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 with PBassign:
$ wget https://zenodo.org/record/259751/files/psi_md_traj_1.gro
$ wget https://zenodo.org/record/259751/files/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://zenodo.org/record/259751/files/psi_md_traj_2.gro
$ wget https://zenodo.org/record/259751/files/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
Example¶
$ PBcount -f psi_md_traj_1.PB.fasta -o psi_md_traj_1
read 90 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.
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)
-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
–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]