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EukPhylo/Utilities/for_fastas/CUB.py
Godwin Ani 922b144de8
Update CUB.py
2024-06-03 15:56:43 -04:00

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#Author, date: Xyrus (last modified by him Sept 17 2020), most recently updated by Auden on July 19 2023
#Motivation: Generate lots of codon usage statistics to aid in identifying useful characteristics for de novo ORF calling
#Intent: Summarize nucleotide composition statistics for a fasta file or folder of fasta files
#Dependencies: Python3, numpy, BioPython
#Inputs: Fasta file or folder of fasta files
#Outputs: A fasta file filtered for properly formatted sequences and several spreadsheets summarizing GC, ENc, RSCU, etc.
#Example: python3 CUB.py -i seqs.fasta
#Dependencies
import os
import re
import sys
import numpy as np
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqUtils import GC
import argparse
class CalcCUB:
"""
Returns the Effective Number of Codons used (observed and expected)
following the equations originally from Wright 1990.
"""
def expWrightENc(gc3):
# Calculates the expected ENc from a sequence's GC3 under Wright 1990
if gc3 > 1:
# If GC3 looks as though it is > 1 (e.g. 100%), converts to a float ≤ 1.
# Calculations expect a value between 0 and 1
gc3 = gc3/100
exp_enc = 2+gc3+(29/((gc3**2)+(1-gc3)**2))
return round(exp_enc, 4)
def nullENcGC3():
# Calculates the expected ENc from the null distribution of GC3
# values (0, 100% GC)
null = [CalcCUB.expWrightENc(n) for n in np.arange(0,.51,0.01)]
null += null[:-1][::-1]
return [str(i)+'\t'+str(j) for i, j in zip([n for n in range(0, 101)],null)]
def calcWrightENc(cdnTable):
# Follows Wright's (1990) calculations for determining ENc scores.
def faCalcWright(aa_counts):
# Returns the codon homozygosity (fa) for a given "type" of AA (e.g.
# 2-fold degeneracy).
counts = [i[2] for i in aa_counts]
# n_aa --> number of this particular AA
n_aa = sum(counts)
# fa --> codon homozygosity
try:
fa = (((n_aa*sum([(i/float(n_aa))**2 for i in counts]))-1)/(n_aa-1))
except:
fa = 0
return fa
def ENcWright_by_Degen(fa_data):
# Same as used in Wright 1990, averages the homozygosity across all codons
# of a given class (e.g. 2-fold degeneracy)
# Codons without any degeneracy (e.g. ATG == M) have 100% homozygosity
# and provide a "base" for the ENc score
enc = 2
for k, v in fa_data.items():
non_zero_vals, non_zero_sum = len([i for i in v if i != 0]), sum([i for i in v if i != 0])
try:
f_aa = non_zero_sum/non_zero_vals
except:
f_aa = 1
enc += k/f_aa
return enc
# Determines the number of degenerate groups to use (i.e. whether 6-Fold
# degeneracy is present).
degen_cdns = {}
for k, v in cdnTable.items():
if v[1] not in degen_cdns.keys():
degen_cdns[v[1]] = [v[0]]
else:
if v[0] not in degen_cdns[v[1]]:
degen_cdns[v[1]] += [v[0]]
