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#!/usr/bin/env python
# -*- coding: utf-8 -*-
### fuse.py - Vidjil utility to parse and regroup list of clones of different timepoints or origins
# This file is part of Vidjil <http://www.vidjil.org>,
# High-throughput Analysis of V(D)J Immune Repertoire.
# Copyright (C) 2011-2017 by Bonsai bioinformatics
# at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
# Contributors:
# Marc Duez <marc.duez@vidjil.org>
# Mathieu Giraud <mathieu.giraud@vidjil.org>
# The Vidjil Team <contact@vidjil.org>
#
# "Vidjil" is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# "Vidjil" is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with "Vidjil". If not, see <http://www.gnu.org/licenses/>
from __future__ import print_function
import check_python_version
import sys
import json
import argparse
import os.path
import os
import datetime
import subprocess
import tempfile
from operator import itemgetter
from utils import *
from defs import *
from collections import defaultdict
FUSE_VERSION = "vidjil fuse"
TOOL_SIMILARITY = "../algo/tools/similarity"
SIMILARITY_LIMIT = 100
GERMLINES_ORDER = ['TRA', 'TRB', 'TRG', 'TRD', 'DD', 'IGH', 'DHJH', 'IJK', 'IJL']
####
class Window:
# Should be renamed "Clone"
'''storage class for sequence informations
with some function to group sequence informations
>>> str(w1)
'<window : [5] 3 aaa>'
>>> str(w3)
'<window : [8] 4 aaa>'
>>> str(w1 + w3)
'<window : [5, 8] 3 aaa>'
check if other information are conserved
>>> (w2 + w4).d["test"]
[0, 'plop']
'''
### init Window with the minimum data required
def __init__(self, size):
self.d={}
self.d["id"] = ""
self.d["top"] = sys.maxsize
self.d["reads"] = []
for i in range(size):
self.d["reads"].append(0)
###
def __iadd__(self, other):
### Not used now
"""Add other.reads to self.reads in-place, without extending lists"""
assert(len(self.d['reads']) == len(other.d['reads']))
self.d['reads'] = [my + her for (my, her) in zip(self.d['reads'], other.d['reads'])]
return self
def __add__(self, other):
"""Concat two windows, extending lists such as 'reads'"""
#data we don't need to duplicate
myList = [ "seg", "top", "id", "sequence", "name", "id", "stats", "germline"]
obj = Window(1)
concatenate_with_padding(obj.d,
self.d, len(self.d["reads"]),
other.d, len(other.d["reads"]),
myList)
#keep other data who don't need to be concat
if other.d["top"] < self.d["top"] :
for key in other.d :
if key in myList :
obj.d[key] = other.d[key]
else :
for key in self.d :
if key in myList :
obj.d[key] = self.d[key]
return obj
def get_nb_reads(self, cid, point=0):
return self[cid]["reads"][point]
def latex(self, point=0, base_germline=10000, base=10000, tag=''):
reads = self.d["reads"][point]
ratio_germline = float(reads)/base_germline
ratio = float(reads)/base
return r" & & %7d & %5.2f\%% & of %-4s & %5.2f\%% & %-50s \\ %% %4s %s" % (reads, ratio_germline * 100, self.d['germline'], ratio * 100,
self.d["name"] if 'name' in self.d else self.d["id"],
tag, self.d["id"])
### print essential info about Window
def __str__(self):
return "<window : %s %s %s>" % ( self.d["reads"], '*' if self.d["top"] == sys.maxsize else self.d["top"], self.d["id"])
class Samples:
def __init__(self):
self.d={}
self.d["number"] = 1
self.d["original_names"] = [""]
def __add__(self, other):
obj=Samples()
concatenate_with_padding(obj.d,
self.d, self.d['number'],
other.d, other.d['number'],
['number'])
obj.d["number"] = int(self.d["number"]) + int(other.d["number"])
return obj
def __str__(self):
return "<Samples: %s>" % self.d
class Diversity:
keys = ["index_H_entropy", "index_E_equitability", "index_Ds_diversity"]
def __init__(self, data=None):
self.d={}
for k in self.keys:
if data == None or not (k in data):
self.d[k] = ["na"]
else:
self.d[k]= [data[k]]
def __add__(self, other):
for k in self.keys:
self.d[k].append(other.d[k][0])
return self
def __str__(self):
return "<Diversity: %s>" % self.d
class Reads:
def __init__(self):
self.d={}
self.d["total"] = ["0"]
self.d["segmented"] = ["0"]
self.d["germline"] = {}
self.d['distribution'] = {}
def __add__(self, other):
obj=Reads()
concatenate_with_padding(obj.d['germline'],
self.d['germline'], len(self.d['total']),
other.d['germline'], len(other.d['total']),
['total'])
concatenate_with_padding(obj.d['distribution'],
self.d['distribution'], len(self.d['total']),
other.d['distribution'], len(other.d['total']),
['total'])
obj.d["total"] = self.d["total"] + other.d["total"]
obj.d["segmented"] = self.d["segmented"] + other.d["segmented"]
return obj
def __str__(self):
return "<Reads: %s>" % self.d
class OtherWindows:
"""Aggregate counts of windows that are discarded (due to too small 'top') for each point into several 'others-' windows."""
