'''
Chengxin's own python/shell scripts repository.
All scripts are licensed under LGPL v2+.
All scripts can be directly called by command line.
When launched without argument, a short documentation will be displayed.
All python scripts are importable by python.
'''
#### sequence parsing ####
fasta2pfam.py # convert FASTA file to Pfam file
pfam2fasta.py # convert Pfam file to FASTA file
NWalign.py # global sequence alignment
seq_similarity.py # sequence identity matrix for MSA
split_fasta.py # split multi sequence FASTA into one sequence FASTA
fasta2len.py # list the length of entries in fasta sequence
#### structure parsing ####
contact_pdb.py # calculate residue contacts
reindex_pdb.py # renumber residue number of PDB file
fixMSE.py # fix MSE and other nonstandard residues in PDB
fetch.py,fetch.sh # fetch PDB from RCSB PDB according to PDB id, Uniprot
# accession, or Pfam family id
reptra2pdb.py # convert I-TASSER format decoy file rep*.tra*.bz2 to PDB
superpose.py # superpose two structures
initdat2pdb.py # convert LOMETS threading result init.dat to PDB
HomologyModelling.py # homology modelling by MODELLER
strip_sidechain.py # remove side
DomainParser.py # partition a PDB chain into domains
split_uniprot.py # partition a PDB file into different uniprot ID
pdb2fasta.py # convert PDB file to fasta file
xvg2png.py # plot gromacs xvf file to png image
batch_pdb_image.py # gallery view of many pdb files
#### GO parsing ####
obo2csv.py # parsing obo format GO defination file
#### regular expression ####
grep-GO.sh # uniquely grep all GO terms in plain text
grep-uniprot.sh # uniquely grep all uniprot accession in plain text
#### mathematics ultility ####
getPvalue.py # calculate Student's T test p-value
#### system ultility ####
read_mail.py # read system mail