def form_submit():
# ENH: pick a unique, informative name -- e.g. date or hostname
name = bottle.request.forms.name
seqfile1 = bottle.request.files.seqfile1
if not hasattr(seqfile1, 'file'):
return "Error: You need to specify at least one sequence file."
seq1fname = handle2temp(seqfile1.file,
suffix=('.cma' if seqfile1.filename.endswith('.cma')
else '.seq'))
# Optional second sequence set -- if missing, do single mode
seqfile2 = bottle.request.files.seqfile2
if hasattr(seqfile2, 'file'):
seq2fname = handle2temp(seqfile2.file,
suffix=('.cma' if
seqfile2.filename.endswith('.cma') else
'.seq'))
if not name:
name = "%s-vs-%s" % (seqfile1.filename.rsplit('.', 1)[0],
seqfile2.filename.rsplit('.', 1)[0])
else:
seq2fname = ''
if not name:
name = seqfile1.filename
# Optional HMM profile for alignment
profile = bottle.request.files.profile
# Optional HMM profile for alignment
profile = bottle.request.files.profile
if hasattr(profile, 'file'):
if not profile.filename.endswith('.hmm'):
return "HMM profile file name must end in .hmm"
profname = handle2temp(profile.file, suffix='.hmm')
logging.info("Aligning %s with profile %s", seq1fname, profname)
fg_aln = core.hmm_align_and_read(profname, seq1fname)
if seq2fname:
logging.info("Aligning %s with profile %s", seq2fname, profname)
bg_aln = core.hmm_align_and_read(profname, seq2fname)
else:
profname = ''
fg_aln = core.read_aln(seq1fname, 'fasta')
if seq2fname:
bg_aln = core.read_aln(seq2fname, 'fasta')
pdbfile = bottle.request.files.pdbfile
if hasattr(pdbfile, 'file'):
if not profname:
return ("Error: to generate a PyMOL script for a PDB file you must"
"also specify an HMM profile")
pdbfname = handle2temp(pdbfile.file)
logging.info("Aligning %s with profile %s", pdbfile.filename, profname)
pdb_rec, pdb_resnums, pdb_inserts = core.pdb_hmm(profname,
pdbfname)
pdb_data = [(pdbfname, pdb_rec, pdb_resnums, pdb_inserts)]
else:
pdbfname = ''
pdb_data = None
# Mutually exclusive with pdbfname (above):
pdbid = bottle.request.forms.pdbid
if pdbid:
# If PDB ID: .pml should use "fetch" instead of "load"?
# Can get this info w/o dl'ing actual PDB file (e.g. via FASTA)?
pass
stat_module = dict(gtest=gtest, urn=urn, jsd=jsd, phospho=phospho,
)[bottle.request.forms.strategy]
try:
alpha = float(bottle.request.forms.alpha)
if not 0.0 <= alpha <= 1.0:
raise ValueError
except ValueError:
return "Error: alpha must be a number between 0 and 1"
_fdo, tmp_output = tempfile.mkstemp(suffix='.out')
os.close(_fdo)
_fdp, tmp_pattern = tempfile.mkstemp(suffix='.pttrn')
os.close(_fdp)
# Run the algorithms...
if seq2fname:
# Pair mode
fg_clean, bg_clean, hits = core.process_pair(fg_aln, bg_aln,
stat_module)
core.process_output(fg_clean, bg_clean, hits, alpha,
tmp_output, tmp_pattern,
pdb_data)
else:
# Single mode
aln, hits = core.process_one(fg_aln, stat_module)
core.process_output(aln, None, hits, alpha,
tmp_output, tmp_pattern,
pdb_data)
# Get the HTML report data
contents = report.do_single(tmp_output, tmp_pattern)[1]
cleanup(seq1fname)
cleanup(seq2fname)
cleanup(profname)
cleanup(tmp_output)
cleanup(tmp_pattern)
return report.html_page_tpl % dict(title=name, contents=contents)
import argparse
import logging
from cladecomparelib.report import do_single, do_multi, html_page_tpl
logging.basicConfig(level=logging.INFO,
format="%(module)s [@%(lineno)s]: %(message)s")
AP = argparse.ArgumentParser(__doc__)
AP.add_argument('outfiles', nargs='+',
help="Output file(s) generated by cladecompare.py")
AP.add_argument('-p', '--pattern',
help="Pattern file (.pttrn) generated by cladecompare.py")
AP.add_argument('-o', '--output',
help="HTML output file name. (Default: stdout)")
args = AP.parse_args()
if len(args.outfiles) == 1:
title, contents = do_single(args.outfiles[0], args.pattern)
else:
title, contents = do_multi(args.outfiles, args.pattern)
html_report = html_page_tpl % dict(title=title, contents=contents)
if args.output:
with open(args.output, 'w') as handle:
handle.write(html_report)
else:
print(html_report)
import logging
from cladecomparelib.report import do_single, do_multi, html_page_tpl
logging.basicConfig(level=logging.INFO,
format="%(module)s [@%(lineno)s]: %(message)s")
AP = argparse.ArgumentParser(__doc__)
AP.add_argument('outfiles',
nargs='+',
help="Output file(s) generated by cladecompare.py")
AP.add_argument('-p',
'--pattern',
help="Pattern file (.pttrn) generated by cladecompare.py")
AP.add_argument('-o',
'--output',
help="HTML output file name. (Default: stdout)")
args = AP.parse_args()
if len(args.outfiles) == 1:
title, contents = do_single(args.outfiles[0], args.pattern)
else:
title, contents = do_multi(args.outfiles, args.pattern)
html_report = html_page_tpl % dict(title=title, contents=contents)
if args.output:
with open(args.output, 'w') as handle:
handle.write(html_report)
else:
print(html_report)
def form_submit():
# ENH: pick a unique, informative name -- e.g. date or hostname
name = bottle.request.forms.name
seqfile1 = bottle.request.files.seqfile1
if not hasattr(seqfile1, 'file'):
return "Error: You need to specify at least one sequence file."