# Calculates codon homozygosity (fa) for each amino acid. Groups the
# resulting values based on the amino acids degeneracy (e.g. 'two-fold').
fa_cdns = {len(v):[] for k, v in degen_cdns.items() if 'one' not in k}
for k, v in degen_cdns.items():
# Skip codons lacking degeneracy
if 'one' in k:
continue
for aa in v:
aa_counts = [cdnTable[k] for k in cdnTable.keys() if cdnTable[k][0] == aa]
fa_cdns[len(v)] += [faCalcWright(aa_counts)]
enc_val = min(61, round(ENcWright_by_Degen(fa_cdns),4))
return enc_val
def SunEq5(cdnTable):
def calcFcf(aa_counts):
counts = [i[2] for i in aa_counts]
pseudocounts = [i+1 for i in counts]
na = sum(pseudocounts)
fcf = sum([(i/float(na))**2 for i in pseudocounts]), sum(pseudocounts)
return fcf
ENcWeightedPsuedo = 0
degen_cdns = {}
for k, v in cdnTable.items():
if v[1] == 'none':
continue
if v[1] not in degen_cdns.keys():
degen_cdns[v[1]] = [v[0]]
else:
if v[0] not in degen_cdns[v[1]]:
degen_cdns[v[1]] += [v[0]]
for k, v in degen_cdns.items():
fcf_nc = []
for aa in v:
aa_counts = [cdnTable[k] for k in cdnTable.keys() if cdnTable[k][0] == aa]
fcf_nc.append(calcFcf(aa_counts))
weightedENc = (len(fcf_nc) /
(sum([i[0]*i[1] for i in fcf_nc]) /
sum([i[1] for i in fcf_nc])))
ENcWeightedPsuedo += weightedENc
return round(ENcWeightedPsuedo,4)
def calcRCSU(cdnTbl):
rscu = {k:[v[0]] for k, v in cdnTbl.items() if v[0].isalpha()}
for k, v in rscu.items():
try:
aa_info = [(key, val[-1]) for key, val in cdnTbl.items() if val[0] == v[0]]
aa_cnts = [x[1] for x in aa_info]
cdn_rscu = (cdnTbl[k][-1]*len(aa_cnts))/sum(aa_cnts)
rscu[k] += [str(round(cdn_rscu,4))]
except:
rscu[k] += ['NA']
return rscu
class GenUtil(object):
"""
"Overflow" of functions for now. Just a precaution to make the code a
little cleaner/easier to manage.
This class inclues means to normalize/check the user-provided genetic code,
which if not valid will default to the "universal" genetic code.
Similarly, This class will return the appropriate
codon count table and provides a function to update its values.
"""
def convertGenCode(gCode):
# Will interpret the user provided genetic code (gcode) and checks that
# it is currently available for use with the NCBI/biopython
# supported translation tables. Default is universal.
# Dictionary of the possible/functional genetic codes that are supported.
# --- Chilodonella and condylostoma are to come!
transTable = {'universal':1, 'blepharisma':4,
'ciliate':6, 'euplotes':10, 'mesodinium':29, 'myrionecta':29, 'peritrich':30,
'1':1, '4':4, '6':6, '10':10, '29':29, '30':30, 'chilo':'chilo'}
if str(gCode).lower() not in transTable:
print("\nWarning: Provided genetic code is not supported (yet).\n")
print("Currently running using the UNIVERSAL genetic code.\n\n")
print("Alternative genetic codes are as follows (Note: numbers "\
"correspond to NCBI genetic code tables):\n")
print('\n'.join(list(transTable.keys()))+'\n')
return 'Universal',1
else:
return gCode,transTable[str(gCode).lower()]
def getCDNtable(gCode):
