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revcom_seq ========== `revcom_seq.pl` is a script to reverse complement (multi-)sequence files. * [Synopsis](#synopsis) * [Description](#description) * [Usage](#usage) * [Options](#options) * [Output](#output) * [Run environment](#run-environment) * [Dependencies](#dependencies) * [Author - contact](#author---contact) * [Citation, installation, and license](#citation-installation-and-license) * [Changelog](#changelog) ## Synopsis perl revcom_seq.pl seq-file.embl > seq-file_revcom.embl **or** perl cat_seq.pl multi-seq_file.embl | perl revcom_seq.pl -i embl > seq_file_cat_revcom.embl ## Description This script reverse complements (multi-)sequence files. The features/annotations in RichSeq files (e.g. EMBL or GENBANK format) will also be adapted accordingly. Use option **-o** to specify a different output sequence format. Input files can be given directly via *STDIN* or as a file. If *STDIN* is used, the input sequence file format has to be given with option **-i**. Be careful to set the correct input format. ## Usage perl revcom_seq.pl -o gbk seq-file.embl > seq-file_revcom.gbk **or** reverse complement all sequence files in the current working directory: for file in *.embl; do perl revcom_seq.pl -o fasta "$file" > "${file%.embl}"_revcom.fasta; done ## Options - **-h**, **-help** Help (perldoc POD) - **-o**=*str*, **-outformat**=*str* Specify different sequence format for the output [fasta, embl, or gbk] - **-i**=*str*, **-informat**=*str* Specify the input sequence file format, only needed for *STDIN* input - **-v**, **-version** Print version number to *STDOUT* ## Output - *STDOUT* The reverse complemented sequence file is printed to *STDOUT*. Redirect or pipe into another tool as needed. ## Run environment The Perl script runs under Windows and UNIX flavors. ## Dependencies - [**BioPerl**](http://www.bioperl.org) (tested version 1.007001) ## Author - contact Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster) ## Citation, installation, and license 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). ## Changelog * v0.2 (2015-12-10) * included a POD instead of a simple usage text * included `pod2usage` with Pod::Usage * included 'use autodie' pragma * options with Getopt::Long * output format now specified with option **-o** * included version switch, **-v** * allowed file and *STDIN* input, instead of only file; thus new option **-i** for input format * output printed to *STDOUT* now, instead of output file * fixed bug, that only first sequence in multi-sequence file is reverse complemented. Now all sequences in a multi-seq file are reverse complemented. * v0.1 (2013-02-08)