# Constants

MIN$\_$CODONS $=5$

MIN$\_$MASS$\_$PERCENTAGE$\_$CG $=30$

NUM$\_$NUCLEOTIDES $=4$

NUCLEOTIDES$\_$PER$\_$CODON $=3$

# Function to convert a nucleotide into an index

def nucleotide$\_$to$\_$index$($nucleotide$)$:

nucleotide $=$ nucleotide.upper$()$

nucleotide$\_$index $=\{\text{'}$A$\text{'}$: $0,\text{'}$C$\text{'}$: $1,\text{'}$G$\text{'}$: $2,\text{'}$T$\text{'}$: $3\}$

return nucleotide$\_$index.get$($nucleotide$,-1)$

# Function to calculate nucleotide counts

def calculate$\_$nucleotide$\_$counts$($sequence$)$:

counts $=[0]*$ NUM$\_$NUCLEOTIDES

for nucleotide in sequence:

index $=$ nucleotide$\_$to$\_$index$($nucleotide$)$

if index $!=-1$:

counts$[$index$]+=1$

return counts

# Function to calculate mass percentages

def calculate$\_$mass$\_$percentages$($sequence$)$:

mass$\_$values $=\{\text{'}$A$\text{'}$: $135\mathrm{.}128,\text{'}$C$\text{'}$: $111\mathrm{.}103,\text{'}$G$\text{'}$: $151\mathrm{.}128,\text{'}$T$\text{'}$: $125\mathrm{.}107,\text{'}-\text{'}$: $100\mathrm{.}000\}$

# Filter out dashes $(\text{'}-\text{'})$ before calculating total mass

total$\_$mass $=$ sum$($mass$\_$values$[$nucleotide$]$ for nucleotide in sequence if nucleotide in mass$\_$values$)$

nucleotide$\_$counts $=$ calculate$\_$nucleotide$\_$counts$($sequence$)$

# Calculate mass percentages based on the total mass of the sequence

mass$\_$percentages $=[$round$(($mass$\_$values$[$nucleotide$]*$ count $/$ total$\_$mass$)*100,1)$ for nucleotide, count in zip$("$ACGT$",$ nucleotide$\_$counts$)]$

return mass$\_$percentages, total$\_$mass

# Function to extract codons from a sequence

def extract$\_$codons$($sequence$)$:

valid$\_$sequence $=[$nucleotide for nucleotide in sequence if nucleotide.isupper$()]$

codons $=[\text{'}\text{'}.$join$($valid$\_$sequence$[$i:i $+$ NUCLEOTIDES$\_$PER$\_$CODON$])$ for i in range$(0,$ len$($valid$\_$sequence$),$ NUCLEOTIDES$\_$PER$\_$CODON$)]$

return codons

# Function to check if a sequence is a protein

def is$\_$protein$($sequence$)$:

start$\_$codon $=$ "ATG"

stop$\_$codons $=["$TAA$",$ "TAG", "TGA"$]$

# Check start codon

if not sequence.startswith$($start$\_$codon$)$:

return False

# Check stop codon

if not any$($sequence$.$endswith$($stop$)$ for stop in stop$\_$codons$)$:

return False

# Check minimum codons

if len$($extract$\_$codons$($sequence$))<$ MIN$\_$CODONS:

return False

# Check minimum mass percentage of C and G

cg$\_$mass$\_$percentage $=$ sum$($calculate$\_$mass$\_$percentages$($sequence$)[1$:$3])$

if cg$\_$mass$\_$percentage $<$ MIN$\_$MASS$\_$PERCENTAGE$\_$CG:

return False

return True

# Function to process a nucleotide sequence

def process$\_$sequence$($region$\_$name, nucleotides$)$:

nucleotide$\_$counts $=$ calculate$\_$nucleotide$\_$counts$($nucleotides$)$

mass$\_$percentages, total$\_$mass $=$ calculate$\_$mass$\_$percentages$($nucleotides$)$

codons$\_$list $=$ extract$\_$codons$($nucleotides$)$

is$\_$protein$\_$result $=$ is$\_$protein$($nucleotides$)$

# Print or write to the output file

print$($f$"$Region Name: $\{$region$\_$name$\}")$

print$($f$"$Nucleotides: $\{$nucleotides$\}")$

print$($f$"$Nuc$.$ Counts: $\{$nucleotide$\_$counts$\}")$

print$($f$"$Total Mass$\%$: $\{$mass$\_$percentages$\}$ of $\{$total$\_$mass:$\mathrm{.}1$f$\}")$

print$($f$"$Codons List: $\{$codons$\_$list$\}")$

print$($f$"$Is Protein?: $\{\text{'}$YES$\text{'}$ if is$\_$protein$\_$result else $\text{'}$NO$\text{'}\}$

$")$

# Main function

def main$()$:

print$("$This program reports information about DNA nucleotide sequences that may encode proteins."$)$

# Input file names

input$\_$file$\_$name $=$ input$("$Input file name? $")$

output$\_$file$\_$name $=$ input$("$Output file name? $")$

# Process input file

with open$($input$\_$file$\_$name, $\text{'}$r$\text{'})$ as input$\_$file:

# Assume each pair of lines represents a region name and nucleotide sequence

lines $=$ input$\_$file.readlines$()$

for i in range$(0,$ len$($lines$),2)$:

region$\_$name $=$ lines$[$i$].$strip$()$

nucleotides $=$ lines$[$i $+1].$strip$().$upper$()$

process$\_$sequence$($region$\_$name, nucleotides$)$

if $\_\_$name$\_\_=="\_\_$main$\_\_"$:

main$()$ what is the pseudocode and flowchart for this python code?