mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
4cbfce361b
Datatypes are defined like: [galaxy:datatypes] bed = galaxy.datatypes.interval:Bed png = galaxy.datatypes.images:Image,image/png where the mime-type (default of text/plain) can be declared after the class name, as is seen with png.
257 lines
11 KiB
Python
257 lines
11 KiB
Python
#build list of available data
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import os, sys
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microbe_info= {}
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def init():
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try:
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orgs = {}
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for line in open( "/depot/data2/galaxy/microbes/microbial_data.loc" ):
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if line[0:1] == "#" : continue
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fields = line.split('\t')
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#read each line, if not enough fields, go to next line
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try:
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info_type = fields.pop(0)
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if info_type.upper() == "ORG":
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#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
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org_num = fields.pop(0)
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name = fields.pop(0)
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kingdom = fields.pop(0)
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group = fields.pop(0)
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chromosomes = fields.pop(0)
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info_url = fields.pop(0)
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link_site = fields.pop(0).replace("\r","").replace("\n","")
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if org_num not in orgs:
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orgs[org_num]={}
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orgs[org_num]['chrs']={}
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orgs[org_num]['name']= name
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orgs[org_num]['kingdom']= kingdom
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orgs[org_num]['group']= group
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orgs[org_num]['chromosomes']= chromosomes
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orgs[org_num]['info_url']= info_url
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orgs[org_num]['link_site']= link_site
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elif info_type.upper() == "CHR":
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#CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
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org_num = fields.pop(0)
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chr_acc = fields.pop(0)
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name = fields.pop(0)
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length = fields.pop(0)
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gi = fields.pop(0)
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gb = fields.pop(0)
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info_url = fields.pop(0).replace("\r","").replace("\n","")
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chr = {}
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chr['name']=name
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chr['length']=length
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chr['gi']=gi
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chr['gb']=gb
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chr['info_url']=info_url
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if org_num not in orgs:
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orgs[org_num]={}
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orgs[org_num]['chrs']={}
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orgs[org_num]['chrs'][chr_acc] = chr
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elif info_type.upper() == "DATA":
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#DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
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uid = fields.pop(0)
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org_num = fields.pop(0)
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chr_acc = fields.pop(0)
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feature = fields.pop(0)
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filetype = fields.pop(0)
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path = fields.pop(0).replace("\r","").replace("\n","")
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data = {}
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data['filetype']=filetype
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data['path']=path
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data['feature']=feature
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if org_num not in orgs:
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orgs[org_num]={}
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orgs[org_num]['chrs']={}
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if 'data' not in orgs[org_num]['chrs'][chr_acc]:
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orgs[org_num]['chrs'][chr_acc]['data']={}
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orgs[org_num]['chrs'][chr_acc]['data'][uid] = data
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else: continue
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except:
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continue
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for org_num in orgs:
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org = orgs[org_num]
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if org['kingdom'] not in microbe_info:
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microbe_info[org['kingdom']]={}
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#if org['group'] not in microbe_info[org['kingdom']]:
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# microbe_info[org['kingdom']][org['group']]={}
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if org_num not in microbe_info[org['kingdom']]:
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microbe_info[org['kingdom']][org_num]=org
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except Exception, exc:
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print >>sys.stdout, 'microbial_import_code.py initialization error -> %s' % exc
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init()
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def get_kingdoms():
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ret_val = []
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kingdoms = microbe_info.keys()
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kingdoms.sort()
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for kingdom in kingdoms:
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ret_val.append((kingdom,kingdom,False))
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if ret_val:
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ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
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return ret_val
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def get_orgs_by_kingdom(kingdom):
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ret_val = []
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orgs = microbe_info[kingdom].keys()
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#need to sort by name
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swap_test = False
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for i in range(0, len(orgs) - 1):
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for j in range(0, len(orgs) - i - 1):
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if microbe_info[kingdom][orgs[j]]['name'] > microbe_info[kingdom][orgs[j + 1]]['name']:
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orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
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swap_test = True
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if swap_test == False:
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break
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for org in orgs:
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if microbe_info[kingdom][org]['link_site'] == "UCSC":
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ret_val.append(("<b>"+microbe_info[kingdom][org]['name']+"</b> <a href=\""+microbe_info[kingdom][org]['info_url']+"\" target=\"_blank\">(about)</a>",org,False))
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else:
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ret_val.append((microbe_info[kingdom][org]['name']+" <a href=\""+microbe_info[kingdom][org]['info_url']+"\" target=\"_blank\">(about)</a>",org,False))
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if ret_val:
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ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
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return ret_val
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def get_data(kingdom,group,org,feature):
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ret_val = []
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chroms = microbe_info[kingdom][group][org]['chrs'].keys()
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chroms.sort()
