## Usage:

## standard layout (gene cluster table and alignment on the same row):

## python add-new-pages.py -fn your_species

## wide layout (gene cluster table for one row and alignment at the bottom):

## python add-new-pages.py -fn your_species -wl

import os, sys, json, argparse

parser = argparse.ArgumentParser(description=\

association score: python ./%(prog)s' ' -fn E_coli -sa')

parser.add_argument('-fn', '--folder_name', type = str, required=True,

help='your folder/species name (without "/", e.g.: E_coli)', metavar='')

parser.add_argument('-wl', '--wide_layout', action='store_true',

help='using wide layout (by default: standard layout)')

parser.add_argument('-sa', '--show_associations', action='store_true',

help='show association scores using wide layout for the cluster datatable (by default: standard layout)')

params = parser.parse_args()

species=params.folder_name

if params.show_associations:

print 'using wide layout showing association scores'

os.system('cp ./views/instance-association.jade ./views/' species '.jade')

elif params.wide_layout==False:

print 'using standard layout'

os.system('cp ./views/instance.jade ./views/' species '.jade')

else: #params.wide_layout True

print 'using wide layout'

os.system('cp ./views/instance-wide.jade ./views/' species '.jade')

##process jade file (in folder ./views/)

os.system('sed -i -- "s/TestSet/' species '/g" ./views/' species '.jade')

##process js file (in folder ./routes/)

os.system('cp ./routes/TestSet.js ./routes/' species '.js')

os.system('sed -i -- "s/TestSet/' species '/g" ./routes/' species '.js')

##process association

if params.show_associations:

with open('./public/dataset/TestSet/metaConfiguration.js'.replace('TestSet',species)) as meta_config:

for row in meta_config:

if 'association_columns=' in row:

cols=row.strip().split('association_columns=')[1].split(';')[0]

association_columns_list = [i for i in json.loads(cols)]

with open('./public/dataset/TestSet/newColumnConfig.js'.replace('TestSet',species),'wb') as newColumnConfig_output:

newColumnConfig_js='var apply_association_cols=true;\nvar new_columns_config=[\n'

## add branch association group

newColumnConfig_js="%s {insertion_pos:'Length', new_col: {'data':'', 'group name':'branch association', 'visible': true, 'tooltip':''}},\n"%(newColumnConfig_js)

## add branch association columns

for i in association_columns_list:

newColumn_BA=" {insertion_pos:'Length', new_col: {'data':'newColumnName BA', 'group':'branch association', 'visible': true, 'name':'newColumnName BA','tooltip':'newColumnName branch association'}},\n".replace('newColumnName',i)

newColumnConfig_js="%s%s"%(newColumnConfig_js,newColumn_BA)

## add presence/absence association group

newColumnConfig_js="%s {insertion_pos:'Length', new_col: {'data':'', 'group name':'presence/absence association', 'visible': true, 'tooltip':''}},\n"%(newColumnConfig_js)

## add presence/absence association columns

for i in association_columns_list:

newColumn_PA=" {insertion_pos:'Length', new_col: {'data':'newColumnName PA', 'group':'presence/absence association', 'visible': true, 'name':'newColumnName PA','tooltip':'newColumnName presence/absence association'}},\n".replace('newColumnName',i)

newColumnConfig_js="%s%s"%(newColumnConfig_js,newColumn_PA)

newColumnConfig_js ='];'

newColumnConfig_output.write(newColumnConfig_js)