def main():
options = interface()
array_alignments = make_align_list(options.input_dir, options.input_file_format)
# DO BOOTSTRAPPING AND WRITE REPLICATES TO OUTFILES
# options.bootstrap_reps += 1
boot_alignments = phylo.bootstrap(array_alignments, options.bootstrap_reps)
bootstrapped_datasets = []
for rep_count, boot_rep in enumerate(boot_alignments):
boot_bases = []
# setup outfile names (make into function?)
if options.output_file_format == 'nexus':
fname = 'bootrep_%s.nex' % rep_count
if options.output_file_format == 'phylip':
fname = 'bootrep_%s.phylip' % rep_count
final_path = os.path.join(options.output_dir,fname)
fout = open(final_path,'a')
for count, align in enumerate(boot_rep):
seqs = copy(align[0]) # lots of copying to be 'safe'
ids = copy(align[1])
bases_by_col = np.column_stack(seqs) # flip rows and columns
bs_bases = phylo.bootstrap(bases_by_col, 1) # bootstrap the bases within the bootstrapped alignments
bs_bases = np.column_stack(bs_bases[0]) # [0] corrects weirdnesss due to extra set of brackets
bs_bases = bs_bases.copy() # copy modified replicate
pair = [bs_bases, ids]
biopy_align = [strarray2biopy(pair)]
AlignIO.write(biopy_align, fout, options.output_file_format)
fout.write('\n')
fout.close()
def main():
options = interface()
alignment = open(options.input_file, "r")
alignment = AlignIO.read(alignment, "nexus")
numpy_alignment = biopy2strarray(alignment)
max_reps = options.bootstrap_reps + 1
rep = 1
while rep != max_reps:
fout_name = os.path.join(options.output_dir, "bootrep_%s")
fout_name = fout_name + "." + options.output_file_format
fout_name = fout_name % rep
fout = open(fout_name, "w")
seqs = copy(numpy_alignment[0]) # lots of copying to be 'safe'
ids = copy(numpy_alignment[1])
bases_by_col = np.column_stack(seqs) # flip rows and columns
bs_bases = phylo.bootstrap(bases_by_col, 1) # bootstrap the bases within the bootstrapped alignments
bs_bases = np.column_stack(bs_bases[0]) # [0] corrects weirdnesss due to extra set of brackets
bs_bases = bs_bases.copy() # copy modified replicate
pair = [bs_bases, ids]
biopy_align = [strarray2biopy(pair)]
AlignIO.write(biopy_align, fout, options.output_file_format)
fout.write("\n")
fout.close()
print "Made boostrap replicate %s" % rep
rep += 1
