Header of first sequence is missing after grep
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,
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Pierre Lindenbaum
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Kai_Qi
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1 answer
you want B BEFORE
grep -i -B1 CCC..C input.fasta
not A AFTER
grep -i -A1 CCC..C input.fasta
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