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Command Line Tool
Contents
| Usage | Back to top |
$ ruby gene_painter.rb -i <alignment> -p <yaml_files> [<options>]
| -i or --input | Path to fasta-formatted multiple sequence alignment |
| -p or --path | Path to folder containing gene structures in YAML or GFF format |
| Standard output format | Mark exons by '-' and introns by '|' |
| Options | Back to top |
Text-based output format
| --intron-phase | Mark introns by their phase instead of '|' |
| --phylo | Mark exons by '0' and introns by '1' |
| --spaces | Mark exons by space (' ') instead of '-' |
| --no-standard-output | Specify to skip standard output format. |
| --alignment | Output the alignment file with additional lines containing intron phases |
| --fuzzy N | Introns at most N base pairs apart from each other are aligned |
Graphical output format
| --svg | Draw a graphical representation of genes in SVG format. |
| --svg-format FORMAT | Switch between different formats. FORMAT must be one of "normal", "reduced" or "both"] "normal" draws details of aligned exons and introns [default] "reduced" focuses on common introns only "both" draws both formats |
| --pdb FILE | Mark consensus or merged gene structure in pdb FILE Consenus gene structure contains introns conserved in N % of all genes Specify N with option --consensus N; [default: 80%] Two scripts for execution in PyMol are provided: 'color_exons.py' to mark consensus exons 'color_splicesites.py' to mark splice junctions of consensus exons |
| --pdb-chain CHAIN | Mark gene structures for chain CHAIN. [default: Use chain A] |
| --pdb-ref-prot PROT | Use protein PROT as reference for alignment with pdb sequence. [default: First protein in alignment] |
| --pdb-ref-prot-struct | Color only intron positions occuring in the reference protein structure. |
| --tree | Generate newick tree file and SVG representation |
Meta information and statistics
| --consensus N | Mark all introns conserved in N % genes. Specify N as decimal number between 0 and 1. |
| --merge | Merge all introns into a single exon intron pattern |
| --statistics | Output additional file with statistics about common introns. To include information about taxomony, specify options --taxomony and ‑‑taxonomy‑to‑fasta. |
Taxonomy
| --taxonomy FILE | Use this option to mark introns by taxonomy. NCBI taxonomy database dump file FILE OR Excerpt of NCBI taxonomy. Lineage must be semicolon-separated list of taxa from root to species. |
| --taxonomy-to-fasta FILE | Text-based file mapping gene structure file names to species names. One or more genes given as semicolon-separated list and species name. Delimiter between gene list and species name must be a colon. The species name itself must be enclosed by double quotes like this "SPECIES" |
| --taxonomy-common-to X,Y,Z | Mark introns common to taxa X,Y,Z. List must consist of at least one NCBI taxon (scientific name) |
| --[no-]exclusively-in-taxa | Mark introns occuring (not) exclusively in listed taxa. [default: not exclusively] |
| --introns-per-taxon | Mark newly gained introns for every inner node in taxonomy. |
Parse NCBI taxonomy
| --no-grep | Read the NCBI taxomony dump into RAM. This will require some additional hundert MBs of RAM. [default: taxomony dump is parsed with grep calls] |
| --nice | Run grep calls with lower priority. Please make sure to have nice in your executable path when using this option. |
Analysis and output of all or subset of data
| --analyse-all-output-all | Analyse all data and provide full output [default] |
| --analyse-all-output-selection | Analyse all data and provide text-based and graphical output for selection only. All introns are analysed, including those not present in selection |
| ‑‑analyse‑selection-output‑selection | Analyse selected data and provide output for selection only |
| ‑‑analyse‑selection‑on‑all‑data-output‑selection | Analyse intron positions of selected data in all data and provide output for selection only. Introns present in selection are analysed in all data |
Selection criteria for data and output selection
| --select-all | No selection applied (default) |
| --selection-based-on-regex "REGEX" | Regular expression applied on gene structure file names. Regex must be enclosed by double quotes |
| --selection-based-on-list X,Y,Z | List of gene structures to be used |
| --selection-based-on-species SPECIES | Use all gene structures associated with species. Specify also --taxonomy-to-fasta to map gene structure file names to species names |
General options
| -o or --outfile FILENAME | Prefix of the output files. |
| --path-to-output PATH | Path to the location where output files should be stored. |
| --range START,STOP | Restrict genes to range START-STOP in alignment |
| --[no-]delete-range | (Not) Delete specified range |
| --keep-common-gaps | Keep common gaps in alignment. This option effects only output of --alignment |
| --no-best-position-introns | Plot introns always onto beginning of a gap. Default: Align introns if their position differs by alignment gaps only |
| --[no-]separate-introns-in-textbased-output | (Not) Separate each consecutive pair of introns by an exon placeholder in text-based output formats. Default: Separate introns unless the output lines get too long. |
| -h or --help | List all options available. |
| Changes in command line parameters from v.1.0 to v.2.0 | Back to top |
| v.1.0 parameter | v.2.0 parameter |
| -a | --alignment |
| -n | --intron-phase |
| -phylo | --phylo |
| -s | --spaces |
| -svg WIDTH,HEIGHT FORMAT | --svg and --svg-format |
| -start START and -stop STOP | --range START,STOP |
| -pdb | --pdb |
| -pdb_prot | --pdb-ref-prot |
| -ref_prot_struct | --pdb-ref-prot-struct |
| -consensus | --consensus, no longer restricted to combination with -pdb |
| -f and -penalize_endgaps | obsolete |
