def term_types_in_paper(paper):
"""For each paper, count how often different term types appear.
Possible term types:
biological_process
molecular_function
cellular_component
"""
# term types (ontologies) in a given paper
tt_count = {}
go_con = mysqlConnect()
go_cursor = go_con.cursor()
for prec in paper:
go_id = prec['go_id']
try:
term_type = gu.go_acc_to_term_type(go_id, go_cursor)
except IndexError:
print go_id, "may be deprecated"
continue
# tt_count[term_type] = count of that term
tt_count[term_type] = tt_count.get(term_type, 0) + 1
go_con.close()
return tt_count # count of term types
def term_types_in_paper(paper):
"""For each paper, count how often different term types appear.
Possible term types:
biological_process
molecular_function
cellular_component
"""
# term types (ontologies) in a given paper
tt_count = {}
go_con = mysqlConnect()
go_cursor = go_con.cursor()
for prec in paper:
go_id = prec['go_id']
try:
term_type = gu.go_acc_to_term_type(go_id, go_cursor)
except IndexError:
print go_id,"may be deprecated"
continue
# tt_count[term_type] = count of that term
tt_count[term_type] = tt_count.get(term_type,0) + 1
go_con.close()
return tt_count # count of term types
outfile = sys.stdout
for o, a in opts:
if o in ('-i','--infile'):
infile = a
elif o in ('-o','--outfile'):
outfile = open(a,"w")
elif o in ('-f','--field'):
go_acc_field = int(a)
print "infile", infile
if infile:
for inline in file(infile):
sp_id = inline.strip().split()[3]
go_acc = inline.strip().split()[go_acc_field-1]
go_level = gu.go_level(go_acc,goc)
try:
go_term_type = gu.go_acc_to_term_type(go_acc, goc)
except IndexError:
outfile.write("%s\t%s\t%.1f\t%s\n" % (go_acc, "NOTERMTYPE",
go_level, sp_id))
continue
outfile.write("%s\t%s\t%.1f\t%s\n" % (go_acc, go_term_type, go_level, sp_id))
else:
go_acc = args[0]
go_level = gu.go_level(go_acc,goc)
go_term_type = gu.go_acc_to_term_type(go_acc, goc)
outfile.write("%s\t%s\t%.1f\n" % (go_acc, go_term_type, go_level))
gocon.close()
if outfile != sys.stdout:
outfile.close()
