Python splitLines Examples

Example #1

File: runMatt.py Project: kmcnamara/sstrees

def runAlignment(pdb1, pdb2):
    Score = 0
    length = -1
    align = matt+' '+pdb_dir+pdb1+':'+pdb1[-5]+' '+pdb_dir+pdb2+':'+pdb2[-5]
    result = commands.getoutput(align)
    # Parse for the score and alignment length 
    result = splitLines('MattAlignment.txt')
    Score = float(result[3][2])
    length = float(result[1][2])
    Score = Score / length
    # Remove output files
    toremove = 'MattAlignment.fasta MattAlignment.pdb MattAlignment.spt '+\
               'MattAlignment.txt'
    removed = commands.getoutput('rm '+toremove)
    # Return the Score
    return str(Score)

Example #2

File: runMatt.py Project: kmcnamara/sstrees

    # Remove output files
    toremove = 'MattAlignment.fasta MattAlignment.pdb MattAlignment.spt '+\
               'MattAlignment.txt'
    removed = commands.getoutput('rm '+toremove)
    # Return the Score
    return str(Score)
# End of runAlignment

### End of Functions ###

### Main ###

print '\nRunning runMatt.py...'

# Read in the .pdb file names
pdbs = splitLines(sys.argv[1])

# Initialize distance matrix with zeros
Score_matrix = []
for row in range( len(pdbs) ):
    Score_matrix.append([])
    for col in range( len(pdbs) ):
        Score_matrix[row].append('0.0')

maxval = -1.0
for A in range( len(pdbs) ):
    for B in range( len(pdbs) ):
        if(B < A):
            # Fill in matrix[A][B] and matrix[B][A] with RMSD value
            Score_matrix[A][B] = runAlignment(pdbs[A][0], pdbs[B][0])
            Score_matrix[B][A] = Score_matrix[A][B]

Example #3

File: handleSeqTree.py Project: kmcnamara/sstrees

#!/usr/bin/python

# handleSeqTree.py
# Handle all the business involved in produced the sequence-based phylogenetic
# tree. Use pullSeqFromPDB.py to get all the needed .fa files. Then use
# runClustal.sh to produce the newick tree file.

# sys.argv[1] -- list of .pdb files

import sys, os, commands
from kmutils import fileToList, splitLines

scripts = '/home/kylem/BIMM185/scripts/'

files = splitLines( sys.argv[1] )

cat = 'cat '
for f in range( len(files) ):
  res = commands.getoutput( 'python '+scripts+'pullSeqFromPDB.py '+files[f][0] )
  cat += files[f][0][:-4] + '.fa '

res = commands.getoutput( cat + ' > allseqs.fa' )

res = commands.getoutput( 'sh '+scripts+'runClustal.sh allseqs.fa seqtree' )