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toggle likesFreqs #153

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Merged
merged 2 commits into from
Oct 20, 2016
Merged

toggle likesFreqs #153

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9f43799
toggle likesFreqs
josephvitti Oct 20, 2016
b411aaf
Merge branch 'master' into jv
josephvitti Oct 20, 2016
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26 changes: 16 additions & 10 deletions cms/composite.py
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Original file line number Diff line number Diff line change
Expand Up @@ -213,26 +213,32 @@ def execute_poppair(args):
subprocess.check_call( cmdstring.split() )
return
def execute_outgroups(args):
"""still possible to toggle likesFreqs vs. not (?)"""
#delihh_hit_filename, delihh_miss_filename, ihs_hit_filename, ihs_miss_filename, xpehh_hit_filename, xpehh_miss_filename, fst_hit_filename, fst_miss_filename, deldaf_hit_filename, deldaf_miss_filename = get_likesfiles_frommaster(args.likesfile)
delihh_hit_hi_filename, delihh_miss_hi_filename, ihs_hit_hi_filename, ihs_miss_hi_filename, xpehh_hit_hi_filename, xpehh_miss_hi_filename, fst_hit_hi_filename, fst_miss_hi_filename, deldaf_hit_hi_filename, deldaf_miss_hi_filename = get_likesfiles_frommaster(args.likesfile)
#HI-FREQ by default
if args.likesfile_mid is not None:
delihh_hit_mid_filename, delihh_miss_mid_filename, ihs_hit_mid_filename, ihs_miss_mid_filename, xpehh_hit_mid_filename, xpehh_miss_mid_filename, fst_hit_mid_filename, fst_miss_mid_filename, deldaf_hit_mid_filename, deldaf_miss_mid_filename = get_likesfiles_frommaster(args.likesfile_mid)
usefreqs = []
if args.likesfile_low is not None:
delihh_hit_low_filename, delihh_miss_low_filename, ihs_hit_low_filename, ihs_miss_low_filename, xpehh_hit_low_filename, xpehh_miss_low_filename, fst_hit_low_filename, fst_miss_low_filename, deldaf_hit_low_filename, deldaf_miss_low_filename = get_likesfiles_frommaster(args.likesfile_low)

usefreqs.append('low')
if args.likesfile_mid is not None:
delihh_hit_mid_filename, delihh_miss_mid_filename, ihs_hit_mid_filename, ihs_miss_mid_filename, xpehh_hit_mid_filename, xpehh_miss_mid_filename, fst_hit_mid_filename, fst_miss_mid_filename, deldaf_hit_mid_filename, deldaf_miss_mid_filename = get_likesfiles_frommaster(args.likesfile_mid)
usefreqs.append('mid')
while len(usefreqs) < 3:
usefreqs.append('hi')

if not args.region: #GENOME-WIDE
cmd = "combine/combine_scores_multiplepops"
argstring = args.outfile + " " + delihh_hit_filename + " " + delihh_miss_filename + " " + ihs_hit_filename + " " + ihs_miss_filename + " " + xpehh_hit_filename + " " + xpehh_miss_filename + " " + fst_hit_filename + " " + fst_miss_filename + " " + deldaf_hit_filename + " " + deldaf_miss_filename
argstring = args.outfile
else: #WITHIN REGION
cmd = "combine/combine_scores_multiplepops_region"
argstring = str(args.startBp) + " " + str(args.endBp) + " " + args.outfile
for score in ['ihs', 'delihh', 'xpehh', 'fst', 'deldaf']:
for dist_type in ['hit', 'miss']:
for freq in ['low', 'mid', 'hi']:
argument = eval(score + "_" + dist_type + "_" + freq)
argstring += " " + argument
#+ delihh_hit_filename + " " + delihh_miss_filename + " " + ihs_hit_filename + " " + ihs_miss_filename + " " + xpehh_hit_filename + " " + xpehh_miss_filename + " " + fst_hit_filename + " " + fst_miss_filename + " " + deldaf_hit_filename + " " + deldaf_miss_filename

for score in ['ihs', 'delihh', 'xpehh', 'fst', 'deldaf']:
for dist_type in ['hit', 'miss']:
for freq in ['low', 'mid', 'hi']:
argument = eval(score + "_" + dist_type + "_" + freq)
argstring += " " + argument

for pairfile in args.infiles.split(','):
argstring += " " + pairfile
Expand Down