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diff alignment/phytab_mview.py @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/phytab_mview.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+## usage: ./phytab_mview.py -i <phytabinput> -d <protein|dna> 
+## splits up an aligned phytab file containing multiple genes into
+## individual files to run mview
+
+import sys, os, os.path, tempfile, shutil, re, shlex, subprocess
+import optparse
+from multiprocessing import Pool
+
+#define some variables to call later:
+
+directory = ""
+extension = ".fs"
+html_header = """<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML>
+<HEAD>
+<TITLE></TITLE>
+</HEAD>
+<BODY BGCOLOR='white' TEXT='black' LINK='blue' ALINK='red' VLINK='purple'>
+<H1>PHYTAB MVIEW ALIGNMENT VIEWER</H1>
+<PRE>Select from below to view aligned sequence as HTML (left) or FASTA (right) in browser.
+</PRE>
+<table border="1" bordercolor="#000000" style="background-color:#FFFFFF" width="300" cellpadding="3" cellspacing="0">
+	<tr>
+		<td>mview HTML</td>
+		<!--<td>FASTA</td>-->
+	</tr>"""
+html_close =  """
+<P><SMALL><A HREF="http://bio-mview.sourceforge.net">MView</A> </SMALL><BR>
+</BODY>
+</HTML>"""	
+
+#define some functions to call in 'main':
+#    first, sanitize problematic characters
+def unescape(string):
+  mapped_chars = {
+        '>': '__gt__',
+        '<': '__lt__',
+        "'": '__sq__',
+        '"': '__dq__',
+        '[': '__ob__',
+        ']': '__cb__',
+        '{': '__oc__',
+        '}': '__cc__',
+        '@': '__at__',
+        '\n': '__cn__',
+        '\r': '__cr__',
+        '\t': '__tc__',
+        '#': '__pd__'
+        }
+
+  for key, value in mapped_chars.iteritems():
+    string = string.replace(value, key)
+
+  return string
+#  next, define tabular --> fasta conversion
+class Sequence:            
+  def __init__(self, string):
+    lis = string.split()
+    self.species = lis[0]
+    self.family = lis[1]
+    self.name = lis[2]
+    self.header = ' '.join(lis[:-1])
+    self.sequence = lis[-1]
+    self.string = string
+
+  def printFASTA(self):
+    return '> ' + self.header + '\n' + self.sequence + '\n'
+
+#  then define function to apply preceding conversion method to all genes
+#  (creates separate file for each gene)
+def saveMulti(tabFile):
+  with open(tabFile) as f:
+    for line in f:
+      seq = Sequence(line)
+      with open(seq.family + extension, "a") as p:
+        p.write(seq.printFASTA())
+                
+#subroutine to write main HTML output containing valid urls to mview htmls
+def resultsto_output_html(html_mainoutput,basepath):
+  htmllist = [f for f in os.listdir(basepath) if 'html' in f]
+  sortedhtmllist = sorted(htmllist)
+  html = open(html_mainoutput, 'w')
+  html.write(html_header)
+  for f in sortedhtmllist:
+    f_path = os.path.join(basepath,f)
+    htmllink = '<tr><td><a href="' + f + '">' + f + '</a></td>\n' 
+    html.write(htmllink)
+  html.write(html_close)
+  html.close()
+
+def main():
+#the command line arguments from the xml:
+  """
+           ##params for galaxy wrapper
+           $input 
+           $dna  
+           $output 
+           "$output.extra_files_path"  #save the htmlfiles here
+  """ 
+  inputphytabfile = sys.argv[1]
+  dnaorprotein = sys.argv[2]
+  output = sys.argv[3]
+  extra_files_path = sys.argv[4]
+  
+  inputFile = unescape(inputphytabfile)
+  ##make the fasta files
+  saveMulti(inputFile) 
+
+  #prepare to put mview htmls into valid path
+
+  if not os.path.isdir(extra_files_path):  #make filepath for alns to go with galaxy info
+      os.makedirs(extra_files_path)    
+  
+  # execute mview on each fasta, storing in extra_files_path as <gene_aln>.html
+  list_of_fastafiles = [f for f in os.listdir(os.getcwd()) if 'fs' in f]
+  sortedfileorder = sorted(list_of_fastafiles)
+  for gene_aln in sortedfileorder:
+    result_htmlfile = gene_aln + '.html'
+    result_path = os.path.join(extra_files_path,result_htmlfile) #puts the htmls in permanent Galaxy directory
+    if dnaorprotein is 'dna':
+      cmd = subprocess.Popen(['mview','-in','pearson','-DNA','-bold','-coloring','group','-html','head', gene_aln],stdout=subprocess.PIPE)
+    else:
+      cmd = subprocess.Popen(['mview','-in','pearson','-bold','-coloring','group','-html','head', gene_aln],stdout=subprocess.PIPE)
+    cmd.wait()  
+    out =  cmd.communicate()[0]
+     
+    with open(result_path, 'wb') as fileout:
+      fileout.write(out)
+    ##now have # of gene htmls in extra_files_path/
+    
+  #write main html output  
+  resultsto_output_html(output,extra_files_path)
+
+
+if __name__ == '__main__':
+    main()
+