def loadMatchResults(infile, outfile):
'''
load the results of the match analysis into sqlite database
'''
temp = P.getTempFile("./match.dir")
temp.write("seq_id\tmatrix_id\tposition\tstrand\t"
"core_score\tmatrix_score\tsequence\n")
for details in PipelineTFM.match_iterator(infile):
temp.write("\t".join(
map(str, [
details.seq_id, details.matrix_id, details.position,
details.strand, details.core_score, details.matrix_score,
details.sequence
])) + "\n")
temp.close()
to_cluster = True
job_options = "-l mem_free=64G"
inf = temp.name
tablename = filenameToTablename(os.path.basename(infile))
statement = ("python %(scriptsdir)s/csv2db.py"
" -t %(tablename)s"
" --log=%(outfile)s.log"
" --index=seq_id"
" %(csv2db_options)s"
" < %(inf)s > %(outfile)s")
P.run()
os.unlink(temp.name)
def loadMatchResults(infile, outfile):
'''
load the results of the match analysis into
sqlite database
'''
temp = P.getTempFile()
temp.write(
"seq_id\tmatrix_id\tposition\tstrand\tcore_score\tmatrix_score\tsequence\n"
)
for details in PipelineTransfacMatch.match_iterator(infile):
temp.write("\t".join(
map(str, [
details.seq_id, details.matrix_id, details.position,
details.strand, details.core_score, details.matrix_score,
details.sequence
])) + "\n")
inf = temp.name
tablename = filenameToTablename(os.path.basename(infile))
statement = '''python %(scriptsdir)s/csv2db.py -t %(tablename)s
--log=%(outfile)s.log
--index=seq_id
%(csv2db_options)s
< %(inf)s > %(outfile)s'''
P.run()
os.remove(inf)
def loadMatchResults(infile, outfile):
'''
load the results of the match analysis into sqlite database
'''
temp = P.getTempFile("./match.dir")
temp.write("seq_id\tmatrix_id\tposition\tstrand\t"
"core_score\tmatrix_score\tsequence\n")
for details in PipelineTFM.match_iterator(infile):
temp.write("\t".join(map(str, [details.seq_id,
details.matrix_id,
details.position,
details.strand,
details.core_score,
details.matrix_score,
details.sequence])) + "\n")
temp.close()
to_cluster = True
job_options = "-l mem_free=64G"
inf = temp.name
tablename = filenameToTablename(os.path.basename(infile))
statement = ("python %(scriptsdir)s/csv2db.py"
" -t %(tablename)s"
" --log=%(outfile)s.log"
" --index=seq_id"
" %(csv2db_options)s"
" < %(inf)s > %(outfile)s")
P.run()
os.unlink(temp.name)
def loadMatchResults(infile, outfile):
'''
load the results of the match analysis into sqlite database
'''
temp = P.getTempFile("./match.dir")
temp.write("seq_id\tmatrix_id\tposition\tstrand\t"
"core_score\tmatrix_score\tsequence\n")
for details in PipelineTFM.match_iterator(infile):
temp.write("\t".join(
map(str, [
details.seq_id, details.matrix_id, details.position,
details.strand, details.core_score, details.matrix_score,
details.sequence
])) + "\n")
temp.close()
P.load(temp.name, outfile, options="--add-index=seq_id")
os.unlink(temp.name)
def loadMatchResults(infile, outfile):
'''
load the results of the match analysis into
sqlite database
'''
temp = P.getTempFile()
temp.write(
"seq_id\tmatrix_id\tposition\tstrand\tcore_score\tmatrix_score\tsequence\n")
for details in PipelineTransfacMatch.match_iterator(infile):
temp.write("\t".join(map(str, [details.seq_id, details.matrix_id, details.position,
details.strand, details.core_score, details.matrix_score, details.sequence])) + "\n")
inf = temp.name
tablename = filenameToTablename(os.path.basename(infile))
statement = '''python %(scriptsdir)s/csv2db.py -t %(tablename)s
--log=%(outfile)s.log
--index=seq_id
%(csv2db_options)s
< %(inf)s > %(outfile)s'''
P.run()
os.remove(inf)
def loadMatchResults(infile, outfile):
'''
load the results of the match analysis into sqlite database
'''
temp = P.getTempFile("./match.dir")
temp.write("seq_id\tmatrix_id\tposition\tstrand\t"
"core_score\tmatrix_score\tsequence\n")
for details in PipelineTFM.match_iterator(infile):
temp.write("\t".join(map(str, [details.seq_id,
details.matrix_id,
details.position,
details.strand,
details.core_score,
details.matrix_score,
details.sequence])) + "\n")
temp.close()
P.load(temp.name,
outfile,
options="--add-index=seq_id")
os.unlink(temp.name)
