#!/usr/bin/env python
import csv
import sys
partis_path = '.' # edit this if you're not running from the main partis dir
sys.path.insert(1, partis_path + '/python')
import utils
import glutils
from clusterpath import ClusterPath
# read default germline info
glfo = glutils.read_glfo(partis_path + '/data/germlines/human', locus='igh')
print 'first parse an annotation csv file:'
with open(partis_path + '/test/reference-results/annotate-new-simu.csv') as csvfile:
reader = csv.DictReader(csvfile)
for line in reader:
if line['v_gene'] == '': # failed (i.e. couldn't find an annotation)
continue
utils.process_input_line(line)
utils.add_implicit_info(glfo, line)
utils.print_reco_event(line)
break
print 'then parse a partition csv file:'
cp = ClusterPath()
cp.readfile(partis_path + '/test/reference-results/seed-partition-new-simu.csv')
cp.print_partitions(abbreviate=True)
def run_bios2mds(n_components, n_clusters, seqfos, base_workdir, seed, aligned=False, reco_info=None, region=None,
max_runs=100, max_iterations=1000, method='euclidean',
plotdir=None, plotname='mds', queries_to_include=None, color_scale_vals=None, labels=None, title=None, remove_duplicates=False, debug=False):
workdir = base_workdir + '/mds'
msafname = workdir + '/msa.fa'
mdsfname = workdir + '/components.txt'
clusterfname = workdir + '/clusters.txt'
if not os.path.exists(workdir):
os.makedirs(workdir)
if len(set([sfo['seq'] for sfo in seqfos])) < len(seqfos): # it'll just crash when it's running mds later, but this is faster
if remove_duplicates:
seq_groups = [list(group) for _, group in itertools.groupby(sorted(seqfos, key=lambda x: x['seq']), key=lambda x: x['seq'])]
seqs_to_remove = []
for sgroup in seq_groups:
seqs_to_remove += [sfo['name'] for sfo in sgroup[1:]] # remove any after the first one
seqfos = [sfo for sfo in seqfos if sfo['name'] not in seqs_to_remove]
else:
raise Exception('duplicate sequences in seqfos')
if aligned: # NOTE unlike the sklearn version below, this doesn't modify <seqfos>
with open(msafname, 'w') as fastafile:
for sfo in seqfos:
fastafile.write('>%s\n%s\n' % (sfo['name'], sfo['seq']))
else:
utils.align_many_seqs(seqfos, outfname=msafname)
# build the R cmd file
cmdlines = [
'options(rgl.useNULL=TRUE)',
'require(bios2mds, quietly=TRUE)',
'set.seed(%d)' % seed,
'human <- import.fasta("%s")' % msafname,
'active <- mat.dif(human, human)', # mat.dif or mat.dis?
]
if n_components is not None:
cmdlines += ['mmds_active <- mmds(active, pc=%d)' % n_components]
cmdlines += ['capture.output(mmds_active$coord, file="%s")' % mdsfname]
else:
raise Exception('need to implement')
if n_clusters is not None:
cmdlines += [
'kmeans.run1 <- kmeans.run(mmds_active$coord, nb.clus=%d, nb.run=%d, iter.max=%d, method="%s")' % (n_clusters, max_runs, max_iterations, method),
# 'kmeans.run1$clusters',
# 'kmeans.run1$elements',
'options(width=10000)',
'capture.output(kmeans.run1$clusters, file="%s")' % clusterfname,
# sil.score(mat, nb.clus = c(2:13), nb.run = 100, iter.max = 1000, # run for every possible number of clusters (?)
# method = "euclidean")
# random.msa # builds a random [...]
]
rstart = time.time()
try:
utils.run_r(cmdlines, workdir) #, print_time='kmeans')
except subprocess.CalledProcessError as e: # typically happens because of complex eigenvalues
print e
print ' mds failed on cluster' # NOTE will still crash in read_kmeans_clusterfile(), but I'm not using that a.t.m.
title = (title if title is not None else '') + ' mds failed'
pcvals = read_component_file(mdsfname, n_components, seqfos)
partition = read_kmeans_clusterfile(clusterfname, seqfos) if n_clusters is not None else None
rstop = time.time()
if debug and partition is not None:
print ' kmeans partition:'
cp = ClusterPath(partition=partition)
cp.print_partitions(abbreviate=False)
os.remove(msafname)
os.rmdir(workdir)
plotstart = time.time()
if plotdir is not None:
# utils.prep_dir(plotdir, wildlings=['*.svg'])
plot_mds(n_components, pcvals, plotdir, plotname, partition=partition if n_clusters is not None else None, queries_to_include=queries_to_include, color_scale_vals=color_scale_vals, labels=labels, title=title)
if reco_info is not None:
labels = {uid : reco_info[uid][region + '_gene'] for uid in pcvals}
plot_mds(n_components, pcvals, plotdir, 'true-genes', labels=labels, queries_to_include=queries_to_include, color_scale_vals=color_scale_vals, title=title)
if not debug: # this isn't a great way to do this, but I don't want to deal with finding all the calling functions, I just want to add some debug printing to this fcn
print ' %5.1f %5.1f' % (rstop - rstart, time.time() - plotstart),
return partition
#!/usr/bin/env python
import sys
sys.path.insert(1, './python')
import csv
csv.field_size_limit(sys.maxsize) # make sure we can write very large csv fields
import argparse
from clusterpath import ClusterPath
from seqfileopener import get_seqfile_info
import utils
parser = argparse.ArgumentParser()
parser.add_argument('--infname', required=True)
parser.add_argument('--dont-abbreviate', action='store_true', help='Print full seq IDs (otherwise just prints an \'o\')')
parser.add_argument('--n-to-print', type=int, help='How many partitions to print (centered on the best partition)')
parser.add_argument('--datadir', default='data/imgt')
parser.add_argument('--simfname')
parser.add_argument('--is-data', action='store_true')
args = parser.parse_args()
glfo = utils.read_germline_set(args.datadir)
reco_info = None
if args.simfname is not None:
input_info, reco_info = get_seqfile_info(args.simfname, args.is_data, glfo=glfo)
cp = ClusterPath()
cp.readfile(args.infname)
cp.print_partitions(abbreviate=(not args.dont_abbreviate), n_to_print=args.n_to_print, reco_info=reco_info)
import sys
partis_path = '.' # edit this if you're not running from the main partis dir
sys.path.insert(1, partis_path + '/python')
import utils
import glutils
from clusterpath import ClusterPath
# read default germline info
glfo = glutils.read_glfo(partis_path + '/data/germlines/human', chain='h')
print 'first parse an annotation csv file:'
with open(partis_path + '/test/reference-results/annotate-new-simu.csv') as csvfile:
reader = csv.DictReader(csvfile)
for line in reader:
utils.process_input_line(line)
utils.add_implicit_info(glfo, line)
utils.print_reco_event(glfo['seqs'], line)
cdr3_bounds = (line['codon_positions']['v'], line['codon_positions']['j'] + 3)
print ''
print ' should match the above:'
print ' %s naive cdr3' % line['naive_seq'][cdr3_bounds[0] : cdr3_bounds[1]]
print ' %s mature' % line['indel_reversed_seqs'][0][cdr3_bounds[0] : cdr3_bounds[1]]
print ''
break
print 'then parse a partition csv file:'
cp = ClusterPath()
cp.readfile(partis_path + '/test/reference-results/seed-partition-new-simu.csv')
cp.print_partitions(abbreviate=True)
