''' 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