#!/usr/bin/python
# Read GLAM2 output: write an HTML version of it
import fileinput, os, tempfile, sys
from string import replace
embed_seqs = 0
version = ''
commandline = ''
alphabet = '?'
alignments = []
text_alignments = []
freq_matrices = []
state = 0
usage = """
USAGE: %s
\tConvert glam2 output to HTML.
\tReads standard input.
\tWrites standard output.
""" % (sys.argv[0])
# parse command line
i=1
while i < len(sys.argv):
arg = sys.argv[i]
print >> sys.stderr, "Unknown command line argument: " + arg; sys.exit(1)
i += 1
for line in sys.stdin.readlines():
fields = line.split()
if state == 0:
if line.startswith('Version'):
version = line
elif line.find('glam2') != -1:
commandline = line
elif line.startswith('Residue counts'):
if len(fields) == 4 + 3:
alphabet = 'n'
alen = 4
elif len(fields) == 20 + 3:
alphabet = 'p'
alen = 20
state += 1
elif state == 1:
if len(fields) > 1 and fields[0] == 'Score:':
score = fields[1]
columns = int(fields[3])
sequences = int(fields[5])
state += 1
elif state == 2:
if len(fields) == 1:
keypos = fields[0]
aln = []
alignments.append([score, keypos, aln])
text_aln = line
text_alignments.append(text_aln)
state += 1
elif state == 3:
if len(fields) == 6:
assert len(fields[2]) == len(keypos)
aln.append(fields)
text_alignments[len(text_alignments)-1] += line
else:
state += 1
elif state == 4:
if len(fields) == alen + 3 and fields[alen] == 'Del':
ipos = 0
pspm = []
freq_matrices.append([pspm, columns, sequences])
state += 1
elif state == 5:
if len(fields) == alen + 2:
pspm.append(fields[:alen])
ipos += 1
if ipos == columns:
state = 1
assert len(alignments) > 0
# print the HTML header:
print ''
print ''
print 'GLAM2'
print ''
print ''
print ''
print 'GLAM2: Gapped Local Alignment of Motifs
'
print '', version, '
', commandline, '
'
print 'If you use this program in your research, please cite: \
MC Frith, NFW Saunders, B Kobe, TL Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008.\
\
[full text]
'
print ''
print ''