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AlnUtility.py
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AlnUtility.py
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#!/usr/bin/
##
# This class is written to manipulate alignment and take care of the calculation
# of dN, dS, and dA
#
# 04/23,03
# This class was modified many many times since maybe 4 months ago. No documen-
# tation. Shame on myself. Anyway, rate_pair() need to be changed somewhat to
# allow the use of full length Ks value as denominator in sliding window ana-
# lysis.
# 05/15,03
# Found a serious bug in rate_pair(). The increment was not correct so every
# step will miss one codon. Fix it.
# 12/15,03
# Problem with paml, some sequence pairs has dS = -1 in Nei & Gojobori method.
# So the paml dN and dS are not generated.
# 08/17,04
# Rate pair now include capability to use Pan's KaKsTools
#
##
import os, sys, FastaManager, Translation, time, TreeUtility, DrawBlocks, \
SVGWriter, FileUtility, string
from kaksToolsHacked import calculate
class aln_util:
def __init__(self):
pass
#
# Getting alingments and neighbor joining trees
#
def batch_nj(self,phydir,alndir):
#phydir = "~/bin/phylip3.66/exe/" # dir for phylip executables
#alndir = "/home/shiu/project/stress_expr_at/1_nj/_aln"
flist = os.listdir(alndir)
c = 1
for alnfile in flist:
if alnfile[-3:] != "phy":
continue
print "#########################"
print "# File %i out of %i" % (c,len(flist))
c += 1
if os.path.isfile("%s/%s.nj.tre" % (alndir,alnfile)) and \
os.path.getsize("%s/%s.nj.tre" % (alndir,alnfile)) == 0:
print " done!"
else:
os.system("rm %s/%s.nj.tre %s/%s.nj.out %s/%s.pd.out" % \
(alndir,alnfile,alndir,alnfile,alndir,alnfile))
# get distance
f = os.popen("%sprotdist" % phydir,"w")
f.write("%s\n" % alnfile) # aln file name
f.write("F\n") # rename file, have a fake outfile ready
f.write("%s.pd.out\n" % alnfile) # output file name
f.write("G\n") # gamma correction
f.write("Y\n") # setting ok
f.write("0.3162\n") # coefficient of var, assume alpha = 10
f.close()
# get nj tree
f = os.popen("%sneighbor" % phydir,"w")
f.write("%s.pd.out\n" % alnfile) # distance file name
f.write("F\n") # rename file, have a fake outfile ready
f.write("%s.nj.out\n" % alnfile) # output file name
f.write("Y\n") # accept default parameters
f.write("F\n") # rename file, have a fake outree ready
f.write("%s.nj.tre\n" % alnfile) # tree file name
f.close()
print "Done!"
##
# This is for getting alignments and bootstrapped phylogeny for each seq
# group.
#
##
def batch_tree(self,group,fasta,clus_dir,bootstrap=0,isdir=0):
# create group fasta files and get group list back
if isdir == 0:
print "Creat group fasta files..."
# originally setting is (fasta,group,0,1), change the
# last to 0 so no outgroup is passed
glist = fasta_manager.get_group_seq(fasta,group,0,0)
else:
print "Run fasta files in dir:",fasta
tmp = os.listdir(fasta)
glist = []
for i in tmp:
if i.find(".fa") != -1:
glist.append(i[:i.find(".fa")])
print "\nAlign and generate phylogeny.."
for i in glist:
print "\n align:",i
# generate alignment
#print "%s/clustalw %s.fa " % (clus_dir,i) + ">> TMP.log"
os.system("%s/clustalw %s.fa " % (clus_dir,i) + ">> TMP.log")
print " tree :",i
if bootstrap != 0:
os.system("%s/clustalw %s.aln /BOOTSTRAP=400 /BOOTLABELS=node" % \
(clus_dir,i) + ">> TMP.log")
else:
os.system("%s/clustalw %s.aln -tree" % \
(clus_dir,i) + ">> TMP.log")
#tree_util.simplify("%s.phb" % i)
#os.system("mv %s.phb.simplify %s.tre" % (i,i))
os.system("rm %s.dnd" % i)
print "Done!"
