#!/usr/bin/python
# Read GLAM2SCAN output: write an HTML version of it
import fileinput
version = ''
commandline = ''
alignments = []
state = 0
for line in fileinput.input():
if state == 0:
if line.startswith('Version'):
version = line
elif line.find('glam2scan') != -1:
commandline = line
state += 1
elif state == 1:
fields = line.split()
if len(fields) == 6:
alignments.append(fields)
# print the HTML header:
print ''
print ''
print 'GLAM2SCAN'
print ''
print ''
print ''
print 'GLAM2SCAN
'
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 ''
print '| NAME | '
print 'START | '
print 'SITE | '
print 'END | '
print 'STRAND | '
print 'SCORE | '
print '
'
print ''
for row in alignments:
print ''
print '| ', row[0], ' | '
print '', row[1], ' | '
print '', row[2], ' | '
print '', row[3], ' | '
print '', row[4], ' | '
print '', row[5], ' | '
print '
'
# close the HTML:
print ''
print '
'
print ''
print ''