klpek / python_scripts Goto Github PK

'''
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

#### 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