Mercurial > repos > dereeper > pangenome_explorer
comparison COG/bac-genomics-scripts/revcom_seq/README.md @ 3:e42d30da7a74 draft
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date | Thu, 30 May 2024 11:52:25 +0000 |
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1 revcom_seq | |
2 ========== | |
3 | |
4 `revcom_seq.pl` is a script to reverse complement (multi-)sequence files. | |
5 | |
6 * [Synopsis](#synopsis) | |
7 * [Description](#description) | |
8 * [Usage](#usage) | |
9 * [Options](#options) | |
10 * [Output](#output) | |
11 * [Run environment](#run-environment) | |
12 * [Dependencies](#dependencies) | |
13 * [Author - contact](#author---contact) | |
14 * [Citation, installation, and license](#citation-installation-and-license) | |
15 * [Changelog](#changelog) | |
16 | |
17 ## Synopsis | |
18 | |
19 perl revcom_seq.pl seq-file.embl > seq-file_revcom.embl | |
20 | |
21 **or** | |
22 | |
23 perl cat_seq.pl multi-seq_file.embl | perl revcom_seq.pl -i embl > seq_file_cat_revcom.embl | |
24 | |
25 ## Description | |
26 | |
27 This script reverse complements (multi-)sequence files. The | |
28 features/annotations in RichSeq files (e.g. EMBL or GENBANK format) | |
29 will also be adapted accordingly. Use option **-o** to specify a | |
30 different output sequence format. Input files can be given directly via | |
31 *STDIN* or as a file. If *STDIN* is used, the input sequence file | |
32 format has to be given with option **-i**. Be careful to set the | |
33 correct input format. | |
34 | |
35 ## Usage | |
36 | |
37 perl revcom_seq.pl -o gbk seq-file.embl > seq-file_revcom.gbk | |
38 | |
39 **or** reverse complement all sequence files in the current working directory: | |
40 | |
41 for file in *.embl; do perl revcom_seq.pl -o fasta "$file" > "${file%.embl}"_revcom.fasta; done | |
42 | |
43 ## Options | |
44 | |
45 - **-h**, **-help** | |
46 | |
47 Help (perldoc POD) | |
48 | |
49 - **-o**=*str*, **-outformat**=*str* | |
50 | |
51 Specify different sequence format for the output [fasta, embl, or gbk] | |
52 | |
53 - **-i**=*str*, **-informat**=*str* | |
54 | |
55 Specify the input sequence file format, only needed for *STDIN* input | |
56 | |
57 - **-v**, **-version** | |
58 | |
59 Print version number to *STDOUT* | |
60 | |
61 ## Output | |
62 | |
63 - *STDOUT* | |
64 | |
65 The reverse complemented sequence file is printed to *STDOUT*. | |
66 Redirect or pipe into another tool as needed. | |
67 | |
68 ## Run environment | |
69 | |
70 The Perl script runs under Windows and UNIX flavors. | |
71 | |
72 ## Dependencies | |
73 | |
74 - [**BioPerl**](http://www.bioperl.org) (tested version 1.007001) | |
75 | |
76 ## Author - contact | |
77 | |
78 Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster) | |
79 | |
80 ## Citation, installation, and license | |
81 | |
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). | |
83 | |
84 ## Changelog | |
85 | |
86 * v0.2 (2015-12-10) | |
87 * included a POD instead of a simple usage text | |
88 * included `pod2usage` with Pod::Usage | |
89 * included 'use autodie' pragma | |
90 * options with Getopt::Long | |
91 * output format now specified with option **-o** | |
92 * included version switch, **-v** | |
93 * allowed file and *STDIN* input, instead of only file; thus new option **-i** for input format | |
94 * output printed to *STDOUT* now, instead of output file | |
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. | |
96 * v0.1 (2013-02-08) |