# Returns the appropriate codon table to be used for the ENc calculations.
# Universal codon table, with 6-fold degenerate codons split
# into four-fold and two-fold groups.
universal_no6fold = {
'GCT': ['A', 'four', 0], 'GCC': ['A', 'four', 0], 'GCA': ['A', 'four', 0],
'GCG': ['A', 'four', 0], 'CGT': ['R', 'four', 0], 'CGC': ['R', 'four', 0],
'CGG': ['R', 'four', 0], 'CGA': ['R', 'four', 0], 'AGA': ['R_', 'two', 0],
'AGG': ['R_', 'two', 0], 'AAT': ['N', 'two', 0], 'AAC': ['N', 'two', 0],
'GAT': ['D', 'two', 0], 'GAC': ['D', 'two', 0], 'TGT': ['C', 'two', 0],
'TGC': ['C', 'two', 0], 'CAA': ['Q', 'two', 0], 'CAG': ['Q', 'two', 0],
'GAA': ['E', 'two', 0], 'GAG': ['E', 'two', 0], 'GGT': ['G', 'four', 0],
'GGC': ['G', 'four', 0], 'GGA': ['G', 'four', 0], 'GGG': ['G', 'four', 0],
'CAT': ['H', 'two', 0], 'CAC': ['H', 'two', 0], 'ATT': ['I', 'three', 0],
'ATC': ['I', 'three', 0], 'ATA': ['I', 'three', 0], 'ATG': ['M', 'one', 0],
'TTA': ['L_', 'two', 0], 'TTG': ['L_', 'two', 0], 'CTT': ['L', 'four', 0],
'CTC': ['L', 'four', 0], 'CTA': ['L', 'four', 0], 'CTG': ['L', 'four', 0],
'AAA': ['K', 'two', 0], 'AAG': ['K', 'two', 0], 'TTT': ['F', 'two', 0],
'TTC': ['F', 'two', 0], 'CCT': ['P', 'four', 0], 'CCC': ['P', 'four', 0],
'CCA': ['P', 'four', 0], 'CCG': ['P', 'four', 0], 'TCT': ['S', 'four', 0],
'TCC': ['S', 'four', 0], 'TCA': ['S', 'four', 0], 'TCG': ['S', 'four', 0],
'AGT': ['S_', 'two', 0], 'AGC': ['S_', 'two', 0], 'ACT': ['T', 'four', 0],
'ACC': ['T', 'four', 0], 'ACA': ['T', 'four', 0], 'ACG': ['T', 'four', 0],
'TGG': ['W', 'one', 0], 'TAT': ['Y', 'two', 0], 'TAC': ['Y', 'two', 0],
'GTT': ['V', 'four', 0], 'GTC': ['V', 'four', 0], 'GTA': ['V', 'four', 0],
'GTG': ['V', 'four', 0], 'TAA': ['*', 'none', 0], 'TGA': ['*', 'none', 0],
'TAG': ['*', 'none', 0], 'XXX': ['_missing', 'none', 0]}
# Universal codon table, with 6-fold degenerate codons kept
# whole, no splitting! Traditional Universal codon table.
universal_6fold = {
'GCT': ['A', 'four', 0], 'GCC': ['A', 'four', 0], 'GCA': ['A', 'four', 0],
'GCG': ['A', 'four', 0], 'CGT': ['R', 'six', 0], 'CGC': ['R', 'six', 0],
'CGG': ['R', 'six', 0], 'CGA': ['R', 'six', 0], 'AGA': ['R', 'six', 0],
'AGG': ['R', 'six', 0], 'AAT': ['N', 'two', 0], 'AAC': ['N', 'two', 0],
'GAT': ['D', 'two', 0], 'GAC': ['D', 'two', 0], 'TGT': ['C', 'two', 0],
'TGC': ['C', 'two', 0], 'CAA': ['Q', 'two', 0], 'CAG': ['Q', 'two', 0],
'GAA': ['E', 'two', 0], 'GAG': ['E', 'two', 0], 'GGT': ['G', 'four', 0],
'GGC': ['G', 'four', 0], 'GGA': ['G', 'four', 0], 'GGG': ['G', 'four', 0],
'CAT': ['H', 'two', 0], 'CAC': ['H', 'two', 0], 'ATT': ['I', 'three', 0],
'ATC': ['I', 'three', 0], 'ATA': ['I', 'three', 0], 'ATG': ['M', 'one', 0],
'TTA': ['L', 'six', 0], 'TTG': ['L', 'six', 0], 'CTT': ['L', 'six', 0],
'CTC': ['L', 'six', 0], 'CTA': ['L', 'six', 0], 'CTG': ['L', 'six', 0],
'AAA': ['K', 'two', 0], 'AAG': ['K', 'two', 0], 'TTT': ['F', 'two', 0],
'TTC': ['F', 'two', 0], 'CCT': ['P', 'four', 0], 'CCC': ['P', 'four', 0],
'CCA': ['P', 'four', 0], 'CCG': ['P', 'four', 0], 'TCT': ['S', 'six', 0],