def __init__(self, length, ranges = None):
self.ranges = ranges if ranges is not None else [1000, 100, 10, 1]
self.length = length
self.sizes = {}
for r in self.ranges:
self.sizes[r] = [0 for i in range(self.length)]
def __iadd__(self, window):
"""Add to self a window. The different points may land into different 'others-' windows."""
for i, s in enumerate(window.d["reads"]):
for r in self.ranges:
if s >= r:
break
self.sizes[r][i] += s
## TODO: add seg_stat
# print window, '-->', self.sizes
return self
def __iter__(self):
"""Yield the 'others-' windows"""
for r in self.ranges:
w = Window(self.length)
w.d['reads'] = self.sizes[r]
w.d['window'] = 'others-%d' % r
w.d['top'] = 0
print(' --[others]-->', w)
yield w
class ListWindows(VidjilJson):
'''storage class for sequences informations
>>> lw1.info()
<ListWindows: [25] 2>
<window : [5] 3 aaa>
<window : [12] 2 bbb>
>>> lw2.info()
<ListWindows: [34] 2>
<window : [8] 4 aaa>
<window : [2] 8 ccc>
>>> lw3 = lw1 + lw2
>>> lw3.info()
<ListWindows: [25, 34] 3>
<window : [12, 0] 2 bbb>
<window : [5, 8] 3 aaa>
<window : [0, 2] 8 ccc>
>>> lw3.build_stat()
>>> lw3.d['reads'].d['distribution']['0.1']
[17, 8]
>>> lw3.d['reads'].d['distribution']['0.01']
[0, 2]
>>> lw3.d['reads'].d['distribution']['0.001']
[0, 0]
>>> lw3.d['reads'].d['distribution']['0.0001']
[0, 0]
'''
def __init__(self):
'''init ListWindows with the minimum data required'''
self.d={}
self.d["samples"] = Samples()
self.d["reads"] = Reads()
self.d["clones"] = []
self.d["clusters"] = []
self.d["germlines"] = {}
self.d["vidjil_json_version"] = VIDJIL_JSON_VERSION
self.d["producer"] = FUSE_VERSION
self.d["timestamp"] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
def __str__(self):
return "<ListWindows: %s %d>" % ( self.d["reads"].d["segmented"], len(self) )
# Iterator and access functions
def __iter__(self):
return self.d["clones"].__iter__()
def __getitem__(self, i):
### not efficient !
for clone in self:
if clone.d["id"] == i:
return clone
def __len__(self):
return len(self.d["clones"])
### print info about each Windows stored
def info(self):
print(self)
for clone in self:
print(clone)
### compute statistics about clones
def build_stat(self):
ranges = [.1, .01, .001, .0001, .00001, .000001, .0000001]
result = [[0 for col in range(len(self.d['reads'].d["segmented"]))] for row in range(len(ranges))]
for clone in self:
for i, s in enumerate(clone.d["reads"]):
for r in range(len(ranges)):
if s*1. / self.d['reads'].d['segmented'][i] >= ranges[r]:
break
result[r][i] += s
for r in range(len(ranges)):
ratio_in_string = '{0:.10f}'.format(ranges[r]).rstrip('0')
self.d['reads'].d['distribution'][ratio_in_string] = result[r]
#TODO V/D/J distrib and more
### save / load to .json
def save_json(self, output):
'''save ListWindows in .json format'''
print("==>", output)
with open(output, "w") as f:
json.dump(self, f, indent=2, default=self.toJson)
def load(self, file_path, *args, **kwargs):
if not '.clntab' in file_path:
self.load_vidjil(file_path, *args, **kwargs)
else:
self.load_clntab(file_path, *args, **kwargs)
def load_vidjil(self, file_path, pipeline, verbose=True):
'''init listWindows with data file
Detects and selects the parser according to the file extension.'''
