#!/usr/bin/env python import locale import os, sys, re locale.setlocale(locale.LC_NUMERIC, "") class Table: def format_num(self, num): """Format a number according to given places. Adds commas, etc. Will truncate floats into ints!""" try: if "." in num: inum = float(num) return locale.format("%.2f", (0, inum), True) else: inum = int(num) return locale.format("%.*f", (0, inum), True) except (ValueError, TypeError): return str(num) def get_max_width(self, table, index): """Get the maximum width of the given column index""" return max([len(self.format_num(row[index])) for row in table]) def pprint_table(self, table): """Prints out a table of data, padded for alignment @param table: The table to print. A list of lists. Each row must have the same number of columns. """ col_paddings = [] out = "" for i in range(len(table[0])): col_paddings.append(self.get_max_width(table, i)) for row in table: # left col out += str(row[0]).ljust(col_paddings[0] + 1) # rest of the cols for i in range(1, len(row)): col = self.format_num(row[i]).rjust(col_paddings[i] + 2) out += col out += "\n" return out # def Xmaketable(self): # """ # DEPRECATED - we just use the resultsTable.dat files # Go through the MRBUMP directories and parse the output files to get the results # """ # table = [] # # if not self.cluster: # for run in os.listdir(self.bumppath): # if re.search('search', run): # # print run # name = re.split('_', run) # sidechains = name[1] # if sidechains == 'SCWRL': # trunc = name[5] # rad = name[7] # else: # trunc = name[4] # rad = name[6] # trunc = str(round(float(trunc))) # #phaser # phasersucc = '' # phaserCC = 'none' # phaserFreeR = 'none' # if os.path.exists(os.path.join(self.bumppath, run, 'phaser_shelx' ) ): # if os.path.exists( os.path.join(self.bumppath, run, 'phaser_shelx', 'orig.pdb' )): # for line in open(os.path.join(self.bumppath, run, 'phaser_shelx', 'orig.pdb' )): # if re.search('CC', line): # split = re.split('CC\s*=\s*(\d*\.\d*)',line) # score = split[1] # phaserCC = score # # if os.path.exists( os.path.join(self.bumppath, run, 'phaser_shelx', 'refined.pdb' )): # for line in open(os.path.join(self.bumppath, run, 'phaser_shelx', 'refined.pdb' )): # if re.search('REMARK\s*(\d*)\s*FREE R VALUE\s*\:', line): # split = re.split('REMARK\s*(\d*)\s*FREE R VALUE\s*\:\s*(\d*\.\d*)',line) # score = split[2] # phaserFreeR = score # # # #print phaserCC # if phaserCC != 'none': # if float(phaserCC) > 25: # phasersucc = 'Solution' # else: # phasersucc = '' # table.append([phasersucc,'',trunc, sidechains, 'Phaser',phaserFreeR,float(phaserCC)]) # # # # # #molrep # molrepsucc = '' # molrepCC = 'none' # molrepFreeR = 'none' # if os.path.exists(os.path.join(self.bumppath, run, 'molrep_shelx' ) ): # if os.path.exists( os.path.join(self.bumppath, run, 'molrep_shelx', 'orig.pdb' )): # for line in open(os.path.join(self.bumppath, run, 'molrep_shelx', 'orig.pdb' )): # if re.search('CC', line): # split = re.split('CC\s*=\s*(\d*\.\d*)',line) # score = split[1] # molrepCC = score # # if os.path.exists( os.path.join(self.bumppath, run, 'molrep_shelx', 'refined.pdb' )): # for line in open(os.path.join(self.bumppath, run, 'molrep_shelx', 'refined.pdb' )): # if re.search('REMARK\s*(\d*)\s*FREE R VALUE\s*\:', line): # split = re.split('REMARK\s*(\d*)\s*FREE R VALUE\s*\:\s*(\d*\.\d*)',line) # score = split[2] # molrepFreeR = score # # #print molrepCC # if molrepCC != 'none': # if float(molrepCC) > 25: # molrepsucc = 'Solution' # else: # molrepsucc = '' # table.append([molrepsucc,'',trunc, sidechains, 'Molrep',molrepFreeR,float(molrepCC)]) # # # # if self.cluster: # table = [] # for run in os.listdir(self.bumppath): # if os.path.isdir(os.path.join(self.bumppath, run )): # #phaser # #print os.path.join(self.bumppath, run ) # for search in os.listdir(os.path.join(self.bumppath, run )): # if re.search('search' , search): # phaser = '' # molrep = '' # phaserCC ='none' # molrepCC ='none' # phasersucc = '' # phaserFreeR = '' # molrepFreeR = '' # if os.path.exists(os.path.join(self.bumppath, run , search, 'phaser_shelx' )): # print 'got' , os.path.join(self.bumppath, run , search, 'phaser_shelx' ) # for pdb in os.listdir(os.path.join(self.bumppath, run , search, 'phaser_shelx' )): # if re.search('refmac_phaser', pdb): # print pdb # # name = re.split('_', pdb) # print name # sidechains = name[4] # if sidechains == 'SCWRL': # trunc = name[8] # else: # trunc = name[7] # print trunc # trunc = str(round(float(trunc))) # if os.path.exists(os.path.join(self.bumppath, run , search, 'phaser_shelx', 'orig.pdb' )): # # for line in open(os.path.join(self.bumppath, run,search, 'phaser_shelx', 'orig.pdb' )): # if re.search('CC', line): # split = re.split('CC\s*=\s*(\d*\.\d*)',line) # score = split[1] # phaserCC = score # if phaserCC != 'none': # if float(phaserCC) > 25: # phasersucc = 'Solution' # else: # phasersucc = '' # table.append([phasersucc,'',trunc, sidechains, 'Phaser',phaserFreeR,float(phaserCC)]) # # # if os.path.exists(os.path.join(self.bumppath, run , search, 'molrep_shelx', 'orig.pdb' )): # # for line in open(os.path.join(self.bumppath, run, search, 'molrep_shelx', 'orig.pdb' )): # if re.search('CC', line): # split = re.split('CC\s*=\s*(\d*\.\d*)',line) # score = split[1] # molrepCC = score # # if molrepCC != 'none': # if float(molrepCC) > 25: # molrepsucc = 'Solution' # else: # molrepsucc = '' # table.append([molrepsucc,'',trunc, sidechains, 'Molrep',molrepFreeR,float(molrepCC)]) # # # # # table.sort(key=lambda x: x[6]) # table = table[::-1] # x=1 # for i in table: # # print i # i[1] = x # x+=1 # table.insert(0,["", "Ensemble No", "Truncation level", "Side chain type", "MR program", "Final Rfree", "Shelxe CC"] ) # return table if __name__ == "__main__": T=Table() T.bumppath = '/home/jmht/ample-dev1/examples/toxd-example/ROSETTA_MR_3/MRBUMP/cluster_run1' T.cluster = True table = T.maketable() out = sys.stdout T.pprint_table(out, table) print 'done' # table = [["", "Ensemble No", "Truncation level", "Side chain type", "MR program", "Final Rfree", "Shelxe CC"], # ["spam", 1, 2, "All", "Phaser", 0.25, 23.51], # ["eggs", 2, 6, "Reliable", "Molrep", 0.45, 4.56], # ["lumberjacks", 3, 10, "Poly", "Phaser", 0.53, 12.12]] # import sys # out = sys.stdout # # T.pprint_table(out, table)