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#!/usr/bin/env python3
"""
Converts TSV files into IgPhyML input files
"""
# Info
__author__ = "Kenneth Hoehn"
from changeo import __version__, __date__
# Imports
import os
import sys
from argparse import ArgumentParser
from collections import OrderedDict
from textwrap import dedent
from time import time
from Bio.Seq import Seq
# Presto and changeo imports
from presto.Defaults import default_out_args
from presto.IO import printLog, printMessage, printWarning, printError, printDebug
from changeo.Defaults import default_format
from changeo.IO import splitName, getDbFields, getFormatOperators, getOutputHandle
from changeo.Alignment import getRegions
from changeo.Commandline import CommonHelpFormatter, checkArgs, getCommonArgParser, parseCommonArgs
def correctMidCodonStart(scodons, qi, debug):
"""
Find and mask split codons
Arguments:
scodons (list): list of codons in IMGT sequence.
qi (str) : input sequence.
spos (int) : starting position of IMGT sequence in input sequence.
debug (bool) : print debugging statements.
Returns:
tuple: (modified input sequence, modified starting position of IMGT sequence in input sequence).
"""
spos = 0
for i in range(0, len(scodons)):
printDebug("%s %s" % (scodons[i], qi[0:3]), debug)
if scodons[i] != "...":
if scodons[i][0:2] == "..":
scodons[i] = "NN" + scodons[i][2]
#sometimes IMGT will just cut off first letter if non-match, at which point we"ll just want to mask the
#first codon in the IMGT seq, other times it will be legitimately absent from the query, at which point
#we have to shift the frame. This attempts to correct for this by looking at the next codon over in the
#alignment
if scodons[i][2:3] != qi[2:3] or scodons[i + 1] != qi[3:6]:
qi = "NN" + qi
spos = i
break
elif scodons[i][0] == ".":
scodons[i] = "N" + scodons[i][1:3]
if scodons[i][1:3] != qi[1:3] or scodons[i+1] != qi[3:6]:
qi = "N" + qi
spos = i
break
else:
spos = i
break
return qi, spos
def checkFrameShifts(receptor, oqpos, ospos, log, debug):
"""
Checks whether a frameshift occured in a sequence
Arguments:
receptor (changeo.Receptor.Receptor): Receptor object.
oqpos (int) : position of interest in input sequence.
ospos (int) : position of interest in IMGT sequence.
log (dict) : log of information for each sequence.
debug (bool) : print debugging statements.
"""
frameshifts = 0
for ins in range(1, 3):
ros = receptor.sequence_input
ris = receptor.sequence_imgt
psite = receptor.v_seq_start - 1 + oqpos*3
pisite = ospos * 3
if (psite + 3 + ins) < len(ros) and (pisite + 3) < len(ris):
#cut out 1 or 2 nucleotides downstream of offending codon
receptor.sequence_input = ros[0:(psite + 3)] + ros[(psite + 3 + ins):]
receptor.sequence_imgt = ris[0:(pisite + 3)] + ris[(pisite + 3):]
# Debug sequence modifications
printDebug(ros, debug)
printDebug(receptor.sequence_input, debug)
printDebug(ris, debug)
printDebug(receptor.sequence_imgt, debug)
printDebug("RUNNING %d" % ins, debug)
mout = maskSplitCodons(receptor, recursive=True)
if mout[1]["PASS"]:
#if debug:
receptor.sequence_input = ros
receptor.sequence_imgt = ris
frameshifts += 1
printDebug("FRAMESHIFT of length %d!" % ins, debug)
log["FAIL"] = "SINGLE FRAME-SHIFTING INSERTION"
break
else:
receptor.sequence_input = ros
receptor.sequence_imgt = ris
return frameshifts
def findAndMask(receptor, scodons, qcodons, spos, s_end, qpos, log, debug, recursive):
"""
Find and mask split codons
Arguments:
receptor (changeo.Receptor.Receptor): Receptor object.
scodons (list): list of codons in IMGT sequence
qcodons (list): list of codons in input sequence
spos (int): starting position of IMGT sequence in input sequence
s_end (int): end of IMGT sequence
qpos (int): starting position of input sequence in IMGT sequence
log (dict): log of information for each sequence
debug (bool): print debugging statements?
