#build list of available data
import os, sys
microbe_info= {}
def init():
try:
orgs = {}
for line in open( "/depot/data2/galaxy/microbes/microbial_data.loc" ):
if line[0:1] == "#" : continue
fields = line.split('\t')
#read each line, if not enough fields, go to next line
try:
info_type = fields.pop(0)
if info_type.upper() == "ORG":
#ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
org_num = fields.pop(0)
name = fields.pop(0)
kingdom = fields.pop(0)
group = fields.pop(0)
chromosomes = fields.pop(0)
info_url = fields.pop(0)
link_site = fields.pop(0).replace("\r","").replace("\n","")
if org_num not in orgs:
orgs[org_num]={}
orgs[org_num]['chrs']={}
orgs[org_num]['name']= name
orgs[org_num]['kingdom']= kingdom
orgs[org_num]['group']= group
orgs[org_num]['chromosomes']= chromosomes
orgs[org_num]['info_url']= info_url
orgs[org_num]['link_site']= link_site
elif info_type.upper() == "CHR":
#CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
org_num = fields.pop(0)
chr_acc = fields.pop(0)
name = fields.pop(0)
length = fields.pop(0)
gi = fields.pop(0)
gb = fields.pop(0)
info_url = fields.pop(0).replace("\r","").replace("\n","")
chr = {}
chr['name']=name
chr['length']=length
chr['gi']=gi
chr['gb']=gb
chr['info_url']=info_url
if org_num not in orgs:
orgs[org_num]={}
orgs[org_num]['chrs']={}
orgs[org_num]['chrs'][chr_acc] = chr
elif info_type.upper() == "DATA":
#DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
uid = fields.pop(0)
org_num = fields.pop(0)
chr_acc = fields.pop(0)
feature = fields.pop(0)
filetype = fields.pop(0)
path = fields.pop(0).replace("\r","").replace("\n","")
data = {}
data['filetype']=filetype
data['path']=path
data['feature']=feature
if org_num not in orgs:
orgs[org_num]={}
orgs[org_num]['chrs']={}
if 'data' not in orgs[org_num]['chrs'][chr_acc]:
orgs[org_num]['chrs'][chr_acc]['data']={}
orgs[org_num]['chrs'][chr_acc]['data'][uid] = data
else: continue
except:
continue
for org_num in orgs:
org = orgs[org_num]
if org['kingdom'] not in microbe_info:
microbe_info[org['kingdom']]={}
#if org['group'] not in microbe_info[org['kingdom']]:
# microbe_info[org['kingdom']][org['group']]={}
if org_num not in microbe_info[org['kingdom']]:
microbe_info[org['kingdom']][org_num]=org
except Exception, exc:
print >>sys.stdout, 'microbial_import_code.py initialization error -> %s' % exc
init()
def get_kingdoms():
ret_val = []
kingdoms = microbe_info.keys()
kingdoms.sort()
for kingdom in kingdoms:
ret_val.append((kingdom,kingdom,False))
if ret_val:
ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
return ret_val
def get_orgs_by_kingdom(kingdom):
ret_val = []
orgs = microbe_info[kingdom].keys()
#need to sort by name
swap_test = False
for i in range(0, len(orgs) - 1):
for j in range(0, len(orgs) - i - 1):
if microbe_info[kingdom][orgs[j]]['name'] > microbe_info[kingdom][orgs[j + 1]]['name']:
orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
swap_test = True
if swap_test == False:
break
for org in orgs:
if microbe_info[kingdom][org]['link_site'] == "UCSC":
ret_val.append((""+microbe_info[kingdom][org]['name']+" (about)",org,False))
else:
ret_val.append((microbe_info[kingdom][org]['name']+" (about)",org,False))
if ret_val:
ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
return ret_val
def get_data(kingdom,group,org,feature):
ret_val = []
chroms = microbe_info[kingdom][group][org]['chrs'].keys()
chroms.sort()
for chr in chroms:
for data in microbe_info[kingdom][group][org]['chrs'][chr]['data']:
if microbe_info[kingdom][group][org]['chrs'][chr]['data'][data]['feature']==feature:
ret_val.append((microbe_info[kingdom][group][org]['chrs'][chr]['name']+" (about)",data,False))
return ret_val
def get_groups(kingdom):
ret_val = []
groups = microbe_info[kingdom].keys()
groups.sort()
for group in groups:
ret_val.append((group,group,False))
if ret_val:
ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
return ret_val
def get_orgs(kingdom,group):
ret_val = []
orgs = microbe_info[kingdom][group].keys()
#need to sort by name
swap_test = False
for i in range(0, len(orgs) - 1):
for j in range(0, len(orgs) - i - 1):
if microbe_info[kingdom][group][orgs[j]]['name'] > microbe_info[kingdom][group][orgs[j + 1]]['name']:
orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
swap_test = True
if swap_test == False:
break
for org in orgs:
if microbe_info[kingdom][group][org]['link_site'] == "UCSC":
ret_val.append((""+microbe_info[kingdom][group][org]['name']+" (about)",org,False))
else:
ret_val.append((microbe_info[kingdom][group][org]['name']+" (about)",org,False))
if ret_val:
ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
return ret_val
def get_data(kingdom,group,org,feature):
ret_val = []
chroms = microbe_info[kingdom][group][org]['chrs'].keys()
chroms.sort()
for chr in chroms:
for data in microbe_info[kingdom][group][org]['chrs'][chr]['data']:
if microbe_info[kingdom][group][org]['chrs'][chr]['data'][data]['feature']==feature:
ret_val.append((microbe_info[kingdom][group][org]['chrs'][chr]['name']+" (about)",data,False))
return ret_val
def get_data_by_kingdom_org_feature(kingdom,org,feature):
ret_val = []
chroms = microbe_info[kingdom][org]['chrs'].keys()
chroms.sort()
for chr in chroms:
for data in microbe_info[kingdom][org]['chrs'][chr]['data']:
if microbe_info[kingdom][org]['chrs'][chr]['data'][data]['feature']==feature:
ret_val.append((microbe_info[kingdom][org]['chrs'][chr]['name']+" (about)",data,False))
return ret_val
#post processing, set build for data and add additional data to history
from galaxy import datatypes, config, jobs
from shutil import copyfile
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
history = out_data.items()[0][1].history
if history == None:
print "unknown history!"
return
kingdom = param_dict.get('kingdom',None)
group = param_dict.get('group',None)
org = param_dict.get('org',None)
if not (kingdom or group or org):
print "Parameters are not available."
new_stdout = ""
split_stdout = stdout.split("\n")
basic_name = ""
for line in split_stdout:
fields = line.split("\t")
if fields[0] == "#File1":
description = fields[1]
chr = fields[2]
dbkey = fields[3]
file_type = fields[4]
name, data = out_data.items()[0]
basic_name = data.name
data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
data.dbkey = dbkey
data.info = data.name
data = app.datatypes_registry.change_datatype( data, file_type )
data.init_meta()
data.set_peek()
app.model.flush()
elif fields[0] == "#NewFile":
description = fields[1]
chr = fields[2]
dbkey = fields[3]
filepath = fields[4]
file_type = fields[5]
newdata = app.model.Dataset()
newdata.extension = file_type
newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
newdata.flush()
history.add_dataset( newdata )
newdata.flush()
app.model.flush()
try:
copyfile(filepath,newdata.file_name)
newdata.info = newdata.name
newdata.state = jobs.JOB_OK
except:
newdata.info = "The requested file is missing from the system."
newdata.state = jobs.JOB_ERROR
newdata.dbkey = dbkey
newdata.init_meta()
newdata.set_peek()
#
app.model.flush()