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genomes_feature_table ===================== `genomes_feature_table.pl` is a script to create a feature table for genomes in EMBL and GENBANK format. * [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 genomes_feature_table.pl path/to/genome_dir > feature_table.tsv ## Description A genome feature table lists basic stats/info (e.g. genome size, GC content, coding percentage, accession number(s)) and the numbers of annotated primary features (e.g. CDS, genes, RNAs) of genomes. It can be used to have an overview of these features in different genomes, e.g. in comparative genomics publications. `genomes_feature_table.pl` is designed to extract (or calculate) these basic stats and **all** annotated primary features from RichSeq files (**EMBL** or **GENBANK** format) in a specified directory (with the correct file extension, see option **-e**). The **default** directory is the current working directory. The primary features are counted and the results for each genome printed in tab-separated format. It is a requirement that each file contains **only one** genome (complete or draft, with or without plasmids). The most important features will be listed first, like genome description, genome size, GC content, coding percentage (calculated based on non-pseudo CDS annotation), CDS and gene numbers, accession number(s) (first..last in the sequence file), RNAs (rRNA, tRNA, tmRNA, ncRNA), and unresolved bases (IUPAC code 'N'). If plasmids are annotated in a sequence file, the number of plasmids are counted and listed as well (needs a */plasmid="plasmid_name"* tag in the *source* primary tag, see e.g. Genbank accession number [CP009167](http://www.ncbi.nlm.nih.gov/nuccore/CP009167)). Use option **-p** to list plasmids as separate entries (lines) in the feature table. For draft genomes the number of contigs/scaffolds are counted. All contigs/scaffolds of draft genomes should be marked with the *WGS* keyword (see e.g. draft NCBI Genbank entry [JSAY00000000](http://www.ncbi.nlm.nih.gov/nuccore/JSAY00000000)). If this is not the case for your file(s) you can add those keywords to each sequence entry with the following Perl one-liners (will edit files in place). For files in **GENBANK** format if 'KEYWORDS .' is present perl -i -pe 's/^KEYWORDS(\s+)\./KEYWORDS$1WGS\./' file or if 'KEYWORDS' isn't present at all perl -i -ne 'if(/^ACCESSION/){ print; print "KEYWORDS WGS.\n";} else{ print;}' file For files in **EMBL** format if 'KW .' is present perl -i -pe 's/^KW(\s+)\./KW$1WGS\./' file or if 'KW' isn't present at all perl -i -ne 'if(/^DE/){ $dw=1; print;} elsif(/^XX/ && $dw){ print; $dw=0; print "KW WGS.\n";} else{ print;}' file ## Usage perl genomes_feature_table.pl -p -e gb,gbk > feature_table_plasmids.tsv perl genomes_feature_table.pl path/to/genome_dir/ -e gbf -e embl > feature_table.tsv ## Options - -h, -help Help (perldoc POD) - -e, -extensions File extensions to include in the analysis (EMBL or GENBANK format), either comma-separated list or multiple occurences of the option [default = ebl,emb,embl,gb,gbf,gbff,gbank,gbk,genbank] - -p, -plasmids Optionally list plasmids as extra entries in the feature table, if they are annotated with a */plasmid="plasmid_name"* tag in the *source* primary tag - -v, -version Print version number to *STDERR* ## Output - *STDOUT* The resulting feature table is printed to *STDOUT*. Redirect or pipe into another tool as needed (e.g. `cut`, `grep`, or `head`). ## Run environment The Perl script runs under Windows and UNIX flavors. ## Dependencies - [BioPerl](http://www.bioperl.org) (tested version 1.006923) ## 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 - v0.5 (14.09.2015) - changed script name to `genomes_feature_table.pl` - included a POD - options with Getopt::Long - included `pod2usage` with Pod::Usage - major code overhaul with restructuring (removing code redundancy, print out without temp file etc.) and Perl syntax changes - changed input options to get folder path from STDIN - as a consequence new option **-e|-extensions** - accession numbers not essential anymore, changed hash key to filename; but requires now only one genome per file - draft genomes should include 'WGS' keyword (warning if not) - option **-p|-plasmids** works now correctly with complete and draft genomes - count plasmids without option **-p** - v0.4 (11.08.2013) - included 'use autodie;' pragma - included version switch - v0.3 (05.11.2012) - new option **p** to report plasmid features in multi-sequence draft files separately - v0.2 (19.09.2012) - v0.1 (25.11.2011) - **original** script name: `get_genome_features.pl`