'TCC': ['S', 'six', 0], 'TCA': ['S', 'six', 0], 'TCG': ['S', 'six', 0],
'AGT': ['S', 'six', 0], 'AGC': ['S', 'six', 0], 'ACT': ['T', 'four', 0],
'ACC': ['T', 'four', 0], 'ACA': ['T', 'four', 0], 'ACG': ['T', 'four', 0],
'TGG': ['W', 'one', 0], 'TAT': ['Y', 'two', 0], 'TAC': ['Y', 'two', 0],
'GTT': ['V', 'four', 0], 'GTC': ['V', 'four', 0], 'GTA': ['V', 'four', 0],
'GTG': ['V', 'four', 0], 'TAA': ['*', 'none', 0], 'TGA': ['*', 'none', 0],
'TAG': ['*', 'none', 0], 'XXX': ['_missing', 'none', 0]}
# Blepharisma (table 4) genetic code codon table, with 6-fold degenerate
# codons kept whole, no splitting!
blepharisma_6fold = {**universal_6fold,
'TGA': ['W', 'two', 0], 'TGG': ['W', 'two', 0],
'TAA': ['*', 'two', 0], 'TAG': ['*', 'two', 0]}
# Blepharisma (table 4) genetic code codon table, with 6-fold degenerate
# codons split into four-fold and two-fold groups.
blepharisma_no6fold = {**universal_no6fold,
'TGA': ['W', 'two', 0], 'TGG': ['W', 'two', 0],
'TAA': ['*', 'two', 0], 'TAG': ['*', 'two', 0]}
# Chilodonella genetic code codon table, with 6-fold degenerate
# codons kept whole, no splitting!
chilo_6fold = {**universal_6fold,
'CAA': ['Q', 'four', 0], 'CAG': ['Q', 'four', 0],
'TAA': ['*', 'one', 0], 'TAG': ['Q', 'four', 0],
'TGA': ['Q', 'four', 0]}
# Chilodonella genetic code codon table, with 6-fold degenerate
# codons split into four-fold and two-fold groups.
# Note that this also splits four-fold degenerate codons that OUGHT to
# be in "different" functional categories (e.g. CAG =/= TAG)
chilo_no6fold = {**universal_no6fold,
'TAA': ['*', 'one', 0], 'TAG': ['Q_', 'one', 0],
'TGA': ['Q_', 'one', 0]}
# Ciliate (table 6) genetic code codon table, with 6-fold degenerate
# codons kept whole, no splitting! Traditional ciliate codon table.
ciliate_6fold = {**universal_6fold,
'CAA': ['Q', 'four', 0], 'CAG': ['Q', 'four', 0],
'TAA': ['Q', 'four', 0], 'TAG': ['Q', 'four', 0],
'TGA': ['*', 'one', 0]}
# Ciliate (table 6) genetic code codon table, with 6-fold degenerate
# codons split into four-fold and two-fold groups.
# Note that this also splits four-fold degenerate codons that OUGHT to
# be in "different" functional categories (e.g. CAA =/= TAA)
ciliate_no6fold = {**universal_no6fold,
'TAA': ['Q_', 'two', 0], 'TAG': ['Q_', 'two', 0],
'TGA': ['*', 'one', 0]}
# Euplotes codon table, with 6-fold degenerate codons kept
# whole, no splitting! Traditional Universal codon table.
euplotes_6fold = {**universal_6fold,
'TGA': ['C', 'three', 0], 'TGT': ['C', 'three', 0],
'TGC': ['C', 'three', 0], 'TAA': ['*', 'two', 0],
'TAG': ['*', 'two',0]}
# Euplotes genetic code codon table, with 6-fold degenerate codons
# split into four-fold and two-fold groups.
euplotes_no6fold = {**universal_no6fold,
'TGA': ['C', 'three', 0], 'TGT': ['C', 'three', 0],
'TGC': ['C', 'three', 0], 'TAA': ['*', 'two', 0],
'TAG': ['*', 'two',0]}
# Mesodinium/Myrionecta (table 29) genetic code codon table, with 6-fold
# degenerate codons kept whole, no splitting! Traditional ciliate codon table.
mesodinium_6fold = {**universal_6fold,
