Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

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

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/env python
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2 ## usage: ./phytab_mview.py -i <phytabinput> -d <protein|dna>
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3 ## splits up an aligned phytab file containing multiple genes into
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4 ## individual files to run mview
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5
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 import sys, os, os.path, tempfile, shutil, re, shlex, subprocess
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 import optparse
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 from multiprocessing import Pool
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9
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10 #define some variables to call later:
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11
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12 directory = ""
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13 extension = ".fs"
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14 html_header = """<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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15 <HTML>
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16 <HEAD>
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17 <TITLE></TITLE>
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18 </HEAD>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 <BODY BGCOLOR='white' TEXT='black' LINK='blue' ALINK='red' VLINK='purple'>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 <H1>PHYTAB MVIEW ALIGNMENT VIEWER</H1>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 <PRE>Select from below to view aligned sequence as HTML (left) or FASTA (right) in browser.
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22 </PRE>
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23 <table border="1" bordercolor="#000000" style="background-color:#FFFFFF" width="300" cellpadding="3" cellspacing="0">
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24 <tr>
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25 <td>mview HTML</td>
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26 <!--<td>FASTA</td>-->
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27 </tr>"""
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28 html_close = """
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29 <P><SMALL><A HREF="http://bio-mview.sourceforge.net">MView</A> </SMALL><BR>
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30 </BODY>
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31 </HTML>"""
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32
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33 #define some functions to call in 'main':
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34 # first, sanitize problematic characters
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35 def unescape(string):
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36 mapped_chars = {
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37 '>': '__gt__',
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38 '<': '__lt__',
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39 "'": '__sq__',
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40 '"': '__dq__',
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41 '[': '__ob__',
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42 ']': '__cb__',
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43 '{': '__oc__',
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44 '}': '__cc__',
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45 '@': '__at__',
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46 '\n': '__cn__',
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47 '\r': '__cr__',
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48 '\t': '__tc__',
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49 '#': '__pd__'
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50 }
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51
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52 for key, value in mapped_chars.iteritems():
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53 string = string.replace(value, key)
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54
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55 return string
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56 # next, define tabular --> fasta conversion
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57 class Sequence:
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58 def __init__(self, string):
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59 lis = string.split()
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60 self.species = lis[0]
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61 self.family = lis[1]
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62 self.name = lis[2]
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63 self.header = ' '.join(lis[:-1])
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64 self.sequence = lis[-1]
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65 self.string = string
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66
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67 def printFASTA(self):
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68 return '> ' + self.header + '\n' + self.sequence + '\n'
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69
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70 # then define function to apply preceding conversion method to all genes
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71 # (creates separate file for each gene)
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72 def saveMulti(tabFile):
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73 with open(tabFile) as f:
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74 for line in f:
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75 seq = Sequence(line)
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76 with open(seq.family + extension, "a") as p:
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77 p.write(seq.printFASTA())
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78
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79 #subroutine to write main HTML output containing valid urls to mview htmls
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80 def resultsto_output_html(html_mainoutput,basepath):
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81 htmllist = [f for f in os.listdir(basepath) if 'html' in f]
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82 sortedhtmllist = sorted(htmllist)
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83 html = open(html_mainoutput, 'w')
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84 html.write(html_header)
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85 for f in sortedhtmllist:
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86 f_path = os.path.join(basepath,f)
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87 htmllink = '<tr><td><a href="' + f + '">' + f + '</a></td>\n'
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88 html.write(htmllink)
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89 html.write(html_close)
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90 html.close()
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91
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92 def main():
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93 #the command line arguments from the xml:
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94 """
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95 ##params for galaxy wrapper
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96 $input
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97 $dna
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98 $output
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99 "$output.extra_files_path" #save the htmlfiles here
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100 """
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101 inputphytabfile = sys.argv[1]
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102 dnaorprotein = sys.argv[2]
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103 output = sys.argv[3]
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104 extra_files_path = sys.argv[4]
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105
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106 inputFile = unescape(inputphytabfile)
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107 ##make the fasta files
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108 saveMulti(inputFile)
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109
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110 #prepare to put mview htmls into valid path
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111
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112 if not os.path.isdir(extra_files_path): #make filepath for alns to go with galaxy info
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113 os.makedirs(extra_files_path)
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114
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115 # execute mview on each fasta, storing in extra_files_path as <gene_aln>.html
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116 list_of_fastafiles = [f for f in os.listdir(os.getcwd()) if 'fs' in f]
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117 sortedfileorder = sorted(list_of_fastafiles)
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118 for gene_aln in sortedfileorder:
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119 result_htmlfile = gene_aln + '.html'
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120 result_path = os.path.join(extra_files_path,result_htmlfile) #puts the htmls in permanent Galaxy directory
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121 if dnaorprotein is 'dna':
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122 cmd = subprocess.Popen(['mview','-in','pearson','-DNA','-bold','-coloring','group','-html','head', gene_aln],stdout=subprocess.PIPE)
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123 else:
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124 cmd = subprocess.Popen(['mview','-in','pearson','-bold','-coloring','group','-html','head', gene_aln],stdout=subprocess.PIPE)
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125 cmd.wait()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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126 out = cmd.communicate()[0]
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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127
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128 with open(result_path, 'wb') as fileout:
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129 fileout.write(out)
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130 ##now have # of gene htmls in extra_files_path/
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131
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132 #write main html output
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133 resultsto_output_html(output,extra_files_path)
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134
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135
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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136 if __name__ == '__main__':
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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137 main()
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138