PBstat¶
PBstat
generates frequency and logo plots, and estimates something similar
to entropy called the equivalent number of PBs (Neq).
Note
The following examples require psi_md_traj_all.PB.count
obtained with PBassign and then PBcount:
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.gro
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.xtc
$ PBassign -x psi_md_traj_1.xtc -g psi_md_traj_1.gro -o psi_md_traj_1
Frame 1/225.
Frame 100/225.
Frame 200/225.
Frame 225/225.
wrote psi_md_traj_1.PB.fasta
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_2.gro
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_2.xtc
$ PBassign -x psi_md_traj_2.xtc -g psi_md_traj_2.gro -o psi_md_traj_2
Frame 1/225.
Frame 100/225.
Frame 200/225.
Frame 225/225.
wrote psi_md_traj_2.PB.fasta
$ PBcount -f psi_md_traj_1.PB.fasta -f psi_md_traj_2.PB.fasta -o psi_md_traj_all
read 225 sequences in psi_md_traj_1.PB.fasta
read 225 sequences in psi_md_traj_2.PB.fasta
wrote psi_md_traj_all.PB.count
Warning
To generate Weblogo-like representations, Weblogo3 is required.
If needed, you can download [psi_md_traj_all.PB.count](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_all.PB.count).
Example¶
$ PBstat -f psi_md_traj_all.PB.count --map --neq --logo -o psi_md_traj_all
Index of first residue in psi_md_traj_all.PB.count is 1
First residue in the output file(s) 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
-v, --version show program's version number and exit
–map option¶
generates map of the distribution of PBs along protein sequence.
$ PBstat -f psi_md_traj_all.PB.count --map -o psi_md_traj_all
Index of first residue in psi_md_traj_all.PB.count is 1
First residue in the output file(s) is 1
wrote psi_md_traj_all.PB.map.png
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.
$ PBstat -f psi_md_traj_all.PB.count --neq -o psi_md_traj_all
Index of first residue in psi_md_traj_all.PB.count is 1
First residue in the output file(s) 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 1.90
4 1.91
5 2.87
6 2.30
[snip]
–logo option¶
generates WebLogo-like representation of PBs frequency along protein sequence.
Warning
This option requires Weblogo3.
$ PBstat -f 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
–residue-min and –residue-max options¶
These options define the lower and upper bound of residue frame.
$ PBstat -f 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 in psi_md_traj_all.PB.count is 1
First residue in the output file(s) is 15
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
–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.