Hi Shane,
I have a script which saves a colored sequence in HTML format. See
attachment.
Example usage:
run save_colored_fasta.py
save_colored_fasta seq.html
It should be possible to copy&paste the colored sequence from your
browser to excel.
Cheers,
Thomas
Shane Neeley wrote, On 02/27/12 01:45:
Hi Pymol Network,
I would appreciate someones help in extracting the sequence in the
viewer above the protein. I have gone through the sequence and
changed AAs to different colors based on their position. I would
ideally like to be able to copy that sequence with the colors that
they are coded so that I could export it to an excel file. Is this
possible?
Thanks very much.
Shane
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
(c) 2012 Thomas Holder, MPI for Developmental Biology
License: BSD-2-Clause
'''
from pymol import cmd
def save_colored_fasta(filename, selection='(all)', gapped=1, quiet=1):
'''
DESCRIPTION
Save a html file with colored (by C-alpha atoms) fasta sequence.
USAGE
save_colored_fasta filename [, selection [, gapped ]]
'''
from pymol.exporting import _resn_to_aa as one_letter
from pymol import Scratch_Storage
gapped = int(gapped)
selection = '(%s) and guide' % (selection)
html = []
stored = Scratch_Storage()
def callback(resv, resn, color):
if stored.resv is None:
stored.resv = resv - (resv % 70)
if gapped:
while stored.resv+1 < resv:
callback(stored.resv+1, '-', 25)
stored.resv += 1
if stored.resv % 70 == 1:
html.append(('</font>\n<br>%4d <font>' % (resv)).replace(' ', ' '))
stored.color = None
c = cmd.get_color_tuple(color)
color = '#%02x%02x%02x' % (c[0]*255, c[1]*255, c[2]*255)
aa = one_letter.get(resn, '-')
if color != stored.color:
html.append('</font><font color="' + color + '">')
stored.color = color
html.append(aa)
for obj in cmd.get_object_list(selection):
for chain in cmd.get_chains('model %s and (%s)' % (obj, selection)):
sele = 'model %s and chain "%s" and (%s)' % (obj, chain, selection)
html.append('\n<br>>%s_%s<font>' % (obj, chain))
stored.resv = None if gapped else 0
stored.color = None
cmd.iterate(sele, 'callback(resv, resn, color)', space=locals())
html.append('</font>')
handle = open(filename, 'w')
print >> handle, '<html><body style="font-family:monospace">'
print >> handle, ''.join(html)
print >> handle, '</body></html>'
handle.close()
cmd.extend('save_colored_fasta', save_colored_fasta)
cmd.auto_arg[1].update([
('save_colored_fasta', cmd.auto_arg[0]['zoom']),
])
# vi: ts=4:sw=4:smarttab:expandtab
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