'TAA': ['Y', 'four', 0], 'TAT': ['Y', 'four', 0],
'TAG': ['Y', 'four', 0], 'TAC': ['Y', 'four', 0],
'TGA': ['*', 'one', 0]}
# Mesodinium/Myrionecta (table 29) genetic code codon table, with 6-fold
# degenerate codons split into four-fold and two-fold groups.
mesodinium_no6fold = {**universal_no6fold,
'TAA': ['Y', 'four', 0], 'TAT': ['Y', 'four', 0],
'TAG': ['Y', 'four', 0], 'TAC': ['Y', 'four', 0],
'TGA': ['*', 'one', 0]}
# Peritrich (table 30) genetic code codon table, with 6-fold degenerate
# codons kept whole, no splitting! Traditional ciliate codon table.
peritrich_6fold = {**universal_6fold,
'GAA': ['E', 'four', 0], 'GAG': ['E', 'four', 0],
'TAA': ['E', 'four', 0], 'TAG': ['E', 'four', 0],
'TGA': ['*', 'one', 0]}
# Peritrich (table 30) genetic code codon table, with 6-fold degenerate
# codons split into four-fold and two-fold groups.
# Note that this also splits four-fold degenerate codons that OUGHT to
# be in "different" functional categories (e.g. CAA =/= TAA)
peritrich_no6fold = {**universal_no6fold,
'TAA': ['E_', 'two', 0], 'TAG': ['E_', 'two', 0],
'TGA': ['*', 'one', 0]}
cdnTableDict = {1:[universal_no6fold,universal_6fold],
4:[blepharisma_no6fold, blepharisma_6fold],
6:[ciliate_no6fold,ciliate_6fold],
10:[euplotes_no6fold,euplotes_6fold],
29:[mesodinium_no6fold,mesodinium_6fold],
30:[peritrich_no6fold,peritrich_6fold],
'chilodonella':[chilo_no6fold,chilo_6fold],
'chilo':[chilo_no6fold,chilo_6fold]}
return cdnTableDict[gCode]
def mapCdns(seq, cdnTable):
# Updates the codon counts for a given sequence to the respective codon
# count table (e.g. with or without 6-fold degeneracy).
codons = [seq[n:n+3] for n in range(0, len(seq)-len(seq)%3, 3)]
amb_cdn = 0
for c in codons:
try:
cdnTable[c][-1] += 1
except:
amb_cdn += 1
if cdnTable['TCC'][1] == 'six':
return cdnTable, amb_cdn
else:
return cdnTable
class GCeval():
"""
Returns %GC values from DNA sequences of various types.
"""
def gcTotal(seq):
# This function returns global GC content
return round(GC(seq), 4)
def gc1(seq):
# This function return the GC content of the first position of a codon
return round(GC(''.join([seq[n] for n in range(0, len(seq), 3)])), 4)
def gc2(seq):
# This function return the GC content of the second position of a codon
return round(GC(''.join([seq[n] for n in
range(1, len(seq)-len(seq[1:]) % 3, 3)])), 4)
def gc3(seq):
# This function return the GC content of the third position of a codon
return round(GC(''.join([seq[n] for n in
range(2, len(seq)-len(seq[2:]) % 3, 3)])), 4)
def gc3_4F(cdnTbl):
# # This function return the GC content of the third position of four-fold
# # degenerate codons
FrFold = round(GC(''.join([k[-1]*v[-1] for k, v in cdnTbl.items() if v[1] == 'four'])), 4)
return FrFold
class SeqInfo(object):
"""
Provides a means to harbor the data for each individual contig/gene in a
given fasta file.
This includes GC content (various types), Effective Number of codons
(ENc; again various calculations), Relative Synonymous Codon Usage (RSCU).
