PBcount¶
PBcount
computes the frequency of PBs at each position along the amino acid sequence.
Note
- The following examples require
psi_md_traj.PB.fasta
and psi_md_traj2.PB.fasta
obtained withPBassign
:
$ 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
If needed, you can download [psi_md_traj_1.PB.fasta](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.PB.fasta) and [psi_md_traj_2.PB.fasta](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_2.PB.fasta).
Example¶
$ PBcount -f psi_md_traj_1.PB.fasta -o psi_md_traj_1
read 225 sequences in psi_md_traj_1.PB.fasta
wrote psi_md_traj_1.PB.count
Content of psi_md_traj_1.PB.count:
a b c d e f g h i j k l m n o p
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 0 4 0 221 0 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 5 0 0 0 0 220 0 0 0 0 0
[snip]
51 0 0 0 0 0 56 0 98 0 0 71 0 0 0 0 0
52 0 56 0 0 0 0 0 0 94 3 3 69 0 0 0 0
53 144 0 60 2 0 0 0 0 0 0 0 0 1 0 0 18
54 0 0 225 0 0 0 0 0 0 0 0 0 0 0 0 0
55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Note that residues 1, 2, 55 and 56 have a null count of all PBs. These residues are the first and last residues of the structure and no PB can be assigned to them.
If needed, you can download [psi_md_traj_1.PB.count](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.PB.count).
Usage¶
Here’s the PBcount
help text.
usage: PBcount [-h] -f F -o O [--first-residue FIRST_RESIDUE]
Compute PB frequency along protein sequence.
optional arguments:
-h, --help show this help message and exit
-f F name(s) of the PBs file (in fasta format)
-o O name for results
--first-residue FIRST_RESIDUE
define first residue number (1 by default)
-v, --version show program's version number and exit
-f option¶
can be used several times:
$ 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
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).
–first-residue option¶
By default, the number of the first residue is 1, this option allows to adjust the number associated to the first residue (and to the followings automaticaly).
$ PBcount --first-residue 5 -f psi_md_traj_1.PB.fasta -o psi_md_traj_1_shifted
read 225 sequences in psi_md_traj_1.PB.fasta
wrote psi_md_traj_1_shifted.PB.count
Content of psi_md_traj_1_shifted.PB.count:
a b c d e f g h i j k l m n o p
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 4 0 221 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 5 0 0 0 0 220 0 0 0 0 0
9 0 222 0 0 0 0 0 0 0 0 0 3 0 0 0 0
10 6 0 201 0 0 5 0 0 0 0 0 0 12 0 1 0
[snip]
If needed, you can download [psi_md_traj_1_shifted.PB.count](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1_shifted.PB.count).