#!/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/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 '<html>'
print '<head>'
print '<title>GLAM2SCAN</title>'
print '<style type="text/css">'
print 'body {background: #D5F0FF}'
print 'th {text-align: left}'
print '</style>'
print '</head>'
print '<body>'
print '<h1>GLAM2SCAN</h1>'
print '<p style="font-family: monospace">', version, '<br><pre>', commandline, '</pre></p>'
print '<p><b>If you use this program in your research, please cite:</b> \
MC Frith, NFW Saunders, B Kobe, TL Bailey, &quot;Discovering sequence motifs with arbitrary insertions and deletions&quot;, <i>PLoS Computational Biology</i>, <b>4</b>(5):e1000071, 2008. \
<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000071">\
[full text]</a></b></p>'
print '<table>'
print '<tr>'
print '<th style="padding-right: 1em">NAME</th>'
print '<th style="padding-right: 1em">START</th>'
print '<th style="text-align: center">SITE</th>'
print '<th style="padding-left: 1em">END</th>'
print '<th style="padding-left: 1em">STRAND</th>'
print '<th style="padding-left: 1em">SCORE</th>'
print '</tr>'
print '<tbody>'

for row in alignments:
    print '<tr>'
    print '<td style="padding-right: 1em">', row[0], '</td>'
    print '<td style="padding-right: 1em;text-align: right">', row[1], '</td>'
    print '<td style="text-align: center;font-family: monospace">', row[2], '</td>'
    print '<td style="padding-left: 1em;text-align: right">', row[3], '</td>'
    print '<td style="padding-left: 1em;text-align: center">', row[4], '</td>'
    print '<td style="padding-left: 1em">', row[5], '</td>'
    print '</tr>'

# close the HTML:
print '</tbody>'
print '</table>'
print '</body>'
print '</html>'
