I have the series of coordinates in
id.txt file, whose coordinates sequences are in
The coordinates of id.txt file is shown below,
Contig3:15-7 Contig2:5-10 Contig1:12-3
The genome.fasta file is shown below,
>Contig1 AAGGCCATCAAGGACGTGGATGAGGTCGTCAAG >Contig2 ACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCC >Contig3 GCTGCGGCGCTGATCCTGGCGGCCCGCGCCGAG
I have used the following codes to extract the sequences from
genome.fasta based on the coordinates in
id.txt by using the following command
xargs samtools faidx genome.fasta <id.txt > result.fasta
It has extracted only
Contig2:5-10sequence. Because, the coordinates of
Contig2:5-10is in proper order. But
Contig1:12-3 coordinates are in inverse/reverse order, So samtools could not fetch those sequences.
I need to extract those sequences from
Contig3:15-7 coordinates and also I want to
reverse complement them. I have larger fasta file and plenty of coordinates sequences to be extracted, So I need to automate this process. So, please help me to automate this process.
The expected output is
>Contig3 GATCAGCGC >Contig2 AGCGCT >Contig1 CTTGATGGCC
Thank you in advance.