def batch_tree_submit(self,groups,fasta,c_dir,w_dir="./",mode=1,spflag=1,pick="",
aln_profile="",bootstrap=0):
# read group info into dict
gdict = file_util.file_to_dict(groups,2)
# filter, if less than 3 taxa or has only one sp, they will be deleted
countT = 0
countU = 0
oup_log = open(groups+".log","w")
for i in gdict.keys():
countT += 1
same_sp = 1
taxa_lm = 2
sp = ""
for j in gdict[i]:
if sp == "":
sp = j[:2]
elif sp != j[:2]:
same_sp = 0
break
if len(gdict[i]) < 3:
oup_log.write("%s\tless than 3 seq\n" % i)
countU += 1
del(gdict[i])
elif spflag and same_sp:
oup_log.write("%s\tsame_sp\n" % i)
countU += 1
del(gdict[i])
for i in gdict:
"""
print "python ~/codes/qsub2.py -s run_%s -c \"python" % i +\
" ~/codes/AlnUtility.py -f batch_tree2 -group %s" % groups+\
" -fasta %s -clustal %s -mode %i -sp %i" % (fasta,c_dir,mode,spflag)+\
" -bootstrap %i -profile %s -pick %s\"" %(bootstrap,aln_profile,i)
"""
os.system("python ~/codes/qsub2.py -s run_%s -c \"python" % i +\
" ~/codes/AlnUtility.py -f batch_tree2 -group %s" % groups+\
" -fasta %s -clustal %s -mode %i -sp %i" % (fasta,c_dir,mode,spflag)+\
" -bootstrap %i -profile %s -pick %s\"" %(bootstrap,aln_profile,i))
##
# Generate alignments based on a passed file with [group][seq_id]
# Then generate a tree for it.
#
# @param mode run alignment only [0] or both [1, default]
# @param spflag run even if seqs are the same sp [0], not [1, default].
# sp is defined as the first two characters of seq names.
# @param pick specify what group(s) to run. Group names seperated by
# ",".
# @param aln_profile name of the profile alignment, if this is not empty
# sequences to profile alignment mode for clustsal will
# be triggered. Assume the profile alignment file is in the
# working dir.
##
def batch_tree2(self,groups,fasta,c_dir,w_dir="./",mode=1,spflag=1,pick="",
aln_profile="",bootstrap=0):
# get working directories, this is for qsub
w_dir = os.getcwd()
print "working_dir:",w_dir
# make directories
if not os.path.isdir("%s/seq" % w_dir):
os.system("mkdir %s/seq" % w_dir)
if not os.path.isdir("%s/aln" % w_dir):
os.system("mkdir %s/aln" % w_dir)
if not os.path.isdir("%s/tre" % w_dir):
os.system("mkdir %s/tre" % w_dir)
# check if the profile alignment file exisit
if aln_profile != "" and \
not os.path.isfile("%s/%s" % (w_dir,aln_profile)):
print "Profile %s does not exist in %s" % (aln_profile,w_dir)
sys.exit(0)
# read group info into dict
gdict = file_util.file_to_dict(groups,2)
# filter, if less than 3 taxa or has only one sp, they will be deleted
countT = 0
countU = 0
oup_log = open(groups+".log","w")
for i in gdict.keys():
countT += 1
same_sp = 1
taxa_lm = 2
sp = ""
for j in gdict[i]:
if j.find("|") != -1:
curr_sp = j.split("|")[0]
else:
curr_sp = j[:2]
if sp == "":
sp = curr_sp
elif sp != curr_sp:
same_sp = 0
break
if len(gdict[i]) < 3:
oup_log.write("%s\tless than 3 seq\n" % i)
countU += 1
del(gdict[i])
elif spflag and same_sp:
oup_log.write("%s\tsame_sp\n" % i)
countU += 1
del(gdict[i])
if pick != "":
print "Pick groups..."
pick = pick.split(",")
pdict = {}
for i in pick:
if gdict.has_key(i):
pdict[i] = gdict[i]
#else:
# print "Family %s not qualified" % i
gdict = pdict
if pdict == {}:
print "No qualified family, quit!"
