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1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.1">
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2 <description>e.g. to get peptides from ESTs</description>
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3 <command interpreter="python">
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4 get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file
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5 </command>
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6 <inputs>
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7 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." />
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8 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
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9 <option value="1">1. Standard</option>
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10 <option value="2">2. Vertebrate Mitochondrial</option>
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11 <option value="3">3. Yeast Mitochondrial</option>
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12 <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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13 <option value="5">5. Invertebrate Mitochondrial</option>
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14 <option value="6">6. Ciliate Macronuclear and Dasycladacean</option>
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15 <option value="9">9. Echinoderm Mitochondrial</option>
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16 <option value="10">10. Euplotid Nuclear</option>
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17 <option value="11">11. Bacterial</option>
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18 <option value="12">12. Alternative Yeast Nuclear</option>
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19 <option value="13">13. Ascidian Mitochondrial</option>
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20 <option value="14">14. Flatworm Mitochondrial</option>
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21 <option value="15">15. Blepharisma Macronuclear</option>
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22 <option value="16">16. Chlorophycean Mitochondrial</option>
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23 <option value="21">21. Trematode Mitochondrial</option>
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24 <option value="22">22. Scenedesmus obliquus</option>
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25 <option value="23">23. Thraustochytrium Mitochondrial</option>
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26 </param>
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27 <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs">
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28 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option>
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29 <option value="CDS">Look for CDSs (with start and stop codons)</option>
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30 </param>
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31 <param name="ends" type="select" value="open" label="Sequence end treatment">
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32 <option value="open">Open ended (will allow missing start/stop codons at the ends)</option>
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33 <option value="closed">Complete (will check for start/stop codons at the ends)</option>
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34 <!-- TODO? Circular, for using this on finished bacteria etc -->
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35 </param>
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36
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37 <param name="mode" type="select" label="Selection criteria" help="Suppose a sequence has ORFs/CDSs of lengths 100, 102 and 102 -- which should be taken? These options would return 3, 2 or 1 ORF.">
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38 <option value="all">All ORFs/CDSs from each sequence</option>
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39 <option value="top">All ORFs/CDSs from each sequence with the maximum length</option>
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40 <option value="one">First ORF/CDS from each sequence with the maximum length</option>
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41 </param>
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42 <param name="min_len" type="integer" size="5" value="30" label="Minimum length ORF/CDS (in amino acids, e.g. 30 aa = 90 bp plus any stop codon)">
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43 </param>
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44 <param name="strand" type="select" label="Strand to search" help="Use the forward only option if your sequence directionality is known (e.g. from poly-A tails, or strand specific RNA sequencing.">
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45 <option value="both">Search both the forward and reverse strand</option>
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46 <option value="forward">Only search the forward strand</option>
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47 <option value="reverse">Only search the reverse strand</option>
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48 </param>
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49 </inputs>
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50 <outputs>
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51 <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" />
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52 <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input_file" value="get_orf_input.fasta" />
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57 <param name="table" value="1" />
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58 <param name="ftype" value="CDS" />
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59 <param name="ends" value="open" />
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60 <param name="mode" value="all" />
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61 <param name="min_len" value="10" />
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62 <param name="strand" value="forward" />
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63 <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" />
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64 <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" />
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65 </test>
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66 <test>
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67 <param name="input_file" value="get_orf_input.fasta" />
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68 <param name="table" value="11" />
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69 <param name="ftype" value="CDS" />
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70 <param name="ends" value="closed" />
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71 <param name="mode" value="all" />
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72 <param name="min_len" value="10" />
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73 <param name="strand" value="forward" />
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74 <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" />
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75 <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" />
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76 </test>
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77 <test>
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78 <param name="input_file" value="get_orf_input.fasta" />
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79 <param name="table" value="11" />
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80 <param name="ftype" value="CDS" />
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81 <param name="ends" value="open" />
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82 <param name="mode" value="all" />
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83 <param name="min_len" value="10" />
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84 <param name="strand" value="forward" />
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85 <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" />
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86 <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" />
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87 </test>
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88 </tests>
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89 <requirements>
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90 <requirement type="python-module">Bio</requirement>
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91 </requirements>
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92 <help>
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93
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94 **What it does**
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95
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96 Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ
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97 and Standard Flowgram Format (SFF) are supported), and searches each sequence
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98 for open reading frames (ORFs) or potential coding sequences (CDSs) of the
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99 given minimum length. These are returned as FASTA files of nucleotides and
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100 protein sequences.
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101
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102 You can choose to have all the ORFs/CDSs above the minimum length for each
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103 sequence (similar to the EMBOSS getorf tool), those with the longest length
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104 equal, or the first ORF/CDS with the longest length (in the special case
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105 where a sequence encodes two or more long ORFs/CDSs of the same length). The
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106 last option is a reasonable choice when the input sequences represent EST or
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107 mRNA sequences, where only one ORF/CDS is expected.
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108
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109 Note that if no ORFs/CDSs in a sequence match the criteria, there will be no
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110 output for that sequence.
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111
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112 Also note that the ORFs/CDSs are assigned modified identifiers to distinguish
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113 them from the original full length sequences, by appending a suffix.
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114
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115 The start and stop codons are taken from the `NCBI Genetic Codes
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116 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_.
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117 When searching for ORFs, the sequences will run from stop codon to stop
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118 codon, and any start codons are ignored. When searching for CDSs, the first
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119 potential start codon will be used, giving the longest possible CDS within
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120 each ORF, and thus the longest possible protein sequence. This is useful
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121 for things like BLAST or domain searching, but since this may not be the
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122 correct start codon may not be appropriate for signal peptide detection
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123 etc.
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124
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125 **Example Usage**
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126
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127 Given some EST sequences (Sanger capillary reads) assembled into unigenes,
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128 or a transcriptome assembly from some RNA-Seq, each of your nucleotide
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129 sequences should (barring sequencing, assembly errors, frame-shifts etc)
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130 encode one protein as a single ORF/CDS, which you wish to extract (and
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131 perhaps translate into amino acids).
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132
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133 If your RNS-Seq data was strand specific, and assembled taking this into
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134 account, you should only search for ORFs/CDSs on the forward strand.
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135
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136 **Citation**
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137
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138 This tool uses Biopython. If you use this tool in scientific work leading
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139 to a publication, please cite the Biopython application note (and Galaxy
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140 too of course):
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141
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142 Cock et al 2009. Biopython: freely available Python tools for computational
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143 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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144 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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145
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146 </help>
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147 </tool>
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