import sys import os from parameter import Parameter p = Parameter("stream.reads.") reads_1 = p._("1") reads_2 = p._("2") os.system("paste -d '\n' {0} {1}".format(reads_1, reads_2))
import sys from parameter import Parameter from common import Dictionary p = Parameter("release.") release = p._("path") dic = Dictionary(p._("dictionary")) for line in sys.stdin: entry = line.strip().split("\t") id = int(entry[0]) l = int(entry[1]) score = entry[2] contig = dic._(id) name = contig[0] cls = contig[2] print "{0}\t{1}\t{2}\t{3}\t{4}\t{5}".format(id, name, cls, contig[1], l, score)
import os from parameter import Parameter p = Parameter() # create dir tree dir = p._('project.dir') name = p._('project.wizard.create.name') project_dir = dir + '/' + name os.system('rm -rf {}'.format(project_dir)) os.system('mkdir {}'.format(project_dir)) os.system('mkdir {}/data'.format(project_dir)) os.system('mkdir {}/data/structure'.format(project_dir)) os.system('mkdir {}/data/structure/receptor'.format(project_dir)) os.system('mkdir {}/data/structure/ligand'.format(project_dir)) os.system('mkdir {}/docking'.format(project_dir)) os.system('mkdir {}/docking/receptor'.format(project_dir)) os.system('mkdir {}/docking/ligand'.format(project_dir)) os.system('mkdir {}/log'.format(project_dir)) os.system('mkdir {}/stage'.format(project_dir)) os.system('mkdir {}/report'.format(project_dir))
from parameter import Parameter from ligand import Ligand from receptor import Receptor def line(id, ligand): ids = [str(id)] ligand.foreachId(lambda id: ids.append(str(id))) return '\t'.join(ids) p = Parameter() ligand = Ligand(p._('project.ligand.db')) receptor = Receptor(p._('project.receptor.db')) receptor.foreachId(lambda id: print(line(id, ligand))) ligand.close() receptor.close()
import re import glob import ntpath import os from parameter import Parameter from receptor import Receptor from path import Path p = Parameter() pt = Path(p) #locate tree dir = p._('project.dir') + '/' name = p._('project.wizard.create.name') project_dir = dir + name data_dir = project_dir + '/data/' filename = '{}/stage/{}'.format(project_dir, p._('project.wizard.load.receptor')) # import ligands molecule = Receptor(data_dir + p._('project.wizard.receptor.db')) molecule.clear() # import data for id in open(filename): id = id.strip('\n') molecule.add(id) molecule.commit()
for item in table.items(): id = item[0] l = item[1][0] data = item[1][1] cls = item[1][2] name = item[1][3] score = feuler_score(l, data, mean, stdv) table[id] = (l,score,cls,name) p = Parameter("feuler.") dict = Dictionary(p._("dictionary")) max_len = 0 table = {} for line in sys.stdin: line = line.strip().split("\t") if (len(line))>2: contig = dict._(int(line[0])) id = int(line[0]) name = contig[0] cls = contig[2] lref = int(line[1]) data = line[2]
from parameter import Parameter p = Parameter("stream.contigs.") for line in open(p._("source")): print line.strip()
from parameter import Parameter def to_binary(str, one): bin = "".join( map(lambda x: "{0}".format(int(string.find(one, x) > -1)), str)) rest = len(bin) % 4 if rest > 0: return bin + "0000"[rest:] else: return bin p = Parameter("encode.") path = p._("dictionary") one = p._("one") # load dictionary file = open(path) code = {} for line in file: entry = line.split("\t") code[entry[0]] = (entry[1], entry[2]) file.close() for line in sys.stdin: entry = line.split() c = code[entry[0]] print "{0} {1} {2}".format(c[1].strip(), c[0], to_binary(entry[1], one))
import sys import string from parameter import Parameter def to_binary(str, one): bin = "".join( map(lambda x: "{0}".format(int(string.find(one, x) > -1)), str)) rest = len(bin) % 4 return bin + "0000"[rest:] p = Parameter("encode.reads.") one = p._("one") for line in sys.stdin: line = line.strip() print to_binary(line, one)
import os from parameter import Parameter from ligand import Ligand p = Parameter() dir = p._('project.dir') + '/' project_dir = dir + p._('project.wizard.create.name') + '/' data_dir = project_dir + 'data/' molecule = Ligand(data_dir + p._('project.wizard.ligand.db')) columns = p._('project.wizard.ligand_report.columns') molecule.foreachRecord(columns, lambda id, fields: print(id, fields, sep='\t')) molecule.close()
