klpek / python_scripts Goto Github PK
View Code? Open in Web Editor NEWThis project forked from kad-ecoli/python_scripts
scripts for parsing PDB, fasta, and GO
This project forked from kad-ecoli/python_scripts
scripts for parsing PDB, fasta, and GO
''' 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
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.