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1 #!/usr/bin/env python
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2
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3 #Copyright 2011-2013 by Peter Cock, James Hutton Institute (formerly SCRI), UK
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4 #
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5 #Licenced under the GPL (GNU General Public Licence) version 3.
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6 #
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7 #Based on Perl script predictNLS v1.3, copyright 2001-2005 and the later
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8 #versions up to predictnls v1.0.20 (copright 2012), by Rajesh Nair
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9 #(nair@rostlab.org) and Burkhard Rost (rost@rostlab.org), Rost Lab,
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10 #Columbia University http://rostlab.org/
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11
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12 """Batch mode predictNLS, for finding nuclear localization signals
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13
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14 This is a Python script re-implementing the predictNLS method, originally
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15 written in Perl, described here:
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16
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17 Murat Cokol, Rajesh Nair, and Burkhard Rost.
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18 Finding nuclear localization signals.
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19 EMBO reports 1(5), 411-415, 2000
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20
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21 http://dx.doi.org/10.1093/embo-reports/kvd092
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22
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23 The original Perl script was designed to work on a single sequence at a time,
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24 but offers quite detailed output, including HTML (webpage).
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25
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26 This Python version is designed to work on a single FASTA file containing
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27 multiple sequences, and produces a single tabular output file, with one line
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28 per NLS found (i.e. zero or more rows per query sequence).
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29
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30 It takes either two or three command line arguments:
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31
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32 predictNLS_batch input_file output_file [nls_motif_file]
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33
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34 The input file should be protein sequences in FASTA format, the output file
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35 is tab separated plain text, and the NLS motif file defaults to using the
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36 plain text My_NLS_list file located next to the script file, or in a data
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37 subdirectory.
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38
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39 For convience if using this outside Galaxy, the input filename can be '-'
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40 to mean stdin, and likewise the output filename can be '-' to mean stdout.
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41
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42 Tested with the My_NLS_list file included with predictnls-1.0.7.tar.gz to
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43 predictnls-1.0.20.tar.gz inclusive (the list was extended in v1.0.7 in
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44 August 2010, see the change log included in those tar-balls).
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45
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46 The Rost Lab provide source code tar balls for predictNLS on the FTP site
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47 ftp://rostlab.org/predictnls/ but for Debian or RedHat based Linux they
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48 recommend their package repository instead,
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49 https://rostlab.org/owiki/index.php/Packages
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50 """
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51
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52 import os
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53 import sys
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54 import re
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55
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56 def stop_err(msg, return_code=1):
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57 sys.stderr.write(msg.rstrip() + "\n")
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58 sys.exit(return_code)
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59
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60 if len(sys.argv) == 4:
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61 fasta_filename, tabular_filename, re_filename = sys.argv[1:]
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62 elif len(sys.argv) == 3:
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63 fasta_filename, tabular_filename = sys.argv[1:]
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64 #Use os.path.realpath(...) to handle being called via a symlink
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65 #Try under subdirectory data:
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66 re_filename = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])),
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67 "data", "My_NLS_list")
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68 if not os.path.isfile(re_filename):
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69 #Try in same directory as this script:
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70 re_filename = os.path.join(os.path.dirname(os.path.realpath(sys.argv[0])),
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71 "My_NLS_list")
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72 else:
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73 stop_err("Expect 2 or 3 arguments: input FASTA file, output tabular file, and NLS motif file")
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74
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75 if not os.path.isfile(fasta_filename):
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76 stop_err("Could not find FASTA input file: %s" % fasta_filename)
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77
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78 if not os.path.isfile(re_filename):
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79 stop_err("Could not find NLS motif file: %s" % re_filename)
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80
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81 def load_re(filename):
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82 """Parse the 5+ column tabular NLS motif file."""
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83 handle = open(filename, "rU")
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84 for line in handle:
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85 line = line.rstrip("\n")
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86 if not line:
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87 continue
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88 parts = line.split("\t")
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89 assert 5 <= len(parts), parts
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90 regex, evidence, p_count, percent_nuc, precent_non_nuc = parts[0:5]
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91 try:
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92 regex = re.compile(regex)
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93 p_count = int(p_count)
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94 except ValueError:
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95 stop_err("Bad data in line: %s" % line)
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96 if 6 <= len(parts):
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97 proteins = parts[5]
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98 assert p_count == len(proteins.split(",")), line
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99 else:
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100 proteins = ""
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101 assert p_count == 0
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102 if 7 <= len(parts):
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103 domains = parts[6]
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104 assert int(p_count) == len(domains.split(",")), line
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105 else:
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106 domains = ""
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107 assert p_count == 0
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108 #There can be further columns (DNA binding?), but we don't use them.
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109 yield regex, evidence, p_count, percent_nuc, proteins, domains
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110 handle.close()
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111
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112 def fasta_iterator(filename):
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113 """Simple FASTA parser yielding tuples of (name, upper case sequence)."""
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114 if filename == "-":
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115 handle = sys.stdin
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116 else:
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117 handle = open(filename)
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118 name, seq = "", ""
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119 for line in handle:
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120 if line.startswith(">"):
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121 if name:
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122 yield name, seq
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123 #Take the first word only as the name:
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124 name = line[1:].rstrip().split(None,1)[0]
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125 seq = ""
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126 elif name:
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127 #Simple way would leave in any internal white space,
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128 #seq += line.strip().upper()
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129 seq += "".join(line.strip().upper().split())
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130 elif not line.strip():
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131 #Ignore blank lines before first record
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132 pass
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133 else:
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134 raise ValueError("Bad FASTA line %r" % line)
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135 if filename != "-":
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136 handle.close()
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137 if name:
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138 yield name, seq
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139 raise StopIteration
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140
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141 motifs = list(load_re(re_filename))
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142 print "Looking for %i NLS motifs" % len(motifs)
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143
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144 if tabular_filename == "-":
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145 out_handle = sys.stdout
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146 else:
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147 out_handle = open(tabular_filename, "w")
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148 out_handle.write("#ID\tNLS start\tNLS seq\tNLS pattern\tType\tProtCount\t%NucProt\tProtList\tProtLoci\n")
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149 count = 0
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150 nls = 0
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151 for idn, seq in fasta_iterator(fasta_filename):
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152 for regex, evidence, p_count, percent_nuc_prot, proteins, domains in motifs:
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153 #Perl predictnls v1.0.17 (and older) take right most hit only, Bug #40
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154 #This has been fixed (v1.0.18 onwards, June 2011), so we return all the matches
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155 for match in regex.finditer(seq):
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156 #Perl predictnls v1.0.17 (and older) return NLS start position with zero
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157 #but changed to one based counting in v1.0.18 (June 2011) onwards, Bug #38
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158 #We therefore also use one based couting, hence the start+1 here:
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159 out_handle.write("%s\t%i\t%s\t%s\t%s\t%i\t%s\t%s\t%s\n" \
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160 % (idn, match.start()+1, match.group(),
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161 regex.pattern, evidence, p_count,
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162 percent_nuc_prot, proteins, domains))
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163 nls += 1
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164 count += 1
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165 if tabular_filename != "-":
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166 out_handle.close()
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167 print "Found %i NLS motifs in %i sequences" % (nls, count)
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