# name = file_path.split("/")[-1]
extension = file_path.split('.')[-1]
if verbose:
print("<==", file_path, "\t", end=' ')
with open(file_path, "r") as f:
tmp = json.load(f, object_hook=self.toPython)
self.d=tmp.d
# Be robust against 'null' values for clones
if not self.d["clones"]:
self.d["clones"] = []
self.check_version(file_path)
if "diversity" in self.d.keys():
self.d["diversity"] = Diversity(self.d["diversity"])
else:
self.d["diversity"] = Diversity()
if 'distribution' not in self.d['reads'].d:
self.d['reads'].d['distribution'] = {}
if pipeline:
# renaming, private pipeline
f = '/'.join(file_path.split('/')[2:-1])
if verbose:
print("[%s]" % f)
else:
f = file_path
if verbose:
print()
time = os.path.getmtime(file_path)
self.d["samples"].d["timestamp"] = [datetime.datetime.fromtimestamp(time).strftime("%Y-%m-%d %H:%M:%S")]
self.id_lengths = defaultdict(int)
print("%%")
for clone in self:
self.id_lengths[len(clone.d['id'])] += 1
print ("%% lengths .vidjil -> ", self.id_lengths)
try:
print("%% run_v ->", self.d["samples"].d["producer"], self.d["samples"].d["run_timestamp"])
except KeyError:
pass
def getTop(self, top):
result = []
for clone in self:
if clone.d["top"] <= top :
result.append(clone.d["id"])
return result
def filter(self, f):
r = []
reverseList = {}
for i,w in enumerate(self.d["clones"]) :
reverseList[w.d["id"]] = i
#filteredList = { k: reverseList[k] for k in f }
filteredList = dict(filter(lambda t: t[0] in f, reverseList.items()))
for i in filteredList:
r.append(self.d["clones"][filteredList[i]])
self.d["clones"] = r
###
def __add__(self, other):
'''Combine two ListWindows into a unique ListWindows'''
obj = ListWindows()
l1 = len(self.d["reads"].d['segmented'])
l2 = len(other.d["reads"].d['segmented'])
concatenate_with_padding(obj.d,
self.d, l1,
other.d, l2,
["clones", "links", "germlines",
"vidjil_json_version"])
obj.d["clones"]=self.fuseWindows(self.d["clones"], other.d["clones"], l1, l2)
obj.d["samples"] = self.d["samples"] + other.d["samples"]
obj.d["reads"] = self.d["reads"] + other.d["reads"]
obj.d["diversity"] = self.d["diversity"] + other.d["diversity"]
return obj
###
def __mul__(self, other):
for i in range(len(self.d["reads_segmented"])):
self.d["reads_segmented"][i] += other.d["reads_segmented"][i]
self.d["clones"] += other.d["clones"]
self.d["vidjil_json_version"] = [VIDJIL_JSON_VERSION]
self.d["system_segmented"].update(other.d["system_segmented"])
return self
###
def fuseWindows(self, w1, w2, l1, l2) :
#store data in dict with "id" as key
dico1 = {}
for i in range(len(w1)) :
dico1[ w1[i].d["id"] ] = w1[i]
dico2 = {}
for i in range(len(w2)) :
dico2[ w2[i].d["id"] ] = w2[i]
#concat data with the same key ("id")
#if some data are missing we concat with an empty Windows()
dico3 = {}
for key in dico1 :
if key in dico2 :
dico3[key] = dico1[key] + dico2[key]
else :
w=Window(l2)
dico3[key] = dico1[key] + w
for key in dico2 :
if key not in dico1 :
w=Window(l1)
dico3[key] = w + dico2[key]
#sort by top
tab = []
for key in dico3 :
tab.append((dico3[key], dico3[key].d["top"]))
tab = sorted(tab, key=itemgetter(1))
#store back in a List
result=[]
for i in range(len(tab)) :
result.append(tab[i][0])
return result
def cut(self, limit, nb_points):
'''Remove information from sequence/windows who never enter in the most represented sequences. Put this information in 'other' windows.'''
w=[]
others = OtherWindows(nb_points)
for clone in self:
if (int(clone.d["top"]) < limit or limit == 0) :
w.append(clone)
#else:
#others += clone
self.d["clones"] = w #+ list(others)
print("### Cut merged file, keeping window in the top %d for at least one point" % limit)
return self
def load_clntab(self, file_path, *args, **kwargs):
'''Parser for .clntab file'''
self.d["vidjil_json_version"] = [VIDJIL_JSON_VERSION]
self.d["samples"].d["original_names"] = [file_path]
self.d["samples"].d["producer"] = ["EC-NGS central pipeline"]
listw = []
listc = []
total_size = 0
fichier = open(file_path,"r")
for ligne in fichier:
if "clonotype" in ligne:
header_map = ligne.replace('\n', '').split('\t')
else :
tab = AccessedDict()
for index, data in enumerate(ligne.split('\t')):
tab[header_map[index]] = data
w=Window(1)
w.d["seg"] = {}
#w.window=tab["sequence.seq id"] #use sequence id as window for .clntab data
w.d["id"]=tab["sequence.raw nt seq"] #use sequence as window for .clntab data
s = int(tab["sequence.size"])
total_size += s
w.d["reads"] = [ s ]
w.d["germline"] = tab["sequence.V-GENE and allele"][:3] #system ...
