--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COG/bac-genomics-scripts/revcom_seq/README.md	Thu May 30 11:52:25 2024 +0000
@@ -0,0 +1,96 @@
+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)