"""
frameshifts = 0
while spos < s_end and qpos < len(qcodons):
if debug:
print(scodons[spos] + "\t" + qcodons[qpos])
if scodons[spos] == "..." and qcodons[qpos] != "...": #if IMGT gap, move forward in imgt
spos += 1
elif scodons[spos] == qcodons[qpos]: # if both are the same, move both forward
spos += 1
qpos += 1
elif qcodons[qpos] == "N": # possible that SEQ-IMGT ends on a bunch of Ns
qpos += 1
spos += 1
else: # if not the same, mask IMGT at that site and scan forward until you find a codon that matches next site
if debug:
print("checking %s at position %d %d" % (scodons[spos], spos, qpos))
ospos=spos
oqpos=qpos
spos += 1
qpos += 1
while spos < s_end and scodons[spos] == "...": #possible next codon is just a gap
spos += 1
while qpos < len(qcodons) and spos < s_end and scodons[spos] != qcodons[qpos]:
printDebug("Checking " + scodons[spos]+ "\t" + qcodons[qpos], debug)
qpos += 1
if qcodons[qpos-1] == scodons[ospos]: #if codon in previous position is equal to original codon, it was preserved
qpos -= 1
spos = ospos
printDebug("But codon was apparently preserved", debug)
if "IN-FRAME" in log:
log["IN-FRAME"] = log["IN-FRAME"] + "," + str(spos)
else:
log["IN-FRAME"] = str(spos)
elif qpos >= len(qcodons) and spos < s_end:
printDebug("FAILING MATCH", debug)
log["PASS"] = False #if no match for the adjacent codon was found, something"s up.
log["FAIL"] = "FAILED_MATCH_QSTRING:"+str(spos)
#figure out if this was due to a frame-shift by repeating this method but with an edited input sequence
if not recursive:
frameshifts += checkFrameShifts(receptor, oqpos, ospos, log, debug)
elif spos >= s_end or qcodons[qpos] != scodons[spos]:
scodons[ospos] = "NNN"
if spos >= s_end:
printDebug("Masked %s at position %d, at end of subject sequence" % (scodons[ospos], ospos), debug)
if "END-MASKED" in log:
log["END-MASKED"] = log["END-MASKED"] + "," + str(spos)
else:
log["END-MASKED"] = str(spos)
else:
printDebug("Masked %s at position %d, but couldn't find upstream match" % (scodons[ospos], ospos), debug)
log["PASS"]=False
log["FAIL"]="FAILED_MATCH:"+str(spos)
elif qcodons[qpos] == scodons[spos]:
printDebug("Masked %s at position %d" % (scodons[ospos], ospos), debug)
scodons[ospos] = "NNN"
if "MASKED" in log:
log["MASKED"] = log["MASKED"] + "," + str(spos)
else:
log["MASKED"] = str(spos)
else:
log["PASS"] = False
log["FAIL"] = "UNKNOWN"
def maskSplitCodons(receptor, recursive=False, mask=True):
"""
Identify junction region by IMGT definition.
Arguments:
receptor (changeo.Receptor.Receptor): Receptor object.
recursive (bool) : was this method part of a recursive call?
mask (bool) : mask split codons for use with igphyml?
Returns:
str: modified IMGT gapped sequence.
log: dict of sequence information
"""
debug = False
qi = receptor.sequence_input
si = receptor.sequence_imgt
log = OrderedDict()
log["ID"]=receptor.sequence_id
log["CLONE"]=receptor.clone
log["PASS"] = True
if debug:
print(receptor.sequence_id)
# adjust starting position of query sequence
qi = qi[(receptor.v_seq_start - 1):]
#tally where --- gaps are in IMGT sequence and remove them for now
gaps = []
nsi = ""
for i in range(0,len(si)):
if si[i] == "-":
gaps.append(1)
else:
gaps.append(0)
nsi = nsi + si[i]
#find any gaps not divisible by three
curgap = 0
for i in gaps:
if i == 1:
curgap += 1
elif i == 0 and curgap != 0:
if curgap % 3 != 0 :
printDebug("Frame-shifting gap detected! Refusing to include sequence.", debug)
log["PASS"] = False
log["FAIL"] = "FRAME-SHIFTING DELETION"
log["SEQ_IN"] = receptor.sequence_input
log["SEQ_IMGT"] = receptor.sequence_imgt
log["SEQ_MASKED"] = receptor.sequence_imgt
return receptor.sequence_imgt, log
else:
curgap = 0
si = nsi
scodons = [si[i:i + 3] for i in range(0, len(si), 3)]
# deal with the fact that it's possible to start mid-codon
qi,spos = correctMidCodonStart(scodons, qi, debug)
qcodons = [qi[i:i + 3] for i in range(0, len(qi), 3)]
frameshifts = 0
s_end = 0 #adjust for the fact that IMGT sequences can end on gaps
for i in range(spos, len(scodons)):
if scodons[i] != "..." and len(scodons[i]) == 3 and scodons[i] != "NNN":
s_end = i
printDebug("%i:%i:%s" % (s_end, len(scodons), scodons[s_end]), debug)
s_end += 1
qpos = 0
if mask:
findAndMask(receptor, scodons, qcodons, spos, s_end, qpos, log, debug, recursive)
if not log["PASS"] and not recursive:
log["FRAMESHIFTS"] = frameshifts
if len(scodons[-1]) != 3:
if scodons[-1] == ".." or scodons[-1] == ".":
scodons[-1] = "..."