w.d["sequence"] = tab["sequence.raw nt seq"]
w.d["seg"]["5"]=tab["sequence.V-GENE and allele"].split('=')[0]
if (tab["sequence.D-GENE and allele"] != "") :
w.d["seg"]["4"]=tab["sequence.D-GENE and allele"].split('=')[0]
w.d["seg"]["3"]=tab["sequence.J-GENE and allele"].split('=')[0]
# use sequence.JUNCTION to colorize output (this is not exactly V/J !)
junction = tab.get("sequence.JUNCTION.raw nt seq")
position = w.d["sequence"].find(junction)
if position >= 0:
w.d["seg"]["3start"] = position + len(junction)
w.d["seg"]["5end"] = position
else:
w.d["seg"]["3start"] = 0
w.d["seg"]["5end"] = len(w.d["sequence"])
w.d["seg"]["3end"]=0
w.d["seg"]["5start"]=0
w.d["seg"]["4end"]=0
w.d["seg"]["4start"]=0
w.d["seg"]["cdr3"] = tab["sequence.JUNCTION.raw nt seq"][3:-3]
listw.append((w , w.d["reads"][0]))
raw_clonotype = tab.get("clonotype")
w.d["name"]=raw_clonotype # w.d["seg"]["5"] + " -x/y/-z " + w.d["seg"]["3"]
clonotype = raw_clonotype.split(' ')
if (len(clonotype) > 1) :
listc.append((w, raw_clonotype))
#keep data that has not already been stored
for header in tab.not_accessed_keys():
w.d["_"+header] = [tab[header]]
#sort by sequence_size
listw = sorted(listw, key=itemgetter(1), reverse=True)
#sort by clonotype
listc = sorted(listc, key=itemgetter(1))
#generate data "top"
for index in range(len(listw)):
listw[index][0].d["top"]=index+1
self.d["clones"].append(listw[index][0])
self.d["reads"].d["segmented"] = [total_size]
self.d["reads"].d["total"] = [total_size]
def toJson(self, obj):
'''Serializer for json module'''
if isinstance(obj, ListWindows) or isinstance(obj, Window) or isinstance(obj, Samples) or isinstance(obj, Reads) or isinstance(obj, Diversity):
result = {}
for key in obj.d :
result[key]= obj.d[key]
return result
raise TypeError(repr(obj) + " fail !")
else:
result = {}
for key in obj :
result[key]= obj[key]
return result
raise TypeError(repr(obj) + " fail !")
def toPython(self, obj_dict):
'''Reverse serializer for json module'''
if "samples" in obj_dict:
obj = ListWindows()
obj.d=obj_dict
return obj
if "id" in obj_dict:
obj = Window(1)
obj.d=obj_dict
return obj
if "total" in obj_dict:
obj = Reads()
obj.d=obj_dict
return obj
if "original_names" in obj_dict:
obj = Samples()
obj.d=obj_dict
return obj
return obj_dict
### some data used for test
w1 = Window(1)
w1.d ={"id" : "aaa", "reads" : [5], "top" : 3 }
w2 = Window(1)
w2.d ={"id" : "bbb", "reads" : [12], "top" : 2 }
w3 = Window(1)
w3.d ={"id" : "aaa", "reads" : [8], "top" : 4 }
w4 = Window(1)
w4.d ={"id" : "ccc", "reads" : [2], "top" : 8, "test" : ["plop"] }
w5 = Window(1)
w5.d ={"id" : "aaa", "reads" : [5], "top" : 3 }
w6 = Window(1)
w6.d ={"id" : "bbb", "reads" : [12], "top" : 2 }
lw1 = ListWindows()
lw1.d["timestamp"] = 'ts'
lw1.d["reads"] = json.loads('{"total": [30], "segmented": [25], "germline": {}, "distribution": {}}', object_hook=lw1.toPython)
lw1.d["clones"].append(w5)
lw1.d["clones"].append(w6)
lw1.d["diversity"] = Diversity()
w7 = Window(1)
w7.d ={"id" : "aaa", "reads" : [8], "top" : 4 }
w8 = Window(1)
w8.d ={"id" : "ccc", "reads" : [2], "top" : 8, "test" : ["plop"] }
lw2 = ListWindows()
lw2.d["timestamp"] = 'ts'
lw2.d["reads"] = json.loads('{"total": [40], "segmented": [34], "germline": {}, "distribution": {}}', object_hook=lw1.toPython)
lw2.d["clones"].append(w7)
lw2.d["clones"].append(w8)
lw2.d["diversity"] = Diversity()
def main():
print("#", ' '.join(sys.argv))
DESCRIPTION = 'Vidjil utility to parse and regroup list of clones of different timepoints or origins'