"""
def __init__(self,seq,gcode='universal'):
self.ntd = str(seq)
self.gcode, self.transTable = GenUtil.convertGenCode(gcode)
# Dictionary of the GC-related functions/calculations
self.gcFuncs = {'gcOverall':GCeval.gcTotal,'gc1':GCeval.gc1,'gc2':GCeval.gc2,'gc3':GCeval.gc3}
def countCodons(self):
# Stores the different codon tables and updates their codon counts
cdnTbls = GenUtil.getCDNtable(self.transTable)
self.cdnCounts_6F,self.amb_cdn = GenUtil.mapCdns(self.ntd, cdnTbls[1])
self.cdnCounts_No6F = GenUtil.mapCdns(self.ntd, cdnTbls[0])
def ENcStats(self):
# Stores the various Effective Number of Codons calculations in the class
self.expENc = CalcCUB.expWrightENc(self.gc3)
self.obsENc_6F = CalcCUB.calcWrightENc(self.cdnCounts_6F)
self.obsENc_No6F = CalcCUB.calcWrightENc(self.cdnCounts_No6F)
self.SunENc_6F = CalcCUB.SunEq5(self.cdnCounts_6F)
self.SunENc_No6F = CalcCUB.SunEq5(self.cdnCounts_No6F)
def GCstats(self):
# Stores the various GC-stats in the class
for k, v in self.gcFuncs.items():
setattr(self,k,v(self.ntd))
self.gc4F = GCeval.gc3_4F(self.cdnCounts_No6F)
def RSCUstats(self):
self.rscu_No6Fold = CalcCUB.RSCU(self.cdnCounts_No6F)
self.rscu_6Fold = CalcCUB.RSCU(self.cdnCounts_6F)
def prepFolders(outName):
if os.path.isdir(outName) == False:
os.mkdir(outName)
if os.path.isdir(outName+'/SpreadSheets') == False:
os.mkdir(outName+'/SpreadSheets')
def CalcRefFasta(fasta, gCode):
seqDB = {i.description:SeqInfo(i.seq, gCode) for i in SeqIO.parse(fasta,'fasta')}
GenCDNtable = {}
for k, v in seqDB.items():
v.countCodons()
v.GCstats()
v.ENcStats()
for k, v in v.cdnCounts_6F.items():
if k.isalpha() and k not in GenCDNtable .keys():
GenCDNtable[k] = [v[0],v[-1]]
else:
GenCDNtable[k][-1] += v[-1]
RSCU = CalcCUB.calcRCSU(GenCDNtable)
return seqDB, RSCU
def WriteWrightOut(seqData, outName, comp):
if comp == False:
with open(outName+'/SpreadSheets/'+outName.split('/')[-1]+'.ENc.Raw.tsv','w+') as w:
w.write('SequenceID\tAmbiguousCodons\tGC-Overall\tGC1\tGC2\tGC3\t'
'GC3-Degen\tExpWrightENc\tObsWrightENc_6Fold\tObsWrightENc_No6Fold\t'
'ObsWeightedENc_6Fold\tObsWeightedENc_No6Fold\n')
for k, v in seqData.items():
name = [k]
gcs = [str(v.gcOverall),str(v.gc1),str(v.gc2),str(v.gc3),str(v.gc4F)]
ENc = [str(v.expENc),str(v.obsENc_6F),str(v.obsENc_No6F),
str(v.SunENc_6F),str(v.SunENc_No6F)]
w.write('\t'.join(name+[str(v.amb_cdn)]+gcs+ENc)+'\n')
else:
with open(outName+'/SpreadSheets/'+outName.split('/')[-1]+'.CompTrans.ENc.Raw.tsv','w+') as w:
w.write('SequenceID\tAmbiguousCodons\tGC-Overall\tGC1\tGC2\tGC3\t'
'GC3-Degen\tExpWrightENc\tObsWrightENc_6Fold\tObsWrightENc_No6Fold\t'
'ObsWeightedENc_6Fold\tObsWeightedENc_No6Fold\n')
for k, v in seqData.items():
name = [k]
gcs = [str(v.gcOverall),str(v.gc1),str(v.gc2),str(v.gc3),str(v.gc4F)]
ENc = [str(v.expENc),str(v.obsENc_6F),str(v.obsENc_No6F),
str(v.SunENc_6F),str(v.SunENc_No6F)]
w.write('\t'.join(name+[str(v.amb_cdn)]+gcs+ENc)+'\n')
def getCompFasta(fasta, gCode, require_start, require_stop):
stopCDNs = {'1':['TAA','TAG','TGA'], '4':['TAA','TAG'], '6':['TGA'], '10':['TAA','TAG'],
'29':['TGA'], '30':['TGA'], 'universal':['TAA','TAG','TGA'], 'blepharisma':['TAA','TAG'],
'ciliate':['TGA'],'euplotes':['TAA','TAG'], 'mesodinium':['TGA'], 'peritrich':['TGA'],
'chilo':['TAA']}
if gCode.lower() not in stopCDNs.keys():
print('\nWARNING: Genetic code not recognized. Defaulting to universal.')
