REDUCE Suite

The LogoGenerator utility program in the REDUCE Suite is a versatile and robust command-line tool that generates logo images in a variety of styles (raw data, frequency, conventional bit information, or affinity logo in ΔΔG). The input can be either a PSAM, or other common formats (such as a PWM, a multiple sequence alignment file in either FASTA or flat format) converted to a pseudo-PSAM via the utility program Convert2PSAM. The output logo image is in EPS format and is converted to PNG format by default for display in a web page (as from HTMLSummary), using the widely and freely available tool GhostScript tool gs. Other supported image formats include PDF, JPEG, and GIF (further utilizing the convert utility program from ImageMagick).

LogoGenerator [options] -file=PSAM_File

  Required parameters:
    -file=PSAM_file     --- name of the PSAM matrix file to get a logo

  Optional parameters:
    [-output=dir_name]  --- path to the output directory (./)
    [-logo=IMAGE_file]  --- name of output logo image file (base-filename.png)
    [-format=IMAGE_FMT] --- image format of the logo: eps|pdf|jpeg|png (png)
                            Note: o pdf, jpeg and png formats make use of "gs",
                                  o check 'pkg_settings.cfg' for settings
    [-style=LOGO_STYLE] --- style of the logo: raw|freq|bits_info|ddG (bits_info)
    [-type=INPUT_TYPE]  --- input type for generating the logo: PSAM|fasta|flat
                            If in 'fasta' or 'flat' format, the sequences must be
                            already aligned and of the same length (PSAM)
    [-title=string]     --- title string of the logo image
    [-width=float]      --- logo width in cm (12)
    [-height=float]     --- logo height in cm (7.5)
    [-ymin=float]       --- minimum value on the y-axis
    [-ymax=float]       --- maximum value on the y-axis
    [-frame]            --- switch for drawing a bounding box around the logo
    [-bw]               --- switch for black-and-white the logo image
    [-reverse_comp]     --- draw logo based on reverse complementary strand
    [-rna]              --- draw RNA logo (i.e., using U instead of T)

  Usage:
      LogoGenerator -file=$REDUCE_SUITE/data/formats/psam_ex.dat -logo=sample.png

  Note:
      For non-PSAM file formats (e.g., PWM), please see 'Convert2PSAM'