else:
scodons[-1] = "NNN"
if "END-MASKED" in log:
log["END-MASKED"] = log["END-MASKED"] + "," + str(len(scodons))
else:
log["END-MASKED"] = str(spos)
concatenated_seq = Seq("")
for i in scodons:
concatenated_seq += i
# add --- gaps back to IMGT sequence
ncon_seq = ""
counter = 0
for i in gaps:
#print(str(i) + ":" + ncon_seq)
if i == 1:
ncon_seq = ncon_seq + "."
elif i == 0:
ncon_seq = ncon_seq + concatenated_seq[counter]
counter += 1
ncon_seq = ncon_seq + concatenated_seq[counter:]
concatenated_seq = ncon_seq
log["SEQ_IN"] = receptor.sequence_input
log["SEQ_IMGT"] = receptor.sequence_imgt
log["SEQ_MASKED"] = concatenated_seq
return concatenated_seq, log
def unAmbigDist(seq1, seq2, fbreak=False):
"""
Calculate the distance between two sequences counting only A,T,C,Gs
Arguments:
seq1 (str): sequence 1
seq2 (str): sequence 2
fbreak (bool): break after first difference found?
Returns:
int: number of ACGT differences.
"""
if len(seq1) != len(seq2):
printError("Sequences are not the same length! %s %s" % (seq1, seq2))
dist = 0
for i in range(0,len(seq1)):
if seq1[i] != "N" and seq1[i] != "-" and seq1[i] != ".":
if seq2[i] != "N" and seq2[i] != "-" and seq2[i] != ".":
if seq1[i] != seq2[i]:
dist += 1
if fbreak:
break
return dist
def deduplicate(useqs, receptors, log=None, meta_data=None, delim=":"):
"""
Collapses identical sequences
Argument:
useqs (dict): unique sequences within a clone. maps sequence to index in Receptor list.
receptors (dict): receptors within a clone (index is value in useqs dict).
log (collections.OrderedDict): log of sequence errors.
meta_data (str): Field to append to sequence IDs. Splits identical sequences with different meta_data.
delim (str): delimited to use when appending meta_data.
Returns:
list: deduplicated receptors within a clone.
"""
keys = list(useqs.keys())
join = {} # id -> sequence id to join with (least ambiguous chars)
joinseqs = {} # id -> useq to join with (least ambiguous chars)
ambigchar = {} #sequence id -> number ATCG nucleotides
for i in range(0,len(keys)-1):
for j in range(i+1,len(keys)):
ki = keys[i]
kj = keys[j]
if meta_data is None:
ski = keys[i]
skj = keys[j]
else:
ski, cid = keys[i].split(delim)
skj, cid = keys[j].split(delim)
ri = receptors[useqs[ki]]
rj = receptors[useqs[kj]]
dist = unAmbigDist(ski, skj, True)
m_match = True
if meta_data is not None and meta_data[0] != "DUPCOUNT":
m_match = ri.getField(meta_data[0]) == rj.getField(meta_data[0])
if dist == 0 and m_match:
ncounti = ki.count("A") + ki.count("T") + ki.count("G") + ki.count("C")
ncountj = kj.count("A") + kj.count("T") + kj.count("G") + kj.count("C")
ambigchar[useqs[ki]] = ncounti
ambigchar[useqs[kj]] = ncountj
# this algorithm depends on the fact that all sequences are compared pairwise, and all are zero
# distance from the sequence they will be collapse to.
if ncountj > ncounti:
nci = 0
if useqs[ki] in join:
nci = ambigchar[join[useqs[ki]]]
if nci < ncountj:
join[useqs[ki]] = useqs[kj]
joinseqs[ki] = kj
else:
ncj = 0
if useqs[kj] in join:
ncj = ambigchar[join[useqs[kj]]]
if ncj < ncounti:
join[useqs[kj]] = useqs[ki]
joinseqs[kj] = ki
# loop through list of joined sequences and collapse
keys = list(useqs.keys())
for k in keys:
if useqs[k] in join:
rfrom = receptors[useqs[k]]
rto = receptors[join[useqs[k]]]
rto.dupcount += rfrom.dupcount
if log is not None:
log[rfrom.sequence_id]["PASS"] = False
log[rfrom.sequence_id]["DUPLICATE"] = True
log[rfrom.sequence_id]["COLLAPSETO"] = joinseqs[k]
log[rfrom.sequence_id]["COLLAPSEFROM"] = k
log[rfrom.sequence_id]["FAIL"] = "Collapsed with " + rto.sequence_id
del useqs[k]
return useqs
def hasPTC(sequence):
"""
Determines whether a PTC exits in a sequence
Arguments:
sequence (str): IMGT gapped sequence in frame 1.
