def libs(args): """ %prog libs libfile Get list of lib_ids to be run by pull(). The SQL commands: select library.lib_id, library.name from library join bac on library.bac_id=bac.id where bac.lib_name="Medicago"; select seq_name from sequence where seq_name like 'MBE%' and trash is null; """ p = OptionParser(libs.__doc__) p.set_db_opts(dbname="track", credentials=None) opts, args = p.parse_args(args) if len(args) != 1: sys.exit(not p.print_help()) libfile, = args sqlcmd = "select library.lib_id, library.name, bac.gb# from library join bac on " + \ "library.bac_id=bac.id where bac.lib_name='Medicago'" cur = connect(opts.dbname) results = fetchall(cur, sqlcmd) fw = open(libfile, "w") for lib_id, name, gb in results: name = name.translate(None, "\n") if not gb: gb = "None" print >> fw, "|".join((lib_id, name, gb)) fw.close()
def libs(args): """ %prog libs libfile Get list of lib_ids to be run by pull(). The SQL commands: select library.lib_id, library.name from library join bac on library.bac_id=bac.id where bac.lib_name="Medicago"; select seq_name from sequence where seq_name like 'MBE%' and trash is null; """ p = OptionParser(libs.__doc__) p.set_db_opts(dbname="track", credentials=None) opts, args = p.parse_args(args) if len(args) != 1: sys.exit(not p.print_help()) libfile, = args sqlcmd = "select library.lib_id, library.name, bac.gb# from library join bac on " + \ "library.bac_id=bac.id where bac.lib_name='Medicago'" cur = connect(opts.dbname) results = fetchall(cur, sqlcmd) fw = open(libfile, "w") for lib_id, name, gb in results: name = name.translate(None, "\n") if not gb: gb = "None" print >> fw, "|".join((lib_id, name, gb)) fw.close()
def pull(args): """ %prog pull libfile Pull the sequences using the first column in the libfile. """ p = OptionParser(pull.__doc__) p.set_db_opts(dbname="mtg2", credentials=None) p.add_option( "--frag", default=False, action="store_true", help="The command to pull sequences from db", ) opts, args = p.parse_args(args) if len(args) != 1: sys.exit(not p.print_help()) (libfile, ) = args dbname = opts.dbname frag = opts.frag fp = open(libfile) hostname, username, password = get_profile() for row in fp: lib_id, name = row.split("|", 1) sqlfile = lib_id + ".sql" if not op.exists(sqlfile): fw = open(sqlfile, "w") print( "select seq_name from sequence where seq_name like" + " '{0}%' and trash is null".format(lib_id), file=fw, ) fw.close() if frag: cmd = "pullfrag -D {0} -n {1}.sql -o {1} -q -S {2}".format( dbname, lib_id, hostname) cmd += " -U {0} -P {1}".format(username, password) else: cmd = "pullseq -D {0} -n {1}.sql -o {1} -q".format(dbname, lib_id) sh(cmd)
def pull(args): """ %prog pull libfile Pull the sequences using the first column in the libfile. """ p = OptionParser(pull.__doc__) p.set_db_opts(dbname="mtg2", credentials=None) p.add_option( "--frag", default=False, action="store_true", help="The command to pull sequences from db [default: %default]" ) opts, args = p.parse_args(args) if len(args) != 1: sys.exit(not p.print_help()) libfile, = args dbname = opts.dbname frag = opts.frag fp = open(libfile) hostname, username, password = get_profile() for row in fp: lib_id, name = row.split("|", 1) sqlfile = lib_id + ".sql" if not op.exists(sqlfile): fw = open(sqlfile, "w") print >> fw, "select seq_name from sequence where seq_name like" + " '{0}%' and trash is null".format( lib_id ) fw.close() if frag: cmd = "pullfrag -D {0} -n {1}.sql -o {1} -q -S {2}".format(dbname, lib_id, hostname) cmd += " -U {0} -P {1}".format(username, password) else: cmd = "pullseq -D {0} -n {1}.sql -o {1} -q".format(dbname, lib_id) sh(cmd)
