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1. BioGetC

   Purpose: In order to use BioTriangle more friendly, we provide this script tool to allow users to download the molecules by providing their IDs such as CAS, NCBI, KEGG, EBI and Drugbank.
   Prerequisites: Python 2.7, Pybel, Python-rdkit
   Sample usage:
   

   from BioGetC import GetMolFromCAS
   cas=['3522-86-9', '106-22-9', '15766-66-2','50-12-4']
   res=[]
   for i in cas:
       temp=GetMolFromCAS(i)
       res.append(temp)
   print res

   Download: Version 1.0
   

2. BioGetP

   Purpose: BioGetP is used to download the protein sequence from the uniprot (http://www.uniprot.org/) website. You can only need input a protein ID or prepare a file (ID.txt) related to ID. You can obtain a .txt (ProteinSequence.txt) file saving protein sequence you need. You can freely use and distribute it. If you hava any problem, you could contact us timely!
   Prerequisites: Python 2.7
   Sample usage:
   

   import BioGetP
   import os
   path=os.getcwd()  ##please run the script in the directory containing the files
   flag=GetProteinSequenceFromTxt(os.getcwd()+'/',"ID.txt","ProteinSequence.txt")
   print flag

   Download: Version 1.0
   

3. BioGetPDB

   Purpose: BioGetPDB is used to download the protein sequence from the PDB (http://www.rcsb.org/pdb) website. You can only need input a PDB ID or prepare a file (ID.txt) related to ID. You can obtain a *.pdb or *.fasta file saving protein sequence you need. Besides, the function BioCPI_txt() allows users to prepare the input file for BioCPI, BioPPI, BioDPI just by one step.
   Prerequisites: Python 2.7, csb
   Sample usage:
   

   import BioGetPDB
   ss = BioGetPDB.fasta_file('/home/cbdd/pdbid.txt', 'pdbentries.fasta')
   mm = BioGetPDB.protein_pdb('1YCR', 'pdbfile.pdb')
   nn = BioGetPDB.protein_pdb_batch('/home/cbdd/pdbid.txt', os.getcwd() + '/pdb/')
   pp = BioGetPDB.BioCPI_txt('/home/cbdd/pdbid.txt', 'biocpitest.txt')

   Download: Version 1.0
   

4. BioGetGenBank

   Purpose: BioGetGenBank is used to download the DNAs/RNAs, mRNAs, protein sequence from the GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) website. You can only need input a GenBank ID (gi) or prepare a file (gilist.txt) related to ID. Then, you can obtain a *.fasta file saving sequences you need.
   Prerequisites: Python 2.7
   Sample usage:
   

   import BioGetGenBank
   BioGetGenBank.get_nucleotide_gi_fasta('392893239')
   print '#' * 20
   
   BioGetGenBank.get_nucleotide_gi_fasta_list('gilist.txt')
   print '#' * 20
   
   BioGetGenBank.get_protein_gi_fasta('344243512')
   print '#' * 20
   
   BioGetGenBank.get_protein_gi_fasta_list('gilist_protein.txt')
   print '#' * 20

   Download: Version 1.0
   

5. BioModel

   Purpose: The script is used to construct the prediction models based on the data matrix generated by BioTriangle. The users could select different machine learning methods to construct their models. It should be noted that all functions are based on the scikit-learn package.
   Prerequisites: Python 2.7, Python-sklearn
   Download: Version 1.0