Returns:
int: negative if not PTCs, position of PTC if found.
"""
ptcs = ("TAA", "TGA", "TAG", "TRA", "TRG", "TAR", "TGR", "TRR")
for i in range(0, len(sequence), 3):
if sequence[i:(i+3)] in ptcs:
return i
return -1
def characterizePartitionErrors(sequences, clones, meta_data):
"""
Characterize potential mismatches between IMGT labels within a clone
Arguments:
sequences (list): list of sequences in clones.
clones (list): list of Receptor objects.
meta_data (str): Field to append to sequence IDs. Splits identical sequences with different meta_data.
Returns:
tuple: tuple of length four containing a list of IMGT positions for first sequence in clones,
the germline sequence of the first receptor in clones, the length of the first sequence in clones,
and the number of sequences in clones.
"""
sites = len(sequences[0])
nseqs = len(sequences)
imgtar = clones[0].getField("imgtpartlabels")
germline = clones[0].getField("germline_imgt_d_mask")
correctseqs = False
for seqi in range(0, len(sequences)):
i = sequences[seqi]
if len(i) != sites or len(clones[seqi].getField("imgtpartlabels")) != len(imgtar):
correctseqs = True
if correctseqs:
maxlen = sites
maximgt = len(imgtar)
for j in range(0,len(sequences)):
if len(sequences[j]) > maxlen:
maxlen = len(sequences[j])
if len(clones[j].getField("imgtpartlabels")) > maximgt:
imgtar = clones[j].getField("imgtpartlabels")
maximgt = len(imgtar)
sites = maxlen
for j in range(0,len(sequences)):
cimgt = clones[j].getField("imgtpartlabels")
seqdiff = maxlen - len(sequences[j])
imgtdiff = len(imgtar)-len(cimgt)
sequences[j] = sequences[j] + "N"*(seqdiff)
last = cimgt[-1]
cimgt.extend([last]*(imgtdiff))
clones[j].setField("imgtpartlabels",cimgt)
if meta_data is not None:
meta_data_ar = meta_data[0].split(",")
for c in clones:
if meta_data is not None:
c.setField(meta_data[0],c.getField(meta_data_ar[0]))
for m in range(1,len(meta_data_ar)):
st = c.getField(meta_data[0])+":"+c.getField(meta_data_ar[m])
c.setField(meta_data[0],st)
if len(c.getField("imgtpartlabels")) != len(imgtar):
printError("IMGT assignments are not the same within clone %d!\n" % c.clone,False)
printError(c.getField("imgtpartlabels"),False)
printError("%s\n%d\n" % (imgtar,j),False)
for j in range(0, len(sequences)):
printError("%s\n%s\n" % (sequences[j],clones[j].getField("imgtpartlabels")),False)
printError("ChangeO file needs to be corrected")
for j in range(0,len(imgtar)):
if c.getField("imgtpartlabels")[j] != imgtar[j]:
printError("IMGT assignments are not the same within clone %d!\n" % c.clone, False)
printError(c.getField("imgtpartlabels"), False)
printError("%s\n%d\n" % (imgtar, j))
#Resolve germline if there are differences, e.g. if reconstruction was done before clonal clustering
resolveglines = False
for c in clones:
if c.getField("germline_imgt_d_mask") != germline:
resolveglines = True
if resolveglines:
printError("%s %s" % ("Predicted germlines are not the same among sequences in the same clone.",
"Be sure to cluster sequences into clones first and then predict germlines using --cloned"))
if sites > (len(germline)):
seqdiff = sites - len(germline)
germline = germline + "N" * (seqdiff)
if sites % 3 != 0:
printError("number of sites must be divisible by 3! len: %d, clone: %s , seq: %s" %(len(sequences[0]),\
clones[0].clone,sequences[0]))
return imgtar, germline, sites, nseqs
def outputSeqPartFiles(out_dir, useqs_f, meta_data, clones, collapse, nseqs, delim, newgerm, conseqs, duplicate, imgt):
"""
Create intermediate sequence alignment and partition files for IgPhyML output
Arguments:
out_dir (str): directory for sequence files.
useqs_f (dict): unique sequences mapped to ids.
meta_data (str): Field to append to sequence IDs. Splits identical sequences with different meta_data.
clones (list) : list of receptor objects.
collpase (bool) : deduplicate sequences.
nseqs (int): number of sequences.
delim (str) : delimiter for extracting metadata from ID.
newgerm (str) : modified germline of clonal lineage.
conseqs (list) : consensus sequences.
duplicate (bool) : duplicate sequence if only one in a clone.
imgt (list) : IMGT numbering of clonal positions .
