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1 trunc_seq
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2 =========
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3
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4 `trunc_seq.pl` is a script to truncate sequence files.
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5
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6 * [Synopsis](#synopsis)
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7 * [Description](#description)
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8 * [Usage](#usage)
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9 * [Options](#options)
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10 * [Output](#output)
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11 * [Run environment](#run-environment)
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12 * [Dependencies](#dependencies)
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13 * [Author - contact](#author---contact)
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14 * [Citation, installation, and license](#citation-installation-and-license)
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15 * [Changelog](#changelog)
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16
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17 ## Synopsis
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18
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19 perl trunc_seq.pl 20 3500 seq-file.embl > seq-file_trunc_20_3500.embl
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20
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21 **or**
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22
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23 perl trunc_seq.pl file_of_filenames_and_coords.tsv
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24
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25 ## Description
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26
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27 This script truncates sequence files according to the given
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28 coordinates. The features/annotations in RichSeq files (e.g. EMBL or
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29 GENBANK format) will also be adapted accordingly. Use option **-o** to
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30 specify a different output sequence format. Input can be given directly
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31 as a file and truncation coordinates to the script, with the start
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32 position as the first argument, stop as the second and (the path to)
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33 the sequence file as the third. In this case the truncated sequence
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34 entry is printed to *STDOUT*. Input sequence files should contain only
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35 one sequence entry, if a multi-sequence file is used as input only the
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36 **first** sequence entry is truncated.
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37
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38 Alternatively, a file of filenames (fof) with respective coordinates
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39 and sequence files in the following **tab-separated** format can be
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40 given to the script (the header is optional):
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41
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42 \#start stop seq-file<br>
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43 300 9000 (path/to/)seq-file<br>
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44 50 1300 (path/to/)seq-file2<br>
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45
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46 With a fof the resulting truncated sequence files are printed into a
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47 results directory. Use option **-r** to specify a different results
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48 directory than the default.
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49
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50 It is also possible to truncate a RichSeq sequence file loaded into the
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51 [Artemis](http://www.sanger.ac.uk/science/tools/artemis) genome browser
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52 from the Sanger Institute: Select a subsequence and then go to Edit ->
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53 Subsequence (and Features)
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54
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55 ## Usage
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56
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57 perl trunc_seq.pl -o gbk 120 30000 seq-file.embl > seq-file_trunc_120_3000.gbk
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58
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59 **or**
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60
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61 perl trunc_seq.pl -o fasta 5300 18500 seq-file.gbk | perl revcom_seq.pl -i fasta > seq-file_trunc_revcom.fasta
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62
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63 **or**
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64
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65 perl trunc_seq.pl -r path/to/trunc_embl_dir -o embl file_of_filenames_and_coords.tsv
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66
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67 ## Options
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68
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69 - **-h**, **-help**
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70
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71 Help (perldoc POD)
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72
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73 - **-o**=*str*, **-outformat**=*str*
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74
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75 Specify different sequence format for the output (files) [fasta, embl, or gbk]
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76
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77 - **-r**=*str*, **-result\_dir**=*str*
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78
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79 Path to result folder for fof input \[default = './trunc\_seq\_results'\]
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80
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81 - **-v**, **-version**
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82
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83 Print version number to *STDOUT*
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84
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85 ## Output
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86
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87 - *STDOUT*
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88
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89 If a single sequence file is given to the script the truncated sequence
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90 file is printed to *STDOUT*. Redirect or pipe into another tool as
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91 needed.
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92
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93 **or**
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94
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95 - ./trunc_seq_results
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96
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97 If a fof is given to the script, all output files are stored in a
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98 results folder
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99
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100 - ./trunc_seq_results/seq-file_trunc_start_stop.format
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101
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102 Truncated output sequence files are named appended with 'trunc' and the
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103 corresponding start and stop positions
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104
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105 ## Run environment
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106
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107 The Perl script runs under Windows and UNIX flavors.
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108
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109 ## Dependencies
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110
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111 - [**BioPerl**](http://www.bioperl.org) (tested version 1.007001)
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112
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113 ## Author - contact
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114
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115 Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)
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116
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117 ## Citation, installation, and license
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118
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119 For [citation](https://github.com/aleimba/bac-genomics-scripts#citation), [installation](https://github.com/aleimba/bac-genomics-scripts#installation-recommendations), and [license](https://github.com/aleimba/bac-genomics-scripts#license) information please see the repository main [*README.md*](https://github.com/aleimba/bac-genomics-scripts/blob/master/README.md).
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120
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121 ## Changelog
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122
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123 * v0.2 (2015-12-07)
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124 * Merged funtionality of `trunc_seq.pl` and `run_trunc_seq.pl` in one single script
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125 * Allows now single file and file of filenames (fof) with coordinates input
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126 * output for single file input printed to *STDOUT* now
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127 * output for fof input printed into files in a result directory, new option **-r** to specify result directory
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128 * included a POD instead of a simple usage text
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129 * included `pod2usage` with Pod::Usage
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130 * included 'use autodie' pragma
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131 * options with Getopt::Long
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132 * output format now specified with option **-o**
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133 * included version switch, **-v**
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134 * fixed bug to remove input filepaths from fof input for output files
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135 * skip empty or comment lines (/^#/) in fof input
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136 * check and warn if input seq file has more than one seq entries
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137 * v0.1 (2013-02-08)
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138 * In v0.1 `trunc_seq.pl` only for single sequence input, but included additional wrapper script `run_trunc_seq.pl` for a fof input
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