annotate COG/bac-genomics-scripts/revcom_seq/README.md @ 14:5a5c9a6b047b draft

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1 revcom_seq
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2 ==========
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4 `revcom_seq.pl` is a script to reverse complement (multi-)sequence files.
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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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17 ## Synopsis
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19 perl revcom_seq.pl seq-file.embl > seq-file_revcom.embl
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21 **or**
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23 perl cat_seq.pl multi-seq_file.embl | perl revcom_seq.pl -i embl > seq_file_cat_revcom.embl
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25 ## Description
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27 This script reverse complements (multi-)sequence files. The
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28 features/annotations in RichSeq files (e.g. EMBL or GENBANK format)
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29 will also be adapted accordingly. Use option **-o** to specify a
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30 different output sequence format. Input files can be given directly via
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31 *STDIN* or as a file. If *STDIN* is used, the input sequence file
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32 format has to be given with option **-i**. Be careful to set the
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33 correct input format.
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34
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35 ## Usage
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36
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37 perl revcom_seq.pl -o gbk seq-file.embl > seq-file_revcom.gbk
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38
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39 **or** reverse complement all sequence files in the current working directory:
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41 for file in *.embl; do perl revcom_seq.pl -o fasta "$file" > "${file%.embl}"_revcom.fasta; done
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43 ## Options
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44
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45 - **-h**, **-help**
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47 Help (perldoc POD)
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48
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49 - **-o**=*str*, **-outformat**=*str*
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50
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51 Specify different sequence format for the output [fasta, embl, or gbk]
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52
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53 - **-i**=*str*, **-informat**=*str*
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54
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55 Specify the input sequence file format, only needed for *STDIN* input
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56
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57 - **-v**, **-version**
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58
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59 Print version number to *STDOUT*
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60
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61 ## Output
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62
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63 - *STDOUT*
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64
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65 The reverse complemented sequence file is printed to *STDOUT*.
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66 Redirect or pipe into another tool as needed.
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68 ## Run environment
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70 The Perl script runs under Windows and UNIX flavors.
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72 ## Dependencies
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74 - [**BioPerl**](http://www.bioperl.org) (tested version 1.007001)
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76 ## Author - contact
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77
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78 Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)
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79
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80 ## Citation, installation, and license
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81
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82 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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83
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84 ## Changelog
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85
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86 * v0.2 (2015-12-10)
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87 * included a POD instead of a simple usage text
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88 * included `pod2usage` with Pod::Usage
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89 * included 'use autodie' pragma
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90 * options with Getopt::Long
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91 * output format now specified with option **-o**
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92 * included version switch, **-v**
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93 * allowed file and *STDIN* input, instead of only file; thus new option **-i** for input format
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94 * output printed to *STDOUT* now, instead of output file
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95 * fixed bug, that only first sequence in multi-sequence file is reverse complemented. Now all sequences in a multi-seq file are reverse complemented.
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96 * v0.1 (2013-02-08)