Hi EveryOne,
I have a multifasta file which is converted from BWA bam file. I want to extract only sequences contains specific forward primer on the start and reverse primer at the end. How can i do it with awk or sed or grep. Thanks in advance.
The Input file looks like this :
>M01015:63:000000000-D2M18:1:1101:17027:1479
TTCTCTCTTCTCTCTTCTTCCTCTTTTCTTTTCTCTCTCTTTTTTTTCTTCTTTTTCTTCTTTTTTTCTT
TTCCTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTCTCCTTTTTCCTTCTTTCTTTTTCTTTTTT
CTCCTCTTCTTTTTTCTTTTTTTTCTTTCTTTTTTTCTCCTTTTTTTTTTTTCTTTTTTTCTTCCCTTTT
TTTTTTTCCCTTTTTTCTTTTTTTTTTTCTTCCTTTTTTT
>M01015:63:000000000-D2M18:1:1101:17027:1479
TCCTCTCTCTCTCTTCTCCCTCCTCCCTTTCTCTCTTCTCTCTTTTCTCTTTCTTTTCTTTTTTCTCTTT
TCCCTTTTTCCCTTCTTTCTTTTCTTTTTTTTTTTCTTTTTTCTTTTCTTTTTTTTTTCTCTTTTTTTCT
TCTTTTTTTTTCTCCTCTTTTTTTTTTTCTTTTTTTTTTTTTTTCTCTTTTTCTTCTTTTTTTTTTTTTT
CTTTTTTTCTTTTTTTTTTTTTTTTTTCTCTCTCTTTTTT
>M01015:63:000000000-D2M18:1:1101:15901:1612
GGCACTCGTATCGATGCGGCCGCGTTCGTTTGTTTATACACCTGCTCGTGCTTGTTTATGCATCTGCCAT
CTCCCTTCTGCTTATTTCTGTCTCCGATGCCTCTGTACTCCTTAGCCTTTCAGCTCCTGCCGCCTGTTTC
CCTGTGATGCAACAAGCTTACTCTGCACCAATGATGCAGCAGCCAGCTCAATCTAACGCAGCCAGTGATT
AGTTAGACGCGTGCCTGTGATTAGTTAGACGCGTGCCAGT
>M01015:63:000000000-D2M18:1:1101:15901:1612
GCCTCTGTCCCTCTTCTACCTATTCCTTGCCCCCCTCTTCCTTATTCCTTCCCCGCCTCTTCCTTATCTC
TGCCTTCTTTCTTTTGACCTCTCTCCTTCCTCATTGGTGCAGCGTTAGCTTGTTGCTTCACTGGGAAACT
TGCGGCAGGAGCTGCCCTGCTTCTGCGTCCTGACTCTTCGCCTTCCGTAATTTCCCGTTCGGTGTTGCCT
GTTTCTTCTACCAGCTCGCTCAGTTTTTTATTCTTTCGA
>M01015:63:000000000-D2M18:1:1101:16395:1620
GGCACTCGTATCGATGCGGCCGCGGTTATCTCTTCCCGCTGCACTGCCTTTTAGGCGTTCTTTTGTTCCG
GCCCCCTCTCCCCCCGGGTTCCCTGCTTTCCCCTGTGCGCTATTCCTGTTCTAGATGCTTTACTGTCCCC
CTCCGCTCCCGGCTTCTCGGTCAGTTTCCCCGTGCTTAGTTAGACGCGTGCTTCTGGC
>M01015:63:000000000-D2M18:1:1101:16395:1620
GCCTCTAGCACGCGTCTAACTAATCACTTTCCCCCTCCCCGTTAATCCGGGTTCTGTCTTGTTCAGTCAT
TCCTCTCGCCCCGCCCTCGCTCACTGGCTCTTGCTGCCTACCCGGGTTCAGTACTCGCCGTCCCTTATGA
ACCCCTCTTTGGCCTTGCTCCGGGTGGTGTTTCCCGCGGCCGCATCGATACGAGTGCCCTGTTTCTTATA
CACTTCTGACGCTGCCGCCGAATATAGCGGTGTCGTTCTT
>M01015:63:000000000-D2M18:1:1101:15366:1643
GGCACTCGTATCGATGCGGCCGCGGTAAACTCCACCCGGACCAACGCCAAATAGTGTTTCATAAGGTACT
TCCCTTACTCCCCCCGTGTAGGCTGCTTTTGCCCCTCTTCTCTTGCTGGCCTAGATGAATTACTGTCCTC
TACCTAACCCTTCTTATCTGTCAGTTTCACCGTTTTTTGTTAGTCGCGTGCTCTTTGCCTTTTTCTTCTA
CCTCTCTCCTCTCTCACTATACTTCTGTCCATCTTTTTTT
>M01015:63:000000000-D2M18:1:1101:15366:1643
GCCTCTAGCACGCGTCTCACTAATCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTT
TCCTCTTTTCTTTCCTTTTCTCTCTTTTTTTTTCTCCTTTCCCTTTTTCTGTTCCTTCCGTCCCTTTTGT
TCCCCTTTTTTTCCTTTCTCCTTTTTTTTTTTTCCCTTGCTCTTTCTTTTCTCTTCTCCTTTTTCTTTTA
CTTATCTTCCGTTTCCTTCGTCTTTCTCTTTTTATATTTT
>M01015:63:000000000-D2M18:1:1101:17421:1643
GGCACTCGTATCGATGCGGCCGCGGTGATGTTAGTCGCGTGCCGTGTTTTGTTACACGCGTGCCAGTGAT
TAGTTAGACGCGTGCTAGAGGC
>M01015:63:000000000-D2M18:1:1101:17421:1643
GCCTCTAGCACGCGTCTAACTAATCACTGGCCCGCGTCTCTCTAATCTCGGCTCGCGTCTCACTTCCCCG
CGGCCGCATCGATACGAGTGCC
>M01015:63:000000000-D2M18:1:1101:16505:1648
GGCACTCGTATCGATGCGGCCGCGTGTGATTTCTTCGACTTGTCCTAGCGTCCTCTCTCTTATCTACTTC
TTCGACCCCTCTCGACTCCTTTTCATCTCCTATTCCCTTTTCTGCTTCCCTATATTCTCTTCTTