os.makedirs(outfilepath)
+    except:
+        pass
+    plink = sys.argv[4]
+    rgConv(inpedfilepath,outhtmlname,outfilepath,plink)
+    f = file(outhtmlname,'w')
+    f.write(galhtmlprefix % prog)
+    flist = os.listdir(outfilepath)
+    s = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
+    print s
+    f.write('<div>%s\n<ol>' % (s))
+    for i, data in enumerate( flist ):
+        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
+    f.write("</div></body></html>")
+    f.close()
+
+  
+
+if __name__ == "__main__":
+   main()
diff -r 639c6b5e0073 -r 1a0bb7d6897c lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
--- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml	Sun Oct 11 15:00:40 2009 -0400
+++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml	Sun Oct 11 15:07:11 2009 -0400
@@ -1,1 +1,16 @@
-/opt/galaxy/tools/rgenetics/converters/pbed_to_lped_converter.xml
\ No newline at end of file
+<tool id="pbed2lpedconvert" name="Convert plink pbed to linkage lped" version="0.01">
+  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <!-- Used on the metadata edit page. -->
+  <command interpreter="python">
+   pbed_to_lped_converter.py '$input1.extra_files_path/$input1.metadata.base_name'
+   '$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+  </command>
+  <inputs>
+    <param format="pbed" name="input1" type="data" label="Choose compressed Plink binary format genotype file"/>
+  </inputs>
+  <outputs>
+    <data format="lped" name="output1" metadata_source="input1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>

    

Greg Von Kuster

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