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1 #!/usr/bin/env python
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2 import os
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3 import sys
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4 import argparse
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5 import logging
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6 import rpy2.robjects as robjects
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7
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8 import utils
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9
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10 rscript = ''
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11 R = robjects.r
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12
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13
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14 def run_rscript(command=None):
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15 """Run R command, log it, append to rscript"""
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16 global rscript
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17 if not command:
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18 return
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19 logging.debug(command)
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20 rscript += '{}\n'.format(command)
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21 R(command)
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22
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23
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24 def find_periodicity(
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25 rdata_load='Prepare.rda', start_codons='ATG', stop_codons='TAG,TAA,TGA',
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26 fasta_file=None, include_lengths='25:30', analyze_plot_lengths='26:30',
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27 text_legend='Frame 0, Frame 1, Frame 2', rdata_save='Periodicity.rda',
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28 html_file='Periodicity-report.html', output_path=os.getcwd()):
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29 """Plot triplet periodicity from prepared R data file. """
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30 logging.debug('{}'.format(R('sessionInfo()')))
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31 cmd = 'library(riboSeqR)'
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32 run_rscript(cmd)
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33
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34 logging.debug('Loading saved R data file')
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35 cmd = 'load("{}")'.format(rdata_load)
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36 run_rscript(cmd)
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37
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38 # R("""options(showTailLines=Inf)""")
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39 starts, stops = (utils.process_args(start_codons, ret_mode='charvector'),
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40 utils.process_args(stop_codons, ret_mode='charvector'))
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41
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42 cmd = ('fastaCDS <- findCDS(fastaFile={0!r}, startCodon={1}, '
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43 'stopCodon={2})'.format(fasta_file, starts, stops))
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44 run_rscript(cmd)
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45
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46 logging.info('Potential coding sequences using start codon (ATG) and stop '
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47 'codons TAG, TAA, TGA')
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48 logging.info('{}\n'.format(R['fastaCDS']))
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49
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50 cmd = """fCs <- frameCounting(riboDat, fastaCDS, lengths={0})
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51 fS <- readingFrame(rC=fCs, lengths={1}); fS""".\
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52 format(include_lengths, analyze_plot_lengths)
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53 run_rscript(cmd)
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54
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55 logging.debug('riboDat \n{}\n'.format(R['riboDat']))
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56 logging.debug('fCs\n{0}\n'.format(R['fCs']))
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57 logging.info('Reading frames for each n-mer\n{}'.format(R['fS']))
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58
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59 legend = utils.process_args(text_legend, ret_mode='charvector')
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60
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61 for fmat in ('pdf', 'png'):
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62 run_rscript('{0}(file="{1}")'.format(fmat, os.path.join(
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63 output_path, '{0}.{1}'.format('Periodicity-plot', fmat))))
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64 run_rscript('plotFS(fS, legend.text = {0})'.format(legend))
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65 run_rscript('dev.off()')
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66
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67 run_rscript('save("fCs", "fS", "riboDat", "fastaCDS", '
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68 'file="{}", compress=FALSE)'.format(rdata_save))
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69
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70 html = '<h2>Triplet periodicity - results</h2><hr>'
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71 html += ('<h4>Results of reading frame analysis</h4>'
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72 '<pre>{}</pre><br>'.format(R['fS']))
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73 html += ('<p>Lengths used for reading frame analysis - <code>{0}</code>'
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74 '<br>Lengths selected for the plot - <code>{1}</code>'
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75 '</p>'.format(include_lengths, analyze_plot_lengths))
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76 html += ('<p><img src="Periodicity-plot.png" border="1" '
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77 'alt="Triplet periodicity plot" />'
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78 '<br><a href="Periodicity-plot.pdf">PDF version</a></p>')
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79
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80 logging.info('\n{:#^80}\n{}\n{:#^80}\n'.format(
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81 ' R script for this session ', rscript, ' End R script '))
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82
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83 with open(os.path.join(output_path, 'periodicity.R'), 'w') as r:
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84 r.write(rscript)
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85
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86 html += ('<h4>R script for this session</h4>'
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87 '<p><a href="periodicity.R">periodicity.R</a></p>'
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88 '<p>Next step: <em>Metagene analysis</em></p>')
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89
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90 with open(html_file, 'w') as f:
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91 f.write(html)
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92
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93
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94 if __name__ == '__main__':
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95
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96 parser = argparse.ArgumentParser(
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97 description='Plot triplet periodicity for different read lengths.')
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98
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99 # required arguments
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100 flags = parser.add_argument_group('required arguments')
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101 flags.add_argument(
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102 '--rdata_load', required=True,
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103 help='riboSeqR data from input preparation step (Prepare.rda)')
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104 flags.add_argument(
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105 '--fasta_file', required=True,
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106 help='FASTA file of the reference transcriptome')
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107
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108 # optional arguments
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109 parser.add_argument(
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110 '--start_codons',
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111 help='Start codon(s) to use. (default: %(default)s)', default='ATG')
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112 parser.add_argument(
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113 '--stop_codons', help='Stop codon(s) to use. (default: %(default)s)',
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114 default='TAG, TAA, TGA')
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115 parser.add_argument(
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116 '--include_lengths',
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117 help='Lengths of ribosome footprints to be included '
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118 '(default: %(default)s)', default='25:30')
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119 parser.add_argument(
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120 '--analyze_plot_lengths',
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121 help='Lenghts of reads to be analyzed for frame-shift and plotting '
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122 '(default: %(default)s)', default='26:30')
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123 parser.add_argument(
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124 '--text_legend',
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125 help='Text for legend used in the plot (default: %(default)s)',
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126 default='Frame 0, Frame 1, Frame 2')
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127 parser.add_argument(
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128 '--rdata_save', help='File to write RData to (default: %(default)s)',
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129 default='Periodicity.rda')
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130 parser.add_argument('--html_file', help='Output file for results (HTML)')
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131 parser.add_argument('--output_path',
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132 help='Files are saved in this directory')
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133 parser.add_argument(
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134 '--debug', help='Produce debug output', action='store_true')
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135
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136 args = parser.parse_args()
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137 if args.debug:
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138 level = logging.DEBUG
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139 else:
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140 level = logging.INFO
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141
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142 logging.basicConfig(format='%(module)s: %(levelname)s - %(message)s',
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143 level=level, stream=sys.stdout)
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144 logging.info('Supplied Arguments\n{}\n'.format(vars(args)))
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145
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146 if not os.path.exists(args.output_path):
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147 os.mkdir(args.output_path)
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148
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149 find_periodicity(
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150 rdata_load=args.rdata_load, start_codons=args.start_codons,
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151 stop_codons=args.stop_codons, fasta_file=args.fasta_file,
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152 include_lengths=args.include_lengths,
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153 analyze_plot_lengths=args.analyze_plot_lengths,
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154 text_legend=args.text_legend,
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155 rdata_save=args.rdata_save, html_file=args.html_file,
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156 output_path=args.output_path)
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157 logging.info("Done!")
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