How to add character at the end of specific line in UNIX/LINUX?-CodePudding

Here is my input file. I want to add a character ":" into the end of lines that have ">" at the beginning of the line. I tried seq -i 's|$|:|' input.txt but ":" was added to all the ending of each line. It is also hard to call out specific line numbers because, in each of my input files, the line contains">" present in different line numbers. I want to run a loop for multiple files so it is useless.

>Pas_pyrG_2
AAAGTCACAATGGTTAAAATGGATCCTTATATTAATGTCGATCCAGGGACAATGAGCCCA
TTCCAGCATGGTGAAGTTTTTGTTACCGAAGATGGTGCAGAAACAGATCTGGATCTGGGT
>Pas_rpoB_4
CAAACTCACTATGGTCGTGTTTGTCCAATTGAAACTCCTGAAGGTCCAAACATTGGTTTG
ATCAACTCGCTTTCTGTATACGCAAAAGCGAATGACTTCGGTTTCTTGGAAACTCCATAC
CGCAAAGTTGTAGATGGTCGTGTAACTGATGATGTTGAATATTTATCTGCAATTGAAGAA
>Pas_cpn60_2
ATGAACCCAATGGATTTAAAACGCGGTATCGACATTGCAGTAAAAACTGTAGTTGAAAAT
ATCCGTTCTATTGCTAAACCAGCTGATGATTTCAAAGCAATTGAACAAGTAGGTTCAATC
TCTGCTAACTCTGATACTACTGTTGGTAAACTTATTGCTCAAGCAATGGAAAAAGTAGGT
AAAGAAGGCGTAATCACTGTAGAAGAAGGCTCAGGCTTCGAAGACGCATTAGACGTTGTA

Here is experted output file:

    >Pas_pyrG_2:
    AAAGTCACAATGGTTAAAATGGATCCTTATATTAATGTCGATCCAGGGACAATGAGCCCA
    TTCCAGCATGGTGAAGTTTTTGTTACCGAAGATGGTGCAGAAACAGATCTGGATCTGGGT
    >Pas_rpoB_4:
    CAAACTCACTATGGTCGTGTTTGTCCAATTGAAACTCCTGAAGGTCCAAACATTGGTTTG
    ATCAACTCGCTTTCTGTATACGCAAAAGCGAATGACTTCGGTTTCTTGGAAACTCCATAC
    CGCAAAGTTGTAGATGGTCGTGTAACTGATGATGTTGAATATTTATCTGCAATTGAAGAA
    >Pas_cpn60_2:
    ATGAACCCAATGGATTTAAAACGCGGTATCGACATTGCAGTAAAAACTGTAGTTGAAAAT
    ATCCGTTCTATTGCTAAACCAGCTGATGATTTCAAAGCAATTGAACAAGTAGGTTCAATC
    TCTGCTAACTCTGATACTACTGTTGGTAAACTTATTGCTCAAGCAATGGAAAAAGTAGGT
    AAAGAAGGCGTAATCACTGTAGAAGAAGGCTCAGGCTTCGAAGACGCATTAGACGTTGTA

Do seq have more option to modify or the other commands can solve this problem?

CodePudding user response：

Using ed to edit the file:

printf "%s\n" 'g/^>/s/$/:/' w | ed -s input.txt

For every line starting with >, add a colon to the end, and then write the changed file back to disk.

CodePudding user response：

sed -i  '/^>/ s/$/:/' input.txt

Search the lines of input for lines that match ^> (regex for "starts with the > character). Those that do substitute : for end-of-line (you got this part right).

/ slashes are the standard separator character in sed. If you wish to use different characters, be sure to pass -e or s|$|:| probably won't work. Since / characters, unlike | characters, are not meaningful character within the shell, it's best to use them unless the pattern also contains slashes, in which case things get unwieldy.

Be careful with sed -i. Make a backup - make sure you know what's changing by using diff to compare the files.

On OSX -i requires an argument.