"""
transtable = clones[0].sequence_id.maketrans(" ", "_")
outfile = os.path.join(out_dir, "%s.fasta" % clones[0].clone)
with open(outfile, "w") as clonef:
if collapse:
for seq_f, num in useqs_f.items():
seq = seq_f
cid = ""
if meta_data is not None:
seq, cid = seq_f.split(delim)
clones[num].setField(meta_data[0], clones[num].getField(meta_data[0]).replace(":", "_"))
cid = delim + str(clones[num].getField(meta_data[0]))
sid = clones[num].sequence_id.translate(transtable) + cid
clonef.write(">%s\n%s\n" % (sid, seq.replace(".", "-")))
if len(useqs_f) == 1 and duplicate:
if meta_data is not None:
if meta_data[0] == "DUPCOUNT":
cid = delim + "0"
sid = clones[num].sequence_id.translate(transtable) + "_1" + cid
clonef.write(">%s\n%s\n" % (sid, seq.replace(".", "-")))
else:
for j in range(0, nseqs):
cid = ""
if meta_data is not None:
clones[j].setField(meta_data[0], clones[j].getField(meta_data[0]).replace(":", "_"))
cid = delim+str(clones[j].getField(meta_data[0]))
sid = clones[j].sequence_id.translate(transtable) + cid
clonef.write(">%s\n%s\n" % (sid, conseqs[j].replace(".", "-")))
if nseqs == 1 and duplicate:
if meta_data is not None:
if meta_data[0] == "DUPCOUNT":
cid = delim + "0"
sid = clones[j].sequence_id.translate(transtable)+"_1" + cid
clonef.write(">%s\n%s\n" % (sid, conseqs[j].replace(".", "-")))
clonef.write(">%s_GERM\n" % clones[0].clone)
for i in range(0, len(newgerm)):
clonef.write("%s" % newgerm[i].replace(".","-"))
clonef.write("\n")
#output partition file
partfile = os.path.join(out_dir, "%s.part.txt" % clones[0].clone)
with open(partfile, "w") as partf:
partf.write("%d %d\n" % (2, len(newgerm)))
partf.write("FWR:IMGT\n")
partf.write("CDR:IMGT\n")
partf.write("%s\n" % (clones[0].v_call.split("*")[0]))
partf.write("%s\n" % (clones[0].j_call.split("*")[0]))
partf.write(",".join(map(str, imgt)))
partf.write("\n")
def outputIgPhyML(clones, sequences, meta_data=None, collapse=False, logs=None,
fail_writer=None, out_dir=None, min_seq=1):
"""
Create intermediate sequence alignment and partition files for IgPhyML output
Arguments:
clones (list): receptor objects within the same clone.
sequences (list): sequences within the same clone (share indexes with clones parameter).
meta_data (str): Field to append to sequence IDs. Splits identical sequences with different meta_data
collapse (bool): if True collapse identical sequences.
logs (dict): contains log information for each sequence
out_dir (str): directory for output files.
fail_writer (changeo.IO.TSVWriter): failed sequences writer object.
min_seq (int): minimum number of data sequences to include.
Returns:
int: number of clones.
"""
s = ""
delim = "_"
duplicate = True # duplicate sequences in clones with only 1 sequence?