import sys from parameter import Parameter from common import Dictionary def reapr_score(l, data, width, mdh, k): return data p = Parameter("reapr.") out_path = p._("out_path") width = p.i("width") mdh = p.i("mdh") # max differential height k = p.i("k") dict = Dictionary(p._("dictionary")) max_len = 0 for line in sys.stdin: line = line.strip().split("\t") if (len(line)) > 2: contig = dict._(int(line[0])) id = line[0] cls = contig[2] lref = int(line[1]) ref = line[2] max_len = max(lref, max_len) print "{0}\t{1}\t{2}\t{3}".format( id, cls, lref, reapr_score(lref, ref, width, mdh, k))
import os from parameter import Parameter from receptor import Receptor p = Parameter() dir = p._('project.dir') + '/' project_dir = dir + p._('project.wizard.create.name') data_dir = project_dir + '/data/' molecule = Receptor(data_dir + p._('project.wizard.receptor.db')) columns = p._('project.wizard.receptor_report.columns') molecule.foreachRecord(columns, lambda id, fields: print(id, fields, sep='\t')) molecule.close()
import os from parameter import Parameter from ligand import Ligand p = Parameter() #locate tree dir = p._('project.dir') name = p._('project.wizard.create.name') project_dir = dir + '/' + name data_dir = project_dir + '/data' filename = '{}/stage/{}'.format(project_dir, p._('project.wizard.load.ligand')) #import data molecule = Ligand(data_dir + '/' + p._('project.wizard.ligand.db')) molecule.clear() for id in open(filename): id = id.strip('\n') molecule.add(id) molecule.commit() # download ligand structures def save(id, s, format, dir): filename = '{}/{}.{}'.format(dir, id, format) with open(filename, 'w') as file: file.write(s) print(id)
import sys import os from pairdaemon import PairDaemon from parameter import Parameter from path import Path from pair import Pair process_name = 'docking' p = Parameter() pt = Path(p) user = p._('user') payload = p.i('daemon.sbatch.payload') db = Pair(pt.receptordb, pt.liganddb) class Matrix(PairDaemon): def __init__(self): PairDaemon.__init__(self, user, db, pt, payload, process_name) def score(self, pid, cid): score_file = pt.pairdir(pid,cid) + '/scoring.log' try: with open(score_file) as file: data = file.read().split('\n')[::-1]
from parameter import Parameter from pair import Pair p = Parameter() root = p._('root') dir = root + '/' + p._('project.wizard.name') pair = Pair(dir + '/pair.db') pair.foreach( lambda pid, cid : print(pid, cid, sep = '\t') ) pair.close()
dm = param[3] dm.update(r, k, th) def flush(dm): print "saving ...\n" dm.save() def jump(current, limit): return current + random.randint(1, limit) p = Parameter("dsbuilder.") path = p._("contigs_path") sim_threshold = p.f("sim_threshold") k = p.i("k") css = p.i("contigs_sample_size") rss = p.i("reads_sample_size") rrj = p.i("reads_random_jump") save_frequency = p.i("save_frequency") out_path = p._("out_path") dm = DataManager(path, out_path, css) print "processing {0} contigs and {1} reads".format(css, rss) #receive reads stream count = 0 pos = 0
def ok(line): field = re.split('\s+', line) if field[0] == 'ANISOU': return False if field[0] in ['ATOM', 'HETATM']: return field[2].upper() not in ['NA'] return True def remove_noise(id, path, incl): if id in incl: content = open(path).read().strip('\n').split('\n') newcontent = [s for s in content if ok(s)] if len(content) != len(newcontent): open(path, 'w').write('\n'.join(newcontent)) print(id) p = Parameter() pt = Path(p) molecule = Receptor(pt.receptordb) incl = p._('project.wizard.receptor_remove_noise.include').split(',') molecule.foreachId(lambda id: remove_noise(id, pt.receptor(id), incl))
import os from parameter import Parameter from ligand import Ligand from receptor import Receptor from path import Path def print_pairs(pid, ligand): ligand.foreachId(lambda cid: print(pid, cid, sep='\t')) p = Parameter() pt = Path(p) ligand = Ligand(pt.data + p._('project.wizard.ligand.db')) receptor = Receptor(pt.data + p._('project.wizard.receptor.db')) receptor.foreachId(lambda id: print_pairs(id, ligand)) ligand.close() receptor.close()
import os from parameter import Parameter from path import Path from ligand import Ligand p = Parameter() pt = Path(p) #locate tree dir = p._('project.dir') name = p._('project.wizard.create.name') project_dir = dir + '/' + name data_dir = project_dir + '/data' filename = '{}/stage/{}'.format(project_dir, p._('project.wizard.load.ligand')) #import data molecule = Ligand(pt.liganddb) molecule.clear() for id in open(filename): id = id.strip('\n') molecule.add(id) molecule.commit() # download ligand structures def instage(id, pt): return pt.filename('{}.pdb'.format(id), pt.stage, '*.pdb') != None