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+po2anno
+=======
+
+`po2anno.pl` is a script to create an annotation comparison matrix from [Proteinortho5](http://www.bioinf.uni-leipzig.de/Software/proteinortho/) output.
+
+* [Synopsis](#synopsis)
+* [Description](#description)
+* [Usage](#usage)
+  * [cds_extractor](#cds_extractor)
+  * [Proteinortho5](#proteinortho5)
+  * [po2anno](#po2anno)
+* [Options](#options)
+  * [Mandatory options](#mandatory-options)
+  * [Optional options](#optional-options)
+* [Output](#output)
+* [Run environment](#run-environment)
+* [Author - contact](#author---contact)
+* [Citation, installation, and license](#citation-installation-and-license)
+* [Changelog](#changelog)
+
+## Synopsis
+
+    perl po2anno.pl -i matrix.proteinortho -d genome_fasta_dir/ -l -a > annotation_comparison.tsv
+
+## Description
+
+Supplement an ortholog/paralog output matrix from a
+[**Proteinortho5**](http://www.bioinf.uni-leipzig.de/Software/proteinortho/)
+calculation with annotation information. The resulting tab-separated
+annotation comparison matrix (ACM) is mainly intended for the
+transfer of high quality annotations from reference genomes to
+homologs (orthologs and co-orthologs/paralogs) in a query genome
+(e.g. in conjunction with [`tbl2tab.pl`](/tbl2tab)). But of course
+it can also be used to have a quick glance at the annotation of
+genes present only in a couple of input genomes in comparison to the
+others.
+
+Annotation is retrieved from multi-FASTA files created with
+[`cds_extractor.pl`](/cds_extractor). See
+[`cds_extractor.pl`](/cds_extractor) for a description of the
+format. These files are used as input for the PO analysis and option
+**-d** for `po2anno.pl`.
+
+**Proteinortho5** (PO) has to be run with option **-singles** to include
+also genes without orthologs, so-called singletons/ORFans, for each
+genome in the PO matrix (see the
+[PO manual](http://www.bioinf.uni-leipzig.de/Software/proteinortho/manual.html)).
+Additionally, option **-selfblast** is recommended to enhance paralog
+detection by PO.
+
+Each orthologous group (OG) is listed in a row of the resulting ACM,
+the first column holds the OG numbers from the PO input matrix (i.e.
+line number minus one). The following columns specify the
+orthologous CDS for each input genome. For each CDS the ID,
+optionally the length in bp (option **-l**), gene, EC number(s), and
+product are shown depending on their presence in the CDS's
+annotation. The ID is in most cases the locus tag (see
+[`cds_extractor.pl`](/cds_extractor)). If several EC numbers exist
+for a single CDS they're separated by ';'. If an OG includes
+paralogs, i.e. co-orthologs from a single genome, these will be
+printed in the following row(s) **without** a new OG number in the
+first column. The order of paralogous CDSs within an OG is
+arbitrarily.
+
+The OGs are sorted numerically via the query ID (see option **-q**).
+If option **-a** is set, the non-query OGs are appended to the output
+after the query OGs, sorted numerically via OG number.
+
+## Usage
+
+### [`cds_extractor`](/cds_extractor)
+
+    for i in *.[gbk|embl]; do perl cds_extractor.pl -i $i [-p|-n]; done
+
+### [**Proteinortho5**](http://www.bioinf.uni-leipzig.de/Software/proteinortho/)
+
+    proteinortho5.pl -graph [-synteny] -cpus=# -selfblast -singles -identity=50 -cov=50 -blastParameters='-use_sw_tback [-seg no|-dust no]' *.[faa|ffn]
+
+### po2anno
+
+    perl po2anno.pl -i matrix.[proteinortho|poff] -d genome_fasta_dir/ -q query.[faa|ffn] -l -a > annotation_comparison.tsv
+
+## Options
+
+### Mandatory options
+
+- **-i**=_str_, **-input**=_str_
+
+    Proteinortho (PO) result matrix (\*.proteinortho or \*.poff), or piped *STDIN* (-)
+
+- **-d**=_str_, **-dir\_genome**=_str_
+
+    Path to the directory including the genome multi-FASTA PO input files (\*.faa or \*.ffn), created with [`cds_extractor.pl`](/cds_extractor)
+
+### Optional options
+
+- **-h**, **-help**
+
+    Help (perldoc POD)
+
+- **-q**=_str_, **-query**=_str_
+
+    Query genome (has to be identical to the string in the PO matrix) [default = first one in alphabetical order]
+
+- **-l**, **-length**
+
+    Include length of each CDS in bp
+
+- **-a**, **-all**
+
+    Append non-query orthologous groups (OGs) to the output
+
+- **-v**, **-version**
+
+    Print version number to *STDERR*
+
+## Output
+
+- *STDOUT*
+
+    The resulting tab-delimited ACM is printed to *STDOUT*. Redirect or pipe into another tool as needed (e.g. `cut`, `grep`, `head`, or `tail`).
+
+## Run environment
+
+The Perl script runs under Windows and UNIX flavors.
+
+## 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
+
+* v0.2.2 (23.10.2015)
+    * minor syntax changes to `po2anno.pl` and README
+    * changed option **-g|-genome_dir** to **-d|-dir_genome** for consistency with [`po2group_stats.pl`](/po2group_stats)
+* v0.2.1 (07.09.2015)
+    * get rid of underscores in product annotation strings (from [`cds_extractor.pl`](/cds_extractor))
+    * debugged hard-coded relative path for `$genome_file_path`
+* v0.2 (15.01.2015)
+    * give number of query-specific OGs and total query singletons/ORFans in final stat output
+    * changed final stat output to an easier readable format
+    * fixed bug: %Query_ID_Seen included also non-query IDs, which luckily had no consequences
+* v0.1 (18.12.2014)