imgtar, germline, sites, nseqs = characterizePartitionErrors(sequences, clones, meta_data)
tallies = []
for i in range(0, sites, 3):
tally = 0
for j in range(0, nseqs):
if sequences[j][i:(i + 3)] != "...":
tally += 1
tallies.append(tally)
newseqs = [] # remove gap only sites from observed data
newgerm = []
imgt = []
for j in range(0, nseqs):
for i in range(0, sites, 3):
if i == 0:
newseqs.append([])
if tallies[i//3] > 0:
newseqs[j].append(sequences[j][i:(i+3)])
lcodon = ""
for i in range(0, sites, 3):
if tallies[i//3] > 0:
newgerm.append(germline[i:(i+3)])
lcodon=germline[i:(i+3)]
imgt.append(imgtar[i])
if len(lcodon) == 2:
newgerm[-1] = newgerm[-1] + "N"
elif len(lcodon) == 1:
newgerm[-1] = newgerm[-1] + "NN"
useqs_f = OrderedDict()
conseqs = []
for j in range(0, nseqs):
conseq = "".join([str(seq_rec) for seq_rec in newseqs[j]])
if meta_data is not None:
if isinstance(clones[j].getField(meta_data[0]), str):
clones[j].setField(meta_data[0],clones[j].getField(meta_data[0]).replace("_", ""))
conseq_f = "".join([str(seq_rec) for seq_rec in newseqs[j]])+delim+str(clones[j].getField(meta_data[0]))
else:
conseq_f = conseq
if conseq_f in useqs_f and collapse:
clones[useqs_f[conseq_f]].dupcount += clones[j].dupcount
logs[clones[j].sequence_id]["PASS"] = False
logs[clones[j].sequence_id]["FAIL"] = "Duplication of " + clones[useqs_f[conseq_f]].sequence_id
logs[clones[j].sequence_id]["DUPLICATE"]=True
if fail_writer is not None:
fail_writer.writeReceptor(clones[j])
else:
useqs_f[conseq_f] = j
conseqs.append(conseq)
if collapse:
useqs_f = deduplicate(useqs_f, clones, logs, meta_data, delim)
if collapse and len(useqs_f) < min_seq:
for seq_f, num in useqs_f.items():
logs[clones[num].sequence_id]["FAIL"] = "Clone too small: " + str(len(useqs_f))
logs[clones[num].sequence_id]["PASS"] = False
return -len(useqs_f)
elif not collapse and len(conseqs) < min_seq:
for j in range(0, nseqs):
logs[clones[j].sequence_id]["FAIL"] = "Clone too small: " + str(len(conseqs))
logs[clones[j].sequence_id]["PASS"] = False
return -len(conseqs)
# Output fasta file of masked, concatenated sequences
outputSeqPartFiles(out_dir, useqs_f, meta_data, clones, collapse, nseqs,
delim, newgerm, conseqs, duplicate, imgt)
if collapse:
return len(useqs_f)
else:
return nseqs
def maskCodonsLoop(r, clones, cloneseqs, logs, fails, out_args, fail_writer):
"""
Masks codons split by alignment to IMGT reference
Arguments:
r (changeo.Receptor.Receptor): receptor object for a particular sequence.
clones (list): list of receptors.
cloneseqs (list): list of masked clone sequences.
logs (dict): contains log information for each sequence.
fails (dict): counts of various sequence processing failures.
Returns:
None: returns None if an error occurs.
"""
if r.clone is None:
printError("Cannot export datasets until sequences are clustered into clones.")
if r.dupcount is None:
r.dupcount = 1
fails["rec_count"] += 1
fails["totalreads"] += 1
#printProgress(rec_count, rec_count, 0.05, start_time)
ptcs = hasPTC(r.sequence_imgt)
gptcs = hasPTC(r.getField("germline_imgt_d_mask"))
if gptcs >= 0:
log = OrderedDict()
log["ID"] = r.sequence_id
log["CLONE"] = r.clone
log["SEQ_IN"] = r.sequence_input
log["SEQ_IMGT"] = r.sequence_imgt
logs[r.sequence_id] = log
logs[r.sequence_id]["PASS"] = False
logs[r.sequence_id]["FAIL"] = "Germline PTC"
fails["seq_fail"] += 1
fails["germlineptc"] += 1
return None
if r.functional and ptcs < 0:
#If IMGT regions are provided, record their positions
regions = getRegions(r.sequence_imgt, r.junction_length)
#print(regions["cdr1_imgt"]+regions["fwr4_imgt"])
if regions["cdr3_imgt"] is not "":
simgt = regions["fwr1_imgt"] + regions["cdr1_imgt"] + regions["fwr2_imgt"] + regions["cdr2_imgt"] + \
regions["fwr3_imgt"] + regions["cdr3_imgt"] + regions["fwr4_imgt"]
if len(simgt) < len(r.sequence_imgt):
r.fwr4_imgt = r.fwr4_imgt + ("."*(len(r.sequence_imgt) - len(simgt)))
simgt = regions["fwr1_imgt"] + regions["cdr1_imgt"] + regions["fwr2_imgt"] + \
regions["cdr2_imgt"] + regions["fwr3_imgt"] + regions["cdr3_imgt"] + regions["fwr4_imgt"]
imgtpartlabels = [13]*len(regions["fwr1_imgt"]) + [30]*len(regions["cdr1_imgt"]) + [45]*len(regions["fwr2_imgt"]) + \