sys.exit(0)
else:
print "%i families qualified out of %i picked" % \
(len(gdict.keys()),len(pick))
oup_log.close()
# this is here so the variable can be reused. Meanwhile, pdict will not
# be read unless ncessary, this is good for large-scale operation
# where I usu get the group sequences ready so there is no need to
# load pdict.
pdict = {}
# iterating groups
count = 1
print "Iterate groups..."
for i in gdict.keys():
print "%i %s, %i seq" % (count,i,len(gdict[i]))
# write sequence into a file
if(os.path.isfile("%s/seq/%s.fa" % (w_dir,i)) and \
os.path.getsize("%s/seq/%s.fa" % (w_dir,i)) != 0):
print " seq exist..."
else:
print " get sequences..."
pdict = fasta_manager.fasta_to_dict(fasta)
oup = open("%s/seq/%s.fa" % (w_dir,i),"w")
for j in gdict[i]:
oup.write(">%s\n%s\n" % (j,pdict[j]))
oup.close()
# generate alignment
if(os.path.isfile("%s/aln/%s.aln" % (w_dir,i)) and \
os.path.getsize("%s/aln/%s.aln" % (w_dir,i)) != 0):
print " aln exist..."
else:
print " align..."
if aln_profile == "":
os.system("%s/clustalw %s/seq/%s.fa" % \
(c_dir,w_dir,i) + ">>%s/TMP_%s.log" % (w_dir,i))
else:
p1 = aln_profile
#print "%sclustalw -sequences -PROFILE1=%s/%s "%(c_dir,w_dir,p1)+\
# "-PROFILE2=%s/seq/%s.fa " %(w_dir,i) +\
# ">> %s/TMP_%s.log" %(w_dir,i)
os.system("%s/clustalw -sequences -PROFILE1=%s/%s "%(c_dir,w_dir,p1)+\
"-PROFILE2=%s/seq/%s.fa " %(w_dir,i) +\
">> TMP_%s.log" %i)
os.system("mv %s/seq/%s.aln %s/aln/" % (w_dir,i,w_dir))
os.system("rm %s/seq/%s.dnd" % (w_dir,i))
time.sleep(2)
# build tree
# 05/06,07 A weird bug. during tree building phase, the aln name
# pass sometimes clustal will complain that it end with "^Y" so the
# file is not found. There is no where that this control-Y is found
# in the code. So I tried rid of the w_dir part of the os.system
# parameter. And it somehow works.
# 05/11,07 Still some trees are just not built for unknown reason.
# Try sleep for 2 sec after alignment but before tree building. Add
# "./" before aln. Somehow worked...??
if mode:
if((os.path.isfile("%s/tre/%s.ph" % (w_dir,i)) and \
os.path.getsize("%s/tre/%s.ph" % (w_dir,i)) != 0) or \
(os.path.isfile("%s/tre/%s.phb" % (w_dir,i)) and \
os.path.getsize("%s/tre/%s.phb"% (w_dir,i)) != 0)):
print " tree exist..."
else:
print " build tree..."
if bootstrap == 0:
os.system("%s/clustalw %s/aln/%s.aln -tree >> %s/TMP_%s.log" % \
(c_dir,w_dir,i,w_dir,i))
else:
os.system("%s/clustalw aln/%s.aln" %(c_dir,i) +\
" /BOOTSTRAP=%i /BOOTLABELS=node"%bootstrap +\
" >> TMP_%s.log" %i)
os.system("mv %s/aln/%s.ph* %s/tre" % (w_dir,i,w_dir))
time.sleep(2)
count+=1
print "Done!"