def query(args): """ %prog query "SELECT feat_name FROM asm_feature WHERE feat_type = \\"{0}\\" AND end5 <= \\"{1}\\" AND end3 >= \\"{2}\\"" ::: datafile1 .... Script takes the data from tab-delimited datafile(s) and replaces the placeholders in the query which is then executed. Depending upon the type of query, results are either printed out (when running `select`) or not (when running `insert`, `update` or `delete`) If the query contains quotes around field values, then these need to be escaped with \\ """ p = OptionParser(query.__doc__) p.set_db_opts() p.add_option( "--dryrun", default=False, action="store_true", help="Don't commit to database. Just print queries [default: %default]" ) p.set_sep(help="Specify output field separator") p.set_verbose(help="Print out all the queries") p.set_outfile() opts, args = p.parse_args(args) if len(args) == 0: sys.exit(not p.print_help()) fieldsep = opts.sep sep = ":::" files = None if sep in args: sepidx = args.index(sep) files = args[sepidx + 1:] args = args[:sepidx] if not files: files = [""] qrys = [] qry = " ".join(args) if ";" in qry: for q in qry.split(";"): if len(q.strip()) > 0: qrys.append(q) else: qrys.append(qry) queries = set() if files: for datafile in files: datafile = datafile.strip() fp = must_open(datafile) for row in fp: for qry in qrys: qry = qry.strip() m = re.findall(r"\{\d+\}", qry) if m: mi = [int(x.strip("{}")) for x in m] atoms = row.strip().split("\t") assert max(mi) <= len(atoms), \ "Number of columns in `datafile`({0})".format(len(atoms)) + \ " != number of `placeholders`({0})".format(len(m)) natoms = [atoms[x] for x in mi] for idx, (match, atom) in enumerate(zip(m, natoms)): qry = qry.replace(match, atom) queries.add(qry) else: for qry in qrys: if re.search(r"\{\d+\}", qry): logging.error( "Query `{0}` contains placeholders, no datafile(s) specified" .format(qry)) sys.exit() queries.add(qry) if not opts.dryrun: fw = must_open(opts.outfile, "w") dbh, cur = connect(opts.dbname, connector=opts.dbconn, hostname=opts.hostname, \ username=opts.username, password=opts.password, port=opts.port) cflag = None for qry in queries: if opts.dryrun or opts.verbose: print qry if not opts.dryrun: if to_commit(qry): execute(cur, qry) cflag = True else: results = fetchall(cur, qry, connector=opts.dbconn) for result in results: print >> fw, fieldsep.join([str(x) for x in result]) if not opts.dryrun and cflag: commit(dbh)
def query(args): """ %prog query "SELECT feat_name FROM asm_feature WHERE feat_type = \\"{0}\\" AND end5 <= \\"{1}\\" AND end3 >= \\"{2}\\"" ::: datafile1 .... Script takes the data from tab-delimited datafile(s) and replaces the placeholders in the query which is then executed. Depending upon the type of query, results are either printed out (when running `select`) or not (when running `insert`, `update` or `delete`) If the query contains quotes around field values, then these need to be escaped with \\ """ p = OptionParser(query.__doc__) p.set_db_opts() p.add_option("--dryrun", default=False, action="store_true", help="Don't commit to database. Just print queries [default: %default]") p.set_sep(help="Specify output field separator") p.set_verbose(help="Print out all the queries") p.set_outfile() opts, args = p.parse_args(args) if len(args) == 0: sys.exit(not p.print_help()) fieldsep = opts.sep sep = ":::" files = None if sep in args: sepidx = args.index(sep) files = args[sepidx + 1:] args = args[:sepidx] if not files: files = [""] qrys = [] qry = " ".join(args) if ";" in qry: for q in qry.split(";"): if len(q.strip()) > 0: qrys.append(q) else: qrys.append(qry) queries = set() if files: for datafile in files: datafile = datafile.strip() fp = must_open(datafile) for row in fp: for qry in qrys: qry = qry.strip() m = re.findall(r"\{\d+\}", qry) if m: mi = [int(x.strip("{}")) for x in m] atoms = row.strip().split("\t") assert max(mi) <= len(atoms), \ "Number of columns in `datafile`({0})".format(len(atoms)) + \ " != number of `placeholders`({0})".format(len(m)) natoms = [atoms[x] for x in mi] for idx, (match, atom) in enumerate(zip(m, natoms)): qry = qry.replace(match, atom) queries.add(qry) else: for qry in qrys: if re.search(r"\{\d+\}", qry): logging.error("Query `{0}` contains placeholders, no datafile(s) specified".format(qry)) sys.exit() queries.add(qry) if not opts.dryrun: fw = must_open(opts.outfile, "w") dbh, cur = connect(opts.dbname, connector=opts.dbconn, hostname=opts.hostname, \ username=opts.username, password=opts.password, port=opts.port) cflag = None for qry in queries: if opts.dryrun or opts.verbose: print qry if not opts.dryrun: if to_commit(qry): execute(cur, qry) cflag = True else: results = fetchall(cur, qry) for result in results: print >> fw, fieldsep.join([str(x) for x in result]) if not opts.dryrun and cflag: commit(dbh)