I have some txt files that look like this (they contain DNA sequences and sample codes):
>SRR1502445.1
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCAACACAGGGGGATAGGNNNNNNNNNNNNNNNNNNNNNNN
>SRR1502445.2
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNN
>SRR1502445.3
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNN
>SRR1502445.4
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNNNNNNNNNN
I would like to remove the first 15 characters of every other line in the file. This would remove the string GACTACACGTAGTAT
from the second, fourth, sixth, eighth lines (etc).
For instance the cut command can remove the first 15characters of every line:
cut -c 1-15 /path/to/file.txt
I'd like to apply to to only every other line, starting with the second.
If you don't mind using sed
and assuming other line starts with >
then the following will remove the first 15 contiguous uppercase characters "A-Z" of the other lines:
sed 's/^[A-Z]\{15\}//' file > new_file
Or, in place edit (GNU sed) use -i
:
sed -i 's/^[A-Z]\{15\}//' file
Or, in place edit (BSD sed) use -i ''
:
sed -i '' 's/^[A-Z]\{15\}//' file
Or, back it up:
sed -i.bak 's/^[A-Z]\{15\}//' file
Example:
$ cat file
>SRR1502445.1
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCAACACAGGGGGATAGGNNNNNNNNNNNNNNNNNNNNNNN
>SRR1502445.2
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNN
>SRR1502445.3
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNN
>SRR1502445.4
GACTACACGTAGTATACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNNNNNNNNNN
$ sed 's/^[A-Z]\{15\}//' file
>SRR1502445.1
ACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCAACACAGGGGGATAGGNNNNNNNNNNNNNNNNNNNNNNN
>SRR1502445.2
ACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNN
>SRR1502445.3
ACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNN
>SRR1502445.4
ACGAGTGCGTTCCTGCGCTTATTGATATGCTTAAGTTCAGCGGGTAGTCTCACCCGATTTGAGGTCAAGGTTTGTGGGTCGAGTCACAACTCGAACATCGTCTTTGTACAAAGACGGTTGGAAGCGGGTTCCAAGGCACACAGGGGATAGGNNNNNNNNNNN
$