##
# Genearte alignments based on a passed file with [group][seq_id]
#q
# @param groups tab delimited file with [organisms][clade_id][subtree]
# @param fasta fasta sequence file. This file should always have a sequence
# named "OUT" for outgroup sequence
##
def batch_align(self,groups,fasta,clus_dir,paml_dir):
# read group info into dict
gdict = {}
trees = {}
inp = open(groups,"r")
lines = inp.readlines()
oup = open(groups+".log","w")
for i in lines:
if i[-2:] == "\r\n":
i = i[:-2]
elif i[-1] == "\n":
i = i[:-1]
llist = i.split("\t")
trees["%s_%s" % (llist[0],llist[2])] = llist[3]
# parse tree into taxa information
tree_str = ""
for j in llist[3]:
if j not in ["(",")",":",";"]:
tree_str += j
tlist = tree_str.split(",")
gdict["%s_%s" % (llist[0],llist[2])] = tlist
for j in tlist:
oup.write("%s_%s\t%s\n" % (llist[0],llist[2],j))
# filter, if less than 3 taxa or has only one sp, they will deleted
countT = 0
countU = 0
for i in gdict.keys():
countT += 1
same_sp = 1
taxa_lm = 2
sp = ""
for j in gdict[i]:
if sp == "":
sp = j[:2]
elif sp != j[:2]:
same_sp = 0
break
if len(gdict[i]) <=2 or same_sp:
countU += 1
del(gdict[i])
print "Total %i groups, %i not qualified" % (countT, countU)
# read seq into dict
pdict = fasta_manager.fasta_to_dict(fasta)
# iterating groups
oup_rate = open("%s.matrix" % group, "w")
for i in gdict.keys():
# write sequence into 2 files.
oup2= open("TMP2.FA","w") # tree for rate calculation
for j in gdict[i]:
oup2.write(">%s\n%s\n" % (j,pdict[j][1]))
oup2.close()
# run clustal for TMP2
print "%s/clustalw /INFILE=TMP2.FA /OUTFILE=TMP2.GDE /OUTPUT=GDE" % \
clus_dir
os.system("%s/clustalw /INFILE=TMP2.FA /OUTFILE=TMP2.GDE /OUTPUT=GDE" % \
clus_dir)
# save tree into temp file
oup2 = open("TMP2.PHB","w")
oup2.write("%s;\n" % trees[i])
# convert alignment GDE to fa and then to phylip format
inp = open("TMP2.GDE","r")
oup = open("TMP2.GDE.FA","w")
tlines = inp.readlines()
for j in tlines:
if j[0] == "%":
oup.write(">%s" % j[1:])
else:
oup.write(j)
oup.close()
self.to_phylip("TMP2.GDE.FA","TMP2")
# run paml
os.system("%s/codeml" % paml_dir)
# get the matrix part
inp = open("TMP2.OUT","r")
inlines = inp.readlines()
found = 0
rdict = {}
nlist = []
for j in inlines:
if j.find("ML distances of aa seqs.") != -1:
found = 1
elif found:
if j[-2:] == "\r\n":
j = j[:-2]
elif j[-1] == "\n":
j = j[:-1]
jlist = j.split(" ")
tlist = []
nlist.append(jlist[0])
for k in jlist[1:]:
if k != "":
tlist.append(k)
rdict[jlist[0]] = tlist
ilist = i.split("_")
for j in range(len(nlist)):
for k in rdict.keys():
if nlist[j] != k:
oup_rate.write("%s\t%s\t%s\t%s\t%s\n" % \
(ilist[0],ilist[1],nlist[j],k,rdict[k][j]))
else:
del(rdict[k])
#os.system("rm -f TMP*")
##
# Back translate alignment sequences
##
def bt_align(self,pep,cds):
# read fasta into dicts
pdict = fasta_manager.fasta_to_dict(pep)
ndict = fasta_manager.fasta_to_dict(cds)
# back translate each and write into GDE
oup = open(cds+".aligned.fa","w")
flag = 0
for j in pdict.keys():
seq, flag = trans.back_translate2(pdict[j][1],ndict[j][1])
if flag:
print "Error:",j
oup.write(">%s\n%s\n" % (j,seq))
oup.close()
