Substituing Nth character in a fasta

# replace 100th character (strings and/or numbers) to "M"
$ sed 's/./M/100' input





###############################
$ awk '{ if ($0 ~ /^>/) { print $0; } \      # if the line starts with ">", print all
else { printf("%s%c%s\n", substr($0, 1, 2), "X", substr($0, 4, length($0))); } }' \    # else
additional.primers.cosmic.ext200.gDNA.fa | less

# INPUT - sequence must be a one line fasta
>APC_c.637C>T_77
aacagacacaatgcagtctCTTAAAAACAAAATCCCTTAATGCTCACAAACCAGTAACCCAGATACAGCCCAGACACTTCAATTCTCTCCATCTTGGAGTATGGTCATGGTCTCATTTTCCATCCTCAGTTTCCAAGAAGGCTGAAGTACCCTTATTTATCTAAGTTCTGAATTGGGTTTAGGGCACCAGATCTAGGGATGTTTGGGAACATCATATACTTAAAATTTCAgaagtcctagggagagcaatcaggcaagagaaataagtaaaaggaatccagataggaaaagaagaagtcaaactatctctctttgctgacaatataattctatacataaagaatcctaaagactccaccagaaggctcccagaactgataaacaatttcagtaaagtttc
>APC_c.646C>T_52
aggttcacgccattctcctgcctcagcctctccaatagctgggactacagtcacccgccaccatgcccagctaatttttttttttttttttttttttttttttagtagagacgaggcttcaccatgttagccaggatggtctcgatctcctgacctcgtgatccacctgcctcggcctcccaaaatgctggtattacaggcgtgagccactgcgcccggccaatgagcactacttttttttttttaattatacttttaagttctagggtacatgtgcacaacgtgcactacttttgagtgtcatgtcagtgctcaaaaagttttagattttggaggatttcagattttcagatttggggtgcctaacctCTATCTCAAGGCATCTATGAAGCAGGGAGGG


# OUTPUT - every third string in each sequence is replced with "X"
>APC_c.637C>T_77
aaXagacacaatgcagtctCTTAAAAACAAAATCCCTTAATGCTCACAAACCAGTAACCCAGATACAGCCCAGACACTTCAATTCTCTCCATCTTGGAGTATGGTCATGGTCTCATTTTCCATCCTCAGTTTCCAAGAAGGCTGAAGTACCCTTATTTATCTAAGTTCTGAATTGGGTTTAGGGCACCAGATCTAGGGATGTTTGGGAACATCATATACTTAAAATTTCAgaagtcctagggagagcaatcaggcaagagaaataagtaaaaggaatccagataggaaaagaagaagtcaaactatctctctttgctgacaatataattctatacataaagaatcctaaagactccaccagaaggctcccagaactgataaacaatttcagtaaagtttc
>APC_c.646C>T_52
agXttcacgccattctcctgcctcagcctctccaatagctgggactacagtcacccgccaccatgcccagctaatttttttttttttttttttttttttttttagtagagacgaggcttcaccatgttagccaggatggtctcgatctcctgacctcgtgatccacctgcctcggcctcccaaaatgctggtattacaggcgtgagccactgcgcccggccaatgagcactacttttttttttttaattatacttttaagttctagggtacatgtgcacaacgtgcactacttttgagtgtcatgtcagtgctcaaaaagttttagattttggaggatttcagattttcagatttggggtgcctaacctCTATCTCAAGGCATCTATGAAGCAGGGAGGG