[60]*len(regions["cdr2_imgt"]) + [80]*len(regions["fwr3_imgt"]) + [108] * len(regions["cdr3_imgt"]) + \
[120] * len(regions["fwr4_imgt"])
r.setField("imgtpartlabels", imgtpartlabels)
if len(r.getField("imgtpartlabels")) != len(r.sequence_imgt) or simgt != r.sequence_imgt:
log = OrderedDict()
log["ID"] = r.sequence_id
log["CLONE"] = r.clone
log["SEQ_IN"] = r.sequence_input
log["SEQ_IMGT"] = r.sequence_imgt
logs[r.sequence_id] = log
logs[r.sequence_id]["PASS"] = False
logs[r.sequence_id]["FAIL"] = "FWR/CDR error"
logs[r.sequence_id]["FWRCDRSEQ"] = simgt
fails["seq_fail"] += 1
fails["region_fail"] += 1
return None
else:
#imgt_warn = "\n! IMGT FWR/CDR sequence columns not detected.\n! Cannot run CDR/FWR partitioned model on this data.\n"
imgtpartlabels = [0] * len(r.sequence_imgt)
r.setField("imgtpartlabels", imgtpartlabels)
#print(r.sequence_imgt)
mout = maskSplitCodons(r)
mask_seq = mout[0]
ptcs = hasPTC(mask_seq)
if ptcs >= 0:
printWarning("Masked sequence suddenly has a PTC.. %s\n" % r.sequence_id)
mout[1]["PASS"] = False
mout[1]["FAIL"] = "PTC_ADDED_FROM_MASKING"
logs[mout[1]["ID"]] = mout[1]
if mout[1]["PASS"]:
#passreads += r.dupcount
if r.clone in clones:
clones[r.clone].append(r)
cloneseqs[r.clone].append(mask_seq)
else:
clones[r.clone] = [r]
cloneseqs[r.clone] = [mask_seq]
else:
if out_args["failed"]:
fail_writer.writeReceptor(r)
fails["seq_fail"] += 1
fails["failreads"] += r.dupcount
if mout[1]["FAIL"] == "FRAME-SHIFTING DELETION":
fails["del_fail"] += 1
elif mout[1]["FAIL"] == "SINGLE FRAME-SHIFTING INSERTION":
fails["in_fail"] += 1
else:
fails["other_fail"] += 1
else:
log = OrderedDict()
log["ID"] = r.sequence_id
log["CLONE"] = r.clone
log["PASS"] = False
log["FAIL"] = "NONFUNCTIONAL/PTC"
log["SEQ_IN"] = r.sequence_input
logs[r.sequence_id] = log
if out_args["failed"]:
fail_writer.writeReceptor(r)
fails["seq_fail"] += 1
fails["nf_fail"] += 1
# Note: Collapse can give misleading dupcount information if some sequences have ambiguous characters at polymorphic sites
def buildTrees(db_file, meta_data=None, collapse=False, min_seq=1, format=default_format, out_args=default_out_args):
"""
Masks codons split by alignment to IMGT reference, then produces input files for IgPhyML
Arguments:
db_file (str): input tab-delimited database file.
meta_data (str): Field to append to sequence IDs. Splits identical sequences with different meta_data
collapse (bool): if True collapse identical sequences.
format (str): input and output format.
out_args (dict): arguments for output preferences.
Returns:
dict: dictionary of output pass and fail files.
"""
# Print parameter info
log = OrderedDict()
log["START"] = "BuildTrees"
log["FILE"] = os.path.basename(db_file)
log["COLLAPSE"] = collapse
printLog(log)
# Open output files
pass_handle = getOutputHandle(db_file,
out_label="lineages",
out_dir=out_args["out_dir"],
out_name=out_args["out_name"],
out_type="tsv")
dir_name, __ = os.path.split(pass_handle.name)
if out_args["out_name"] is None:
__, clone_name, __ = splitName(db_file)
else:
clone_name = out_args["out_name"]
# clone_dir = outdir/out_name
if dir_name is None:
clone_dir = clone_name
else:
clone_dir = os.path.join(dir_name, clone_name)
if not os.path.exists(clone_dir):
os.makedirs(clone_dir)
# Format options
try:
reader, writer, __ = getFormatOperators(format)
except ValueError:
printError("Invalid format %s." % format)
out_fields = getDbFields(db_file, reader=reader)
# open input file
handle = open(db_file, "r")
records = reader(handle)
fail_handle, fail_writer = None, None
if out_args["failed"]:
fail_handle = getOutputHandle(db_file,
out_label="lineages-fail",
out_dir=out_args["out_dir"],
out_name=out_args["out_name"],
out_type=out_args["out_type"])
fail_writer = writer(fail_handle, fields=out_fields)
cloneseqs = {}
clones = {}
logs = OrderedDict()
fails = {"rec_count":0, "seq_fail":0, "nf_fail":0, "del_fail":0, "in_fail":0, "minseq_fail":0,
"other_fail":0, "region_fail":0, "germlineptc":0, "fdcount":0, "totalreads":0,
"passreads":0, "failreads":0}
# Mask codons split by indels
start_time = time()
printMessage("Correcting frames and indels of sequences", start_time=start_time, width=50)
for r in records:
