Header of first sequence is missing after grep

Question

[Kai_Qi]

Hi All:

I have a fasta file and I used grep to get all the sequences and the coordinates that contain a certain motif:

$ head input.fasta

>16:23107820-23108019(+)
GTACGGCGCTCCCGGGGCGGCCGGTGGCCTGTAGTCAAGGTCACTAGGACCCGCGTTGAGGTGGGTTGCTTGGCGGCCACACTGCAGGTATGCGGGCTTTTTCTTAGGGCACACACTTCTCCTTGTGCCCTTCGAGAAGCTTCCATGATGGTAAGACTCCAGATGTTGGGGAGACAGGACGGATACAAGAACGGAGTAT
>14:54909471-54909670(-)
GTAAGTGGCACCCTGCCAGAGATCCCTCTCTGCCCTGGGTCTCATGCCTTCCTTTCTGCACCTCCAGACAATTTCTGCTGCCCCTAGGTCCCAGATTTCAGCTGTCCAGATGTCCAGGCCTTTTAAAGGGTCTAGGCAGGGGGTCCTACTGCTCACACAGTCCTCCCACTGGCTGTTATGTTTAAAATCCTAACCTGGC
>7:127020805-127021004(-)
GTAGGTGTGGACGACAGACAGCTGGGTGGCATGAGAATGCAGGTGCCAGGCGAACTAGAGGGTGGTGCTGGGTGCGTCGTACCATCGGGAGAAGATCCCCTCCCCCTCAGCCTCTGCTGAAAGCAACAAGGGAACCCCTAAAAGAAGGGCTAAGAAGGTATGCACAAGATACTGGGTCTTCCCCAAGAATGGGGCTGGA
>X:20848619-20848818(+)
GTGAGGGCAGGCCCGGTAGGGTTCGGGTTTTGGAGCGGCTGCGGGACCCGGGTATGAAGTCCAGACCGAAAGCTCAGCTCCAAGATGCTTCCGTCTGAATCTCAGCGTTCTCCCGCCCGGAACCAAAGGAGTGGTTTGACCAGGGCGAGACCGTCGTCATCGACCGTGGGAGTGGATGGAGGAGTCGGCCTGCAGGCTG
>1:75547398-75547597(+)
GTGGGTAGCCTGGGGACCCCTAGCACCCCAGCCTTCACCACCATCACCTTCATCGCCACCATTACTGCGCTCACCTCCGGCTTGATCACTCAGTGTCATCCTGTGCTGGACGCTGTGCTGGGCCACCATGCCATGTTAAGTCATCCTGCCTCTCATACCATCATCACCTTGTTCACCTGTCAGGGGAGATGTAGGGGAG

$ grep -i -A1 CCC..C input.fasta > 1.fasta   #search motif CCC[A/U/G][C/G]C using grep since the sequence is 1 line, don't need to pre-process

The problem is that when I looked into the output file the title(coordinates) of the fist line is missing:

head 1.fasta 

GTACGGCGCTCCCGGGGCGGCCGGTGGCCTGTAGTCAAGGTCACTAGGACCCGCGTTGAGGTGGGTTGCTTGGCGGCCACACTGCAGGTATGCGGGCTTTTTCTTAGGGCACACACTTCTCCTTGTGCCCTTCGAGAAGCTTCCATGATGGTAAGACTCCAGATGTTGGGGAGACAGGACGGATACAAGAACGGAGTAT
>14:54909471-54909670(-)
GTAAGTGGCACCCTGCCAGAGATCCCTCTCTGCCCTGGGTCTCATGCCTTCCTTTCTGCACCTCCAGACAATTTCTGCTGCCCCTAGGTCCCAGATTTCAGCTGTCCAGATGTCCAGGCCTTTTAAAGGGTCTAGGCAGGGGGTCCTACTGCTCACACAGTCCTCCCACTGGCTGTTATGTTTAAAATCCTAACCTGGC
>7:127020805-127021004(-)
GTAGGTGTGGACGACAGACAGCTGGGTGGCATGAGAATGCAGGTGCCAGGCGAACTAGAGGGTGGTGCTGGGTGCGTCGTACCATCGGGAGAAGATCCCCTCCCCCTCAGCCTCTGCTGAAAGCAACAAGGGAACCCCTAAAAGAAGGGCTAAGAAGGTATGCACAAGATACTGGGTCTTCCCCAAGAATGGGGCTGGA
>X:20848619-20848818(+)
GTGAGGGCAGGCCCGGTAGGGTTCGGGTTTTGGAGCGGCTGCGGGACCCGGGTATGAAGTCCAGACCGAAAGCTCAGCTCCAAGATGCTTCCGTCTGAATCTCAGCGTTCTCCCGCCCGGAACCAAAGGAGTGGTTTGACCAGGGCGAGACCGTCGTCATCGACCGTGGGAGTGGATGGAGGAGTCGGCCTGCAGGCTG
>1:75547398-75547597(+)
GTGGGTAGCCTGGGGACCCCTAGCACCCCAGCCTTCACCACCATCACCTTCATCGCCACCATTACTGCGCTCACCTCCGGCTTGATCACTCAGTGTCATCCTGTGCTGGACGCTGTGCTGGGCCACCATGCCATGTTAAGTCATCCTGCCTCTCATACCATCATCACCTTGTTCACCTGTCAGGGGAGATGTAGGGGAG
>11:102777648-102777847(+)

What should I do to make the first line also have its title?

Thank you,

Answer 1

[Pierre Lindenbaum]

you want B BEFORE

grep -i -B1 CCC..C input.fasta

not A AFTER

grep -i -A1 CCC..C input.fasta

[Kai_Qi]

Thank you very much. It worked