PBstat

PBstat generates frequency and logo plots, and estimates something similar to entropy called the equivalent number of PBs (Neq).

Note

The following examples use PBdata and the demo files. See Demo files for more information.

Warning

To generate map or Neq plot, Matplotlib is required.

Warning

To generate Weblogo-like representations, Weblogo3 is required.

Example

$ PBstat -f `PBdata`/psi_md_traj_all.PB.count --map --neq --logo -o psi_md_traj_all
Index of first residue is: 1
wrote psi_md_traj_all.PB.map.png
wrote psi_md_traj_all.PB.Neq
wrote psi_md_traj_all.PB.Neq.png
wrote psi_md_traj_all.PB.logo.png

Usage

Here’s the PBstat help text.

usage: PBstat [-h] -f F -o O [--map] [--neq] [--logo]
              [--image-format {pdf,png,jpg}] [--residue-min RESIDUE_MIN]
              [--residue-max RESIDUE_MAX]

Statistical analysis and graphical representations of PBs.

optional arguments:
  -h, --help            show this help message and exit
  -f F                  name of file that contains PBs frequency (count)
  -o O                  name for results
  --map                 generate map of the distribution of PBs along protein
                        sequence
  --neq                 compute Neq and generate Neq plot along protein
                        sequence
  --logo                generate logo representation of PBs frequency along
                        protein sequence
  --image-format {pdf,png,jpg}
                        File format for all image output.
  --residue-min RESIDUE_MIN
                        defines lower bound of residue frame
  --residue-max RESIDUE_MAX
                        defines upper bound of residue frame

–map option

generates map of the distribution of PBs along protein sequence.

Warning

This option requires Matplotlib.

$ PBstat -f `PBdata`/psi_md_traj_all.PB.count --map -o psi_md_traj_all
Index of first residue is: 1
wrote psi_md_traj_all.PB.map.png

Distribution of PBs

The color range goes from red to blue. For a given position in the protein sequence, blue corresponds to a null frequency (meaning the particular PB is never met a this position) and red corresponds to a frequency of 1 (meaning the particular PB is always found at this position).

–neq option

computes Neq and generates Neq plot along protein sequence.

Warning

This option requires Matplotlib.

$ PBstat -f `PBdata`/psi_md_traj_all.PB.count --neq -o psi_md_traj_all
Index of first residue is: 1
wrote psi_md_traj_all.PB.Neq
wrote psi_md_traj_all.PB.Neq.png

Content of psi_md_traj_all.PB.Neq:

resid       Neq
1          1.00
2          1.00
3          2.03
4          1.92
5          3.12
6          2.14
[snip]

Neq versus residue number

–logo option

generates WebLogo-like representation of PBs frequency along protein sequence.

Warning

This option requires Weblogo3.

$ PBstat -f `PBdata`/psi_md_traj_all.PB.count --logo -o psi_md_traj_all
Index of first residue is: 1
wrote psi_md_traj_all.PB.logo.png

Logo representation of PBs frequency

–residue-min and –residue-max options

These options define the lower and upper bound of residue frame.

$ PBstat -f `PBdata`/psi_md_traj_all.PB.count --map --neq --logo -o psi_md_traj_all_frame --residue-min 15 --residue-max 42
Index of first residue is: 1
wrote psi_md_traj_all_frame.PB.map.15-42.png
wrote psi_md_traj_all_frame.PB.Neq.15-42
wrote psi_md_traj_all_frame.PB.Neq.15-42.png
wrote psi_md_traj_all_frame.PB.logo.15-42.png

PBs distribution with residue frame

Neq versus residue number with residue frame

Logo representation of PBs frequency

–image-format option

All figure can be produced in either PNG, PDF, or JPEG format. The –image-format option allows to control the file format of the image outputs.