seq1fname = handle2temp(
seqfile1.file,
suffix=('.cma' if seqfile1.filename.endswith('.cma') else '.seq'))
# Optional second sequence set -- if missing, do single mode
seqfile2 = bottle.request.files.seqfile2
if hasattr(seqfile2, 'file'):
seq2fname = handle2temp(
seqfile2.file,
suffix=('.cma' if seqfile2.filename.endswith('.cma') else '.seq'))
if not name:
name = "%s-vs-%s" % (seqfile1.filename.rsplit(
'.', 1)[0], seqfile2.filename.rsplit('.', 1)[0])
else:
seq2fname = ''
if not name:
name = seqfile1.filename
# Optional HMM profile for alignment
profile = bottle.request.files.profile
# Optional HMM profile for alignment
profile = bottle.request.files.profile
if hasattr(profile, 'file'):
if not profile.filename.endswith('.hmm'):
return "HMM profile file name must end in .hmm"
profname = handle2temp(profile.file, suffix='.hmm')
logging.info("Aligning %s with profile %s", seq1fname, profname)
fg_aln = core.hmm_align_and_read(profname, seq1fname)
if seq2fname:
logging.info("Aligning %s with profile %s", seq2fname, profname)
bg_aln = core.hmm_align_and_read(profname, seq2fname)
else:
profname = ''
fg_aln = core.read_aln(seq1fname, 'fasta')
if seq2fname:
bg_aln = core.read_aln(seq2fname, 'fasta')
pdbfile = bottle.request.files.pdbfile
if hasattr(pdbfile, 'file'):
if not profname:
return ("Error: to generate a PyMOL script for a PDB file you must"
"also specify an HMM profile")
pdbfname = handle2temp(pdbfile.file)
logging.info("Aligning %s with profile %s", pdbfile.filename, profname)
pdb_rec, pdb_resnums, pdb_inserts = core.pdb_hmm(profname, pdbfname)
pdb_data = [(pdbfname, pdb_rec, pdb_resnums, pdb_inserts)]
else:
pdbfname = ''
pdb_data = None
# Mutually exclusive with pdbfname (above):
pdbid = bottle.request.forms.pdbid
if pdbid:
# If PDB ID: .pml should use "fetch" instead of "load"?
# Can get this info w/o dl'ing actual PDB file (e.g. via FASTA)?
pass
stat_module = dict(
gtest=gtest,
urn=urn,
jsd=jsd,
phospho=phospho,
)[bottle.request.forms.strategy]
try:
alpha = float(bottle.request.forms.alpha)
if not 0.0 <= alpha <= 1.0:
raise ValueError
except ValueError:
return "Error: alpha must be a number between 0 and 1"
_fdo, tmp_output = tempfile.mkstemp(suffix='.out')
os.close(_fdo)
_fdp, tmp_pattern = tempfile.mkstemp(suffix='.pttrn')
os.close(_fdp)
# Run the algorithms...
if seq2fname:
# Pair mode
fg_clean, bg_clean, hits = core.process_pair(fg_aln, bg_aln,
stat_module, False)
core.process_output(fg_clean, bg_clean, hits, alpha, tmp_output,
tmp_pattern, pdb_data)
else:
# Single mode
aln, hits = core.process_one(fg_aln, stat_module, False)
core.process_output(aln, None, hits, alpha, tmp_output, tmp_pattern,
pdb_data)
# Get the HTML report data
contents = report.do_single(tmp_output, tmp_pattern)[1]
cleanup(seq1fname)
cleanup(seq2fname)
cleanup(profname)
cleanup(tmp_output)
cleanup(tmp_pattern)
return report.html_page_tpl % dict(title=name, contents=contents)