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for chr in chroms:
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for data in microbe_info[kingdom][group][org]['chrs'][chr]['data']:
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if microbe_info[kingdom][group][org]['chrs'][chr]['data'][data]['feature']==feature:
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ret_val.append((microbe_info[kingdom][group][org]['chrs'][chr]['name']+" <a href=\""+microbe_info[kingdom][group][org]['chrs'][chr]['info_url']+"\" target=\"_blank\">(about)</a>",data,False))
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return ret_val
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def get_groups(kingdom):
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ret_val = []
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groups = microbe_info[kingdom].keys()
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groups.sort()
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for group in groups:
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ret_val.append((group,group,False))
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if ret_val:
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ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
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return ret_val
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def get_orgs(kingdom,group):
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ret_val = []
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orgs = microbe_info[kingdom][group].keys()
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#need to sort by name
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swap_test = False
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for i in range(0, len(orgs) - 1):
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for j in range(0, len(orgs) - i - 1):
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if microbe_info[kingdom][group][orgs[j]]['name'] > microbe_info[kingdom][group][orgs[j + 1]]['name']:
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orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
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swap_test = True
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if swap_test == False:
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break
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for org in orgs:
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if microbe_info[kingdom][group][org]['link_site'] == "UCSC":
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ret_val.append(("<b>"+microbe_info[kingdom][group][org]['name']+"</b> <a href=\""+microbe_info[kingdom][group][org]['info_url']+"\" target=\"_blank\">(about)</a>",org,False))
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else:
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ret_val.append((microbe_info[kingdom][group][org]['name']+" <a href=\""+microbe_info[kingdom][group][org]['info_url']+"\" target=\"_blank\">(about)</a>",org,False))
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if ret_val:
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ret_val[0]= (ret_val[0][0],ret_val[0][1],True)
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return ret_val
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def get_data(kingdom,group,org,feature):
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ret_val = []
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chroms = microbe_info[kingdom][group][org]['chrs'].keys()
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chroms.sort()
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for chr in chroms:
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for data in microbe_info[kingdom][group][org]['chrs'][chr]['data']:
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if microbe_info[kingdom][group][org]['chrs'][chr]['data'][data]['feature']==feature:
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ret_val.append((microbe_info[kingdom][group][org]['chrs'][chr]['name']+" <a href=\""+microbe_info[kingdom][group][org]['chrs'][chr]['info_url']+"\" target=\"_blank\">(about)</a>",data,False))
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return ret_val
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def get_data_by_kingdom_org_feature(kingdom,org,feature):
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ret_val = []
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chroms = microbe_info[kingdom][org]['chrs'].keys()
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chroms.sort()
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for chr in chroms:
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for data in microbe_info[kingdom][org]['chrs'][chr]['data']:
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if microbe_info[kingdom][org]['chrs'][chr]['data'][data]['feature']==feature:
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ret_val.append((microbe_info[kingdom][org]['chrs'][chr]['name']+" <a href=\""+microbe_info[kingdom][org]['chrs'][chr]['info_url']+"\" target=\"_blank\">(about)</a>",data,False))
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return ret_val
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#post processing, set build for data and add additional data to history
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from galaxy import datatypes, config, jobs
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from shutil import copyfile
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def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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history = out_data.items()[0][1].history
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if history == None:
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print "unknown history!"
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return
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kingdom = param_dict.get('kingdom',None)
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group = param_dict.get('group',None)
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org = param_dict.get('org',None)
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if not (kingdom or group or org):
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print "Parameters are not available."
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new_stdout = ""
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split_stdout = stdout.split("\n")
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basic_name = ""
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for line in split_stdout:
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fields = line.split("\t")
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if fields[0] == "#File1":
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description = fields[1]
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chr = fields[2]
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dbkey = fields[3]
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file_type = fields[4]
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name, data = out_data.items()[0]
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basic_name = data.name
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data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
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data.dbkey = dbkey
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data.info = data.name
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data = app.datatypes_registry.change_datatype( data, file_type )
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data.init_meta()
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data.set_peek()
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app.model.flush()
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elif fields[0] == "#NewFile":
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description = fields[1]
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chr = fields[2]
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dbkey = fields[3]
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filepath = fields[4]
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file_type = fields[5]
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newdata = app.model.Dataset()
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newdata.extension = file_type
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newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
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newdata.flush()
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history.add_dataset( newdata )
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newdata.flush()
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app.model.flush()
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try:
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copyfile(filepath,newdata.file_name)
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newdata.info = newdata.name
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newdata.state = jobs.JOB_OK
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except:
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newdata.info = "The requested file is missing from the system."
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newdata.state = jobs.JOB_ERROR
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newdata.dbkey = dbkey
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newdata.init_meta()
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newdata.set_peek()
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#
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app.model.flush()
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