stops = stopCDNs['1']
else:
stops = stopCDNs[gCode]
with open(fasta.replace('.fasta','.Comp.fasta'),'w+') as w:
for i in SeqIO.parse(fasta,'fasta'):
if len(i.seq) % 3 == 0:
if ((require_start and str(i.seq).upper().startswith('ATG')) or not require_start) and ((require_stop and str(i.seq).upper()[-3:] in stops) or not require_stop):
w.write('>'+i.description+'\n'+str(i.seq)+'\n')
return fasta.replace('.fasta','.Comp.fasta')
def WriteNullENcOut(outName):
with open(outName+'/SpreadSheets/' + outName.split('/')[-1] + '.ENc.Null.tsv','w+') as w:
w.write('GC3\tENc\n')
w.write('\n'.join(CalcCUB.nullENcGC3()))
def WriteRSCUtbl(RSCUtbl, outName):
with open(outName+'/SpreadSheets/' + outName.split('/')[-1] + '.RSCU.tsv','w+') as w:
w.write('Codon\tAmino Acid\tRSCU\n')
for k,v in RSCUtbl.items():
w.write(k+'\t'+'\t'.join(v)+'\n')
def get_args():
parser = argparse.ArgumentParser(
prog = 'Codon Usage Bias Statistic Calculator version 2.1',
description = "Written by Xyrus Maurer-Alcala, updated July 19, 2023 by Auden Cote-L'Heureux"
)
parser.add_argument('--input', '-i', required = True, default = None, type = str, help = 'Path to a fasta file of nucleotide sequences OR to a folder containing multiple fasta files')
parser.add_argument('--genetic_code', '-g', default = 'universal', choices = { 'universal', 'blepharisma', 'ciliate', 'euplotes', 'mesodinium', 'peritrich', 'chilo'}, help = 'Genetic code to use (be careful if you are working with ciliates). Available codes are: "universal" (TAA, TAG, TGA), "blepharisma" (TAA, TAG), "ciliate" (TGA), "euplotes" (TAA, TAG), "mesodinium" (TGA), "peritrich" (TGA) and "chilo" (TAA). Ask someone if you are not sure what this means.')
parser.add_argument('--require_start', action = 'store_true', help = 'Filter for sequences that begin with a start codon')
parser.add_argument('--require_stop', action = 'store_true', help = 'Filter for sequences that end with a stop codon')
return parser.parse_args()
if __name__ == "__main__":
args = get_args()
#If only one file was input
if os.path.isfile(args.input) and args.input.split('.')[-1] in ('fasta', 'fas', 'fa', 'fna'):
outName = args.input.split('.')[0]
compFasta = getCompFasta(args.input, args.genetic_code, args.require_start, args.require_stop)
prepFolders(outName)
fastaDataRaw, RSCUtbl = CalcRefFasta(args.input, args.genetic_code)
fastaDataComp, RSCUtbl = CalcRefFasta(compFasta, args.genetic_code)
WriteWrightOut(fastaDataRaw, outName, comp=False)
WriteWrightOut(fastaDataComp, outName, comp=True)
WriteNullENcOut(outName)
WriteRSCUtbl(RSCUtbl, outName)
os.system('mv ' + compFasta + ' ' + outName + '/')
#If a folder of files was input
elif os.path.isdir(args.input):
if not os.path.isdir('TemporaryCUBOutput'):
os.mkdir('TemporaryCUBOutput')
for file in os.listdir(args.input):
if file != '.DS_Store':
if os.path.isfile(args.input + '/' + file) and file.split('.')[-1] in ('fasta', 'fas', 'fa', 'fna'):
outName = 'TemporaryCUBOutput/' + file.split('.')[0]