maskCodonsLoop(r, clones, cloneseqs, logs, fails, out_args, fail_writer)
# Start processing clones
clonesizes = {}
pass_count, nclones = 0, 0
printMessage("Processing clones", start_time=start_time, width=50)
for k in clones.keys():
if len(clones[str(k)]) < min_seq:
for j in range(0, len(clones[str(k)])):
logs[clones[str(k)][j].sequence_id]["FAIL"] = "Clone too small: " + str(len(cloneseqs[str(k)]))
logs[clones[str(k)][j].sequence_id]["PASS"] = False
clonesizes[str(k)] = -len(cloneseqs[str(k)])
else:
clonesizes[str(k)] = outputIgPhyML(clones[str(k)], cloneseqs[str(k)], meta_data=meta_data, collapse=collapse,
logs=logs, fail_writer=fail_writer, out_dir=clone_dir, min_seq=min_seq)
#If clone is too small, size is returned as a negative
if clonesizes[str(k)] > 0:
nclones += 1
pass_count += clonesizes[str(k)]
else:
fails["seq_fail"] -= clonesizes[str(k)]
fails["minseq_fail"] -= clonesizes[str(k)]
fail_count = fails["rec_count"] - pass_count
# End clone processing
printMessage("Done", start_time=start_time, end=True, width=50)
log_handle = None
if out_args["log_file"] is not None:
log_handle = open(out_args["log_file"], "w")
for j in logs.keys():
printLog(logs[j], handle=log_handle)
pass_handle.write(str(nclones)+"\n")
for key in sorted(clonesizes, key=clonesizes.get, reverse=True):
#print(key + "\t" + str(clonesizes[key]))
outfile = os.path.join(clone_dir, "%s.fasta" % key)
partfile = os.path.join(clone_dir, "%s.part.txt" % key)
if clonesizes[key] > 0:
pass_handle.write("%s\t%s\t%s\t%s\n" % (outfile, "N", key+"_GERM", partfile))
handle.close()
output = {"pass": None, "fail": None}
if pass_handle is not None:
output["pass"] = pass_handle.name
pass_handle.close()
if fail_handle is not None:
output["fail"] = fail_handle.name
fail_handle.close()
if log_handle is not None:
log_handle.close()
#printProgress(rec_count, rec_count, 0.05, start_time)
log = OrderedDict()
log["OUTPUT"] = os.path.basename(pass_handle.name) if pass_handle is not None else None
log["RECORDS"] = fails["rec_count"]
log["PASS"] = pass_count
log["FAIL"] = fail_count
log["NONFUNCTIONAL"] = fails["nf_fail"]
log["FRAMESHIFT_DEL"] = fails["del_fail"]
log["FRAMESHIFT_INS"] = fails["in_fail"]
log["CLONETOOSMALL"] = fails["minseq_fail"]
log["CDRFWR_ERROR"] = fails["region_fail"]
log["GERMLINE_PTC"] = fails["germlineptc"]
log["OTHER_FAIL"] = fails["other_fail"]
if collapse:
log["DUPLICATE"] = fail_count - fails["seq_fail"]
log["END"] = "BuildTrees"
printLog(log)
return output
def getArgParser():
"""
Defines the ArgumentParser
Returns:
argparse.ArgumentParser: argument parsers.
"""
# Define input and output field help message
fields = dedent(
"""
output files:
<folder>
folder containing fasta and partition files for each clone.
lineages
successfully processed records.
lineages-fail
database records failed processing.
required fields:
SEQUENCE_ID, SEQUENCE_INPUT, SEQUENCE_IMGT,
GERMLINE_IMGT_D_MASK, V_CALL, J_CALL
""")
# Parent parser
parser_parent = getCommonArgParser(out_file=False, log=True, format=False)
# Define argument parser
parser = ArgumentParser(description=__doc__, epilog=fields,
parents=[parser_parent],
formatter_class=CommonHelpFormatter, add_help=False)
group = parser.add_argument_group("tree building arguments")
group.add_argument("--collapse", action="store_true", dest="collapse",
help="""If specified, collapse identical sequences before exporting to fasta.""")
group.add_argument("--md", nargs="+", action="store", dest="meta_data",
help="""List of fields to containing metadata to include in output fasta file
sequence headers.""")
group.add_argument("--minseq", action="store", dest="min_seq", type=int, default=1,
help="""Minimum number of data sequences. Any clones with fewer than the specified
number of sequences will be excluded.""")
return parser
if __name__ == "__main__":
"""
Parses command line arguments and calls main
"""
# Parse command line arguments
parser = getArgParser()
checkArgs(parser)
args = parser.parse_args()
args_dict = parseCommonArgs(args)
del args_dict["db_files"]
# Call main for each input file
for f in args.__dict__["db_files"]:
args_dict["db_file"] = f
buildTrees(**args_dict)
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