#### Argument parser (argparse)
parser = argparse.ArgumentParser(description= DESCRIPTION,
epilog='''Example:
python2 %(prog)s --germline IGH out/Diag/vidjil.data out/MRD-1/vidjil.data out/MRD-2/vidjil.data''',
formatter_class=argparse.RawTextHelpFormatter)
group_options = parser.add_argument_group() # title='Options and parameters')
group_options.add_argument('--test', action='store_true', help='run self-tests')
group_options.add_argument('--multi', action='store_true', help='merge different systems from a same timepoint (deprecated, do not use)')
group_options.add_argument('--compress', '-c', action='store_true', help='compress point names, removing common substrings')
group_options.add_argument('--pipeline', '-p', action='store_true', help='compress point names (internal Bonsai pipeline)')
group_options.add_argument('--output', '-o', type=str, default='fused.vidjil', help='output file (%(default)s)')
group_options.add_argument('--top', '-t', type=int, default=50, help='keep only clones in the top TOP of some point (%(default)s)')
group_options.add_argument('--first', '-f', type=int, default=0, help='take only into account the first FIRST files (0 for all) (%(default)s)')
parser.add_argument('file', nargs='+', help='''input files (.vidjil/.cnltab)''')
args = parser.parse_args()
# print args
if args.test:
import doctest
doctest.testmod(verbose = True)
sys.exit(0)
jlist_fused = None
print("### fuse.py -- " + DESCRIPTION)
print()
files = args.file
if args.first:
if len(files) > args.first:
print("! %d files were given. We take into account the first %d files." % (len(files), args.first))
files = files[:args.first]
#filtre
f = []
for path_name in files:
jlist = ListWindows()
jlist.load(path_name, args.pipeline)
f += jlist.getTop(args.top)
f = sorted(set(f))
if args.multi:
for path_name in files:
jlist = ListWindows()
jlist.load(path_name, args.pipeline)
jlist.build_stat()
print("\t", jlist, end=' ')
if jlist_fused is None:
jlist_fused = jlist
else:
jlist_fused = jlist_fused * jlist
print('\t==> merge to', jlist_fused)
jlist_fused.d["system_segmented"] = ordered(jlist_fused.d["system_segmented"], key=lambda sys: ((GERMLINES_ORDER + [sys]).index(sys), sys))
else:
print("### Read and merge input files")
for path_name in files:
jlist = ListWindows()
jlist.load(path_name, args.pipeline)
jlist.build_stat()
jlist.filter(f)
w1 = Window(1)
w2 = Window(2)
w3 = w1+w2
print("\t", jlist, end=' ')
# Merge lists
if jlist_fused is None:
jlist_fused = jlist
else:
jlist_fused = jlist_fused + jlist
print('\t==> merge to', jlist_fused)
if args.compress:
print()
print("### Select point names")
l = jlist_fused.d["samples"].d["original_names"]
ll = interesting_substrings(l)
print(" <==", l)
print(" ==>", ll)
jlist_fused.d["samples"].d["names"] = ll
print()
if not args.multi:
jlist_fused.cut(args.top, jlist_fused.d["samples"].d["number"])
print("\t", jlist_fused)
print()
#compute similarity matrix
if len(jlist_fused.d["clones"]) < SIMILARITY_LIMIT :
fasta = ""
for i in range(len(jlist_fused.d["clones"])) :
fasta += ">>" + str(i) + "\n"
fasta += jlist_fused.d["clones"][i].d["id"] + "\n"
fasta_file = tempfile.NamedTemporaryFile(delete=False)
fasta_file.write(fasta)
try:
out = subprocess.check_output([TOOL_SIMILARITY, "-j", fasta_file.name])
jlist_fused.d["similarity"] = json.loads(out)
except OSError:
print("! failed: %s" % TOOL_SIMILARITY)
finally:
os.unlink(fasta_file.name)
else :
jlist_fused.d["similarity"] = [];
print("### Save merged file")
jlist_fused.save_json(args.output)
if __name__ =='__main__':
main()