compFasta = getCompFasta(args.input + '/' + file, args.genetic_code, args.require_start, args.require_stop)
prepFolders(outName)
fastaDataRaw, RSCUtbl = CalcRefFasta(args.input + '/' + file, args.genetic_code)
fastaDataComp, RSCUtbl = CalcRefFasta(compFasta, args.genetic_code)
WriteWrightOut(fastaDataRaw, outName, comp=False)
WriteWrightOut(fastaDataComp, outName, comp=True)
WriteNullENcOut(outName)
WriteRSCUtbl(RSCUtbl, outName)
os.system('mv ' + compFasta + ' ' + outName + '/')
else:
print('\nWARNING: One of the files in your input folder (' + file + ') is not formatted correctly. These should be nucleotide fasta files with a file extension fasta, fas, fa, or fna. Skipping this file.\n')
folders = ['TemporaryCUBOutput/' + folder for folder in os.listdir('TemporaryCUBOutput') if os.path.isfile('TemporaryCUBOutput/' + folder + '/SpreadSheets/' + folder + '.CompTrans.ENc.Raw.tsv')]
#Combining information from all input files into one set of outputs
if len(folders) > 0:
if not os.path.isdir('CUBOutput'):
os.mkdir('CUBOutput')
if not os.path.isdir('CUBOutput/SpreadSheets'):
os.mkdir('CUBOutput/SpreadSheets')
os.system('cat TemporaryCUBOutput/*/*.Comp.fasta > CUBOutput/AllFiles.Comp.fasta')
os.system('cp ' + folders[0] + '/SpreadSheets/*.ENc.Null.tsv CUBOutput/SpreadSheets/ENc.Null.tsv')
with open('CUBOutput/SpreadSheets/RSCU.tsv', 'w') as o:
o.write('File\tCodon\tAmino Acid\tRSCU\n')
for folder in folders:
for line in open(folder + '/SpreadSheets/' + folder.split('/')[-1] + '.RSCU.tsv'):
if 'Amino Acid' not in line:
o.write(folder.split('/')[-1] + '\t' + line)
with open('CUBOutput/SpreadSheets/ENc.Raw.tsv', 'w') as o:
o.write('File\tSequenceID\tAmbiguousCodons\tGC-Overall\tGC1\tGC2\tGC3\tGC3-Degen\tExpWrightENc\tObsWrightENc_6Fold\tObsWrightENc_No6Fold\tObsWeightedENc_6Fold\tObsWeightedENc_No6Fold\n')
for folder in folders:
for line in open(folder + '/SpreadSheets/' + folder.split('/')[-1] + '.ENc.Raw.tsv'):
if 'SequenceID' not in line:
o.write(folder.split('/')[-1] + '\t' + line)
with open('CUBOutput/SpreadSheets/CompTrans.ENc.Raw.tsv', 'w') as o:
o.write('File\tSequenceID\tAmbiguousCodons\tGC-Overall\tGC1\tGC2\tGC3\tGC3-Degen\tExpWrightENc\tObsWrightENc_6Fold\tObsWrightENc_No6Fold\tObsWeightedENc_6Fold\tObsWeightedENc_No6Fold\n')
for folder in folders:
for line in open(folder + '/SpreadSheets/' + folder.split('/')[-1] + '.CompTrans.ENc.Raw.tsv'):
if 'SequenceID' not in line:
o.write(folder.split('/')[-1] + '\t' + line)
os.system('rm -r TemporaryCUBOutput')
else:
print('\nERROR: No composition information was created -- something probably went wrong with the formatting and/or filtering of the input fasta files. Make sure that this contains properly formatted nucleotide sequences (divisible by 3, etc).')
else:
print('\nERROR: Invalid --input. This should be a nucleotide fasta file with a file extension fasta, fas, fa, or fna or a folder of such files.\n')
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