#
# This function take a list of pairs, conduct pairwise alignment with
# clustal, then parse the gap information out of the alignments.
#
def parse_gap(self,pairs,fasta,clus_dir):
inp = open(pairs,"r")
inlines = inp.readlines()
pdict = fasta_manager.fasta_to_dict(fasta)
# find -, and return a list of coordinates (alignment-based)
def gap(astr):
c = 1
gL = gR = 0
glist = []
for i in astr:
if i == "-":
if gL == 0:
gL = gR = c
else:
gR += 1
else:
if gL != 0:
glist.append("%i-%i" % (gL,gR))
gL = gR = 0
c += 1
if gL != 0:
glist.append("%i-%i" % (gL,gR))
return glist
oup1= open(pairs+".gap","w")
oup2= open(pairs+".seqpair","w")
count = 1
for i in inlines:
# write sequences into temp fasta file and align sequences
i = self.rmlb(i)
# line list, contain ids for each pair
L = i.split("\t")
print " %i %s-%s" % (count,L[0],L[1])
count += 1
# align
error = self.do_clustal(L[0],L[1],pdict,"TMP",clus_dir)
if error:
print " sequence absent"
oup_rate.write("%s\t%s\t" % (llist[0],llist[1]))
oup_rate.write("-\t-\tsequence_absent\n")
else:
# read alignment GDE file
inp = open("TMP.GDE","r")
tmp = inp.readlines()
inp.close()
tag = 0
aln = ["",""]
for i in tmp:
if i[0] == "%":
tag += 1
if tag == 1 and i[0] != "%":
aln[0] += self.rmlb(i)
if tag == 2 and i[0] != "%":
aln[1] += self.rmlb(i)
qlist = gap(aln[0])
slist = gap(aln[1])
qlen = len(pdict[L[0]][1])
slen = len(pdict[L[1]][1])
# should be the same as sline
alen = len(aln[0])
# [q][s][qStr][qEnd][sStr][sEnd][alnL][qGaps][sGaps]
oup1.write("%s\t%s\t1\t%s\t1\t%s\t%i\t%s\t%s\n" % \
(L[0],L[1],qlen,slen,alen,string.joinfields(qlist,","),
string.joinfields(slist,",")))
# 2 lines, each pair seperate by an empty line
oup2.write("%s\t%s\n%s\t%s\n\n" % (L[0],aln[0],L[1],aln[1]))
os.system("rm TMP*")
print "Done!"
##
# Find 4x degenerate sites. The sequences passed should be aligned already.
#
#
# @param seq1 cds seq for gene1
# @param seq2 cds seq for gene2
# @return a list of two modified sequence
##
def find_x4(self,seq1,seq2):
#print seq1
#print seq2
x4 = trans.get_x4()
code = trans.get_nt_code()
nseq1 = nseq2 = ""
for i in range(0,len(seq1),3):
#print seq1[i:i+3],code[seq1[i:i+3]],
#print seq2[i:i+3],code[seq2[i:i+3]],
# both codons are 4fold
if x4.has_key(seq1[i:i+3]) and x4.has_key(seq2[i:i+3]):
# synonymous
if x4[seq1[i:i+3]] == x4[seq2[i:i+3]]:
nseq1 += seq1[i:i+3]
nseq2 += seq2[i:i+3]
#print "4x",
#print ""
#print nseq1
#print nseq2
return [nseq1,nseq2]
