import numpy as np

# Function to read sequences from a FASTA file def read$\_$fasta$($file$)$: with open$($file$,\text{'}$r$\text{'})$ as f:

sequences $=[]$ sequence $=\text{'}\text{'}$ for line in f: if line.startswith$(\text{'}>\text{'})$: if sequence:

sequences.append$($sequence$)$ sequence $=\text{'}\text{'}$ else:

sequence $+=$ line.strip$()$ if sequence: sequences.append$($sequence$)$ return sequences

# Needleman$-$Wunsch algorithm implementation for global alignment def needleman$\_$wunsch$($seq$1,$ seq$2,$ match$\_$score$=1,$ gap$\_$cost$=1,$ mismatch$\_$cost$=1)$:

n $=$ len$($seq$1)$ m $=$ len$($seq$2)$ score$\_$matrix $=$ np$.$zeros$(($n $+1,$ m $+1))$

for i in range$($n $+1)$:

score$\_$matrix$[$i$][0]=-$i $*$ gap$\_$cost for j in range$($m $+1)$:

score$\_$matrix$[0][$j$]=-$j $*$ gap$\_$cost

for i in range$(1,$ n $+1)$: for j in range$(1,$ m $+1)$:

match $=$ score$\_$matrix$[$i $-1][$j $-1]+($match$\_$score if seq$1[$i $-1]==$ seq$2[$j $-1]$ else $-$mismatch$\_$cost$)$ delete $=$ score$\_$matrix$[$i $-1][$j$]-$ gap$\_$cost insert $=$ score$\_$matrix$[$i$][$j $-1]-$ gap$\_$cost score$\_$matrix$[$i$][$j$]=$ max$($match$,$ delete, insert$)$

align$1,$ align$2=\text{'}\text{'},\text{'}\text{'}$ i$,$ j $=$ n$,$ m

while i $>0$ and j $>0$:

score$\_$current $=$ score$\_$matrix$[$i$][$j$]$ score$\_$diagonal $=$ score$\_$matrix$[$i $-1][$j $-1]$ score$\_$up $=$ score$\_$matrix$[$i$][$j $-1]$ score$\_$left $=$ score$\_$matrix$[$i $-1][$j$]$

if score$\_$current $==$ score$\_$diagonal $+($match$\_$score if seq$1[$i $-1]==$ seq$2[$j $-1]$ else $-$mismatch$\_$cost$)$:

align$1+=$ seq$1[$i $-1]$ align$2+=$ seq$2[$j $-1]$ i $-=1$ j $-=1$ elif score$\_$current $==$ score$\_$left $-$ gap$\_$cost:

align$1+=$ seq$1[$i $-1]$ align$2+=\text{'}-\text{'}$ i $-=1$ elif score$\_$current $==$ score$\_$up $-$ gap$\_$cost:

align$1+=\text{'}-\text{'}$ align$2+=$ seq$2[$j $-1]$ j $-=1$

while i $>0$:

align$1+=$ seq$1[$i $-1]$ align$2+=\text{'}-\text{'}$ i $-=1$

while j $>0$:

align$1+=\text{'}-\text{'}$ align$2+=$ seq$2[$j $-1]$ j $-=1$

align$1=$ align$1[$::$-1]$ align$2=$ align$2[$::$-1]$

return align$1,$ align$2,$ score$\_$matrix$[$n$][$m$]$

# Function to find differential indices def find$\_$differential$\_$indices$($align$1,$ align$2)$:

differential$\_$indices $=[]$ for i in range$($len$($align$1))$: if align$1[$i$]!=$ align$2[$i$]$: differential$\_$indices.append$($i$)$ return differential$\_$indices

# Main function to execute the workflow def main$()$:

# Example sequences in FASTA format query$\_$fasta $=$ 'query.fasta' database$\_$fasta $=$ 'database.fasta'

# Read sequences from FASTA files query$\_$sequences $=$ read$\_$fasta$($query$\_$fasta$)$ database$\_$sequences $=$ read$\_$fasta$($database$\_$fasta$)$

query$\_$seq $=$ query$\_$sequences$[0]$ database$\_$seq $=$ database$\_$sequences$[0]$

# Perform global alignment using Needleman$-$Wunsch algorithm align$1,$ align$2,$ score $=$ needleman$\_$wunsch$($query$\_$seq, database$\_$seq$)$

# Find differential indices differential$\_$indices $=$ find$\_$differential$\_$indices$($align$1,$ align$2)$

# Print results print$($f$"$Query Sequence: $\{$query$\_$seq$\}")$ print$($f$"$Database Sequence: $\{$database$\_$seq$\}")$ print$($f$"$Aligned Query Sequence: $\{$align$1\}")$ print$($f$"$Aligned Database Sequence: $\{$align$2\}")$ print$($f$"$Alignment Score: $\{$score$\}")$ print$($f$"$Differential Indices: $\{$differential$\_$indices$\}")$

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

main$()$

$*$It needs to get gapped allignment