##
# Do the following:
# 1. get each pair of orthologs from a pep fasta file based on a table
# 2. clustalw
# 3. back translate NT sequences based on pep alignment. Still in GDE
# 4. parse GDE output and convert into "simple" PHYLIP format
# default output is TMP.GDE.phy
# 5. run yn00 based on the control file yn00.ctl, default output is TMP.out
# in PAML dir.
# 6. parse yn00 output, generate another output file with rates with
# [org1_geneA][org2_geneA][dN/Ds][dN][dS]
#
# !!!!!! FOR THIS TO WORK, THE PAML CONTROL FILE NEED TO BE COPIED TO THE
# WORKING DIR!!!!!!!!
#
# @param wdir working directory, default local
# @param pep polypeptide sequence file to get pairs from
# @param cds nucleotide sequence file. The id should be exactly the same
# as that in pep. All sequences should also be in the same
# frame.
# @param prog program to use paml or tpl (Tzeng,Pan,Li, 2004)
# @param pairs tab delimited file with ortholog relationships
# @param windows the sliding-window size for getting Ka, Ks. Default 0
# @param step step size of the sliding window
# @param gdom graphic domain file
# @param ks the Ks value used to calculate Ka/Ks ratio. Default is
# "full" which is the Ks for the whole gene, or "window" for
# Ks from the sequence of each window.
# @param justka 0 [default] or 1, just show Ka.
# @param x4 Only calculate Ka Ks for 4x sites [1] or all [0, default],
# will not allow window calculation if 4x = 1
# @param debug turn file deletion off (1). Default 0.
##
def rate_pair(self,pep,cds,pairs,clus_dir,prog,paml_dir,window,step,
gdom,ks,justka,x4=0,idxpairs=0,debug=0):
print "Calculate pairwise evol rate:"
print " pep :",pep
print " cds :",cds
print " pairs :",pairs
print " clustal:",clus_dir
print " 4fold :",x4
print " program:",prog
if prog == "paml":
print " paml :",paml_dir
if window != 0:
print " window :",window
print " step :",step
print " ks_full:",ks
# read fasta into dicts
print "Read:",pep
pdict = fasta_manager.fasta_to_dict(pep,verbose=0)
print "Read:",cds
ndict = fasta_manager.fasta_to_dict(cds,verbose=0)
if prog == "paml":
try:
inp = open("yn00.ctl","r")
except IOError:
print "Control file missing, can't do anything... QUIT!"
sys.exit(0)
# read and process sequences pair by pair
inlines = []
if pairs != "":
inp = open(pairs,"r")
inlines = inp.readlines()
oup_rate = open(pairs+".rate","w")
if window != 0:
oup_rate2 = open(pairs+".rate_windows","w")
# no pair info passed, look at all combo
else:
print "No pair info passed, all combination..."
keys = pdict.keys()
for i in range(len(keys)):
for j in range(i+1,len(keys)):
inlines.append("%s\t%s" % (keys[i],keys[j]))
oup_rate = open("all_pairs.rate","w")
if window != 0:
oup_rate2 = open("all_pairs.rate_windows","w")
errors = []
# if window size is specified
if window != 0:
# read gdom file into dict
if gdom == "":
gdict = {}
else:
gdict = file_util.file_to_dict(gdom,1)
Xsize = 2000
Ysize = 300 * (len(inlines)+2)
svg_writer = SVGWriter.svg_writer(pairs+".svg")
svg_writer.write_header(Xsize,Ysize)
oup_rate.write("Seq1\tSeq2\tKa\tKs\tvKa\tvKs\n")
if window != 0:
oup_rate2.write("Window(cds):%i, Step(cds):%i\n" % (window,step))
oup_rate2.write("Seq1\tSeq2\tKa\tKs\tvKa\tvKs\tfull_Ks\tStartAA\n")
# start to process pairs
print "\nProcess pairs:"
count = 1
for i in inlines:
# write sequences into temp fasta file and align sequences
i = self.rmlb(i)
# line list, contain ids for each pair
llist = i.split("\t")
print " %i %s vs %s" % (count,llist[0],llist[1])
if len(llist[0]) > 30 or len(llist[1]) > 30:
print " ERR: seq name too long, clustal cannot deal with it"
continue
error = self.do_clustal(llist[0],llist[1],pdict,"TMP",clus_dir)
if error:
print " sequence absent"
oup_rate.write("%s\t%s\t" % (llist[0],llist[1]))
oup_rate.write("-\t-\t-\t-\tsequence_absent\n")
else:
# convert aligned sequence to fasta, then to dict again
inp = open("TMP.GDE","r")
oup = open("TMP.GDE.FA","w")
tlines = inp.readlines()
inp.close()
for j in tlines:
if j[0] in ["%","#"]:
oup.write(">%s" % j[1:])
else:
oup.write(j)
oup.close()
tdict = fasta_manager.fasta_to_dict("TMP.GDE.FA",verbose=0)
# back translate each and write into GDE
flag = 0
seqs = ""
tkeys = tdict.keys()
tkeys.sort()
for j in tkeys:
try:
seq, flag = trans.back_translate2(tdict[j],
ndict[j])
#print ">>>",flag
except KeyError:
flag = 2
print ">>>",j,j in tdict, j in ndict
if flag != 0:
errors.append(j)
break
seqs += ">%s\n%s\n" % (j,seq)
# problem black translate sequences
if flag != 0:
oup_rate.write("%s\t%s\t-\t-\t-\t-\t" % (llist[0],llist[1]))
if flag == 1:
print " size discrepancy between pep and cds seq"
oup_rate.write("pep_cds_discrepancy\n")
elif flag == 2:
print " sequence not found"
oup_rate.write("seq_absent\n")
count += 1
continue
# no problem, generate output
else:
S = seqs.split("\n")
# if asking for 4fold sites
if x4 == 1:
newseq = self.find_x4(S[1],S[3])
S[1] = newseq[0]
S[3] = newseq[1]
# no 4x sites
if len(S[1]) == 0:
oup_rate.write("%s\t%s\t-\t-\t-\t-\tno_4x_site\n"%\
(llist[0],llist[1]))
continue
if len(S[1]) == 0 or len(S[2]) == 0:
oup_rate.write("%s\t%s\t-\t-\t-\t-\tno_common_site\n"%\
(llist[0],llist[1]))
continue
oup = open("TMP.NT.FA","w")
oup.write(string.joinfields(S,"\n"))
###############################################################
# If sequence absent or size discrepancy, won't get past here
###############################################################
oup.close()
# calculate full length rate
if prog == "paml":
# convert FA into "simple PHYLIP"
self.to_phylip("TMP.NT.FA","TMP")
rate = self.do_yn00(paml_dir,llist)
else:
tmp = calculate(seqs)
rate = []
for i in tmp:
rate.append(str(i))
# deal with situations where no Ka or Ks is generated.
prog_error = 0
try:
Ka_full = float(rate[0])
Ks_full = float(rate[1])
except ValueError:
prog_error = 1
except IndexError:
prog_error = 2
#########################
# deal with window size
#########################
# program error
if prog_error != 0:
oup_rate.write("%s\t%s\t%sprog_err%i\n" %
(llist[0],llist[1],"-\t"*4,prog_error))
# output full length only
elif window == 0:
oup_rate.write("%s\t%s\t%s\n" % (llist[0],llist[1],
string.joinfields(rate,"\t")))
# go through windows
elif window > 0 and x4 == 0:
# generate a full length ka ks output as well
oup_rate.write("%s\t%s\t%s\n" % (llist[0],llist[1],
string.joinfields(rate,"\t")))
# make sure the window and step sizes are multiple of 3
if window%3 != 0:
window += (3-window%3)
if step % 3 != 0:
step += (3-step%3)
# cds sequence dict for a pair
sdict = fasta_manager.fasta_to_dict("TMP.NT.FA")
keys = sdict.keys()
leng = len(sdict[keys[0]][1])
idx = 0
while idx+window < leng:
#print "\n>>>>> WINDOW:",(idx/3+1)
#print sdict[keys[0]][1][idx:idx+window]
#print sdict[keys[1]][1][idx:idx+window]
oup_rate2.write("%s\t%s\t" % (llist[0],llist[1]))
seqs = ">%s\n%s\n>%s\n%s\n" % \
(keys[0],sdict[keys[0]][1][idx:idx+window],
keys[1],sdict[keys[1]][1][idx:idx+window])
if prog == "paml":
oup = open("TMP.NT.FA","w")
oup.write(seqs)
oup.close()
self.to_phylip("TMP.NT.FA","TMP")
rate = self.do_yn00(paml_dir,llist)
else:
#print seqs
tmp = calculate(seqs)
rate = []
for i in tmp:
rate.append(str(i))
# so far, the rate is empty if two sequences are exactly
# the same, paml throws Error: DistanceF84: input err..
# so the Ka/Ks is set to *
if rate == []:
oup_rate2.write("%s%s\t%i\n" % \
("-\t"*4,Ks_full,(idx/3+1)))
else:
oup_rate2.write("%s\t%f\t%i\n" % \
(string.joinfields(rate,"\t"),Ks_full,idx/3+1))
idx += step # because idx start from 0, no need to +1
#######################
# DISABLED!!!
"""
# modify gdom line
try:
glist = self.modify_gdom([llist[0]+"\t"+gdict[llist[0]],
llist[1]+"\t"+gdict[llist[1]]],
"TMP.GDE.FA")
except KeyError:
glist = [llist[0]+"\terror",
llist[1]+"\terror"]
# generate graphics
rkeys = rdict.keys()
rkeys.sort()
print "\nKa/Ks values:"
for k in rkeys:
print k/3+1,"\t",rdict[k]
draw_block.combine(glist,rdict,svg_writer,count,step)
"""
########################
if prog == "paml":
# Delete tmp files
if debug == 0:
os.system("rm TMP* 2YN* rst* rub")
pass
count += 1
if window != 0:
svg_writer.write_footer()
print "Size discrepancies between Nt and Pep:",
if error != []:
for i in errors:
print "",i
else:
print " none..."
print "\nDone!\n"
#
# Assume that the CDS is aligned with no stop like output of Translation.
# tl_mindless(). Pairs file is also generated with the same function.
#
def rate_pair2(self,pairs,cds,prog,paml_dir):
print "Read sequences into dict..."
cds = fasta_manager.fasta_to_dict(cds,verbose=0)
print "Process pairs:",
inp = open(pairs,"r")
inlines = inp.readlines()
np = len(inlines) # number of pairs
print np
oup_rate = open(pairs+".rate","w")
oup_rate.write("Seq1\tSeq2\tKa\tKs\tvKa\tvKs\n")
count = 0
for i in inlines:
i = i.strip()
if count % 1e2 == 0:
print " %i x100, %f%s" % (count/1e2,count*100.0/np,"%")
count += 1
PAIR = i.split("\t")
# Check if sequence is present
noseq1 = noseq2 = 0
if PAIR[0] not in cds:
print " no seq:",PAIR[0]
noseq1 = 1
if PAIR[1] not in cds:
print " no seq:",PAIR[1]
noseq2 = 1
if noseq1 or noseq2:
oup_rate.write("%s\t%s\t" % (PAIR[0],PAIR[1]))
oup_rate.write("-\t-\t-\t-\tno_seq:%i,%i\n" % (noseq1,noseq2))
continue
seqs = ">seq1\n%s\n>seq2\n%s\n" % (cds[PAIR[0]],cds[PAIR[1]])
if len(cds[PAIR[0]]) != len(cds[PAIR[1]]):
print "Err: length discrepancy",
print PAIR,len(cds[PAIR[0]]),len(cds[PAIR[1]])
print cds[PAIR[0]]
print cds[PAIR[1]]
sys.exit(0)
# calculate full length rate
if prog == "paml":
# convert FA into "simple PHYLIP"
oup = open("TMP.NT.FA","w")
oup.write(seqs)
oup.close()
self.to_phylip("TMP.NT.FA","TMP")
rate = self.do_yn00(paml_dir,PAIR)
else:
tmp = calculate(seqs)
rate = []
for i in tmp:
rate.append(str(i))
# deal with situations where no Ka or Ks is generated.
prog_error = 0
try:
Ka_full = float(rate[0])
Ks_full = float(rate[1])
except ValueError:
prog_error = 1
except IndexError:
prog_error = 2
sys.exit(0)
# program error
if prog_error != 0:
oup_rate.write("%s\t%s\t%sprog_err%i\n" %
(PAIR[0],PAIR[1],"-\t"*4,prog_error))
else:
oup_rate.write("%s\t%s\t%s\n" % (PAIR[0],PAIR[1],
string.joinfields(rate,"\t")))
if prog == "paml":
# Delete tmp files
if debug == 0:
os.system("rm TMP* 2YN* rst* rub")
pass
##
# subroutine for synchronize alignments and gdom coordinates THERE ARE BUGS
# IN THIS THING. SOME DON'T QUITE ALIGN RIGHT.
#
#
# @param glist a list of gdom lines
# @param aligned the fasta file of polypeptide alignments
##
def modify_gdom(self,glist,aligned):
adict = fasta_manager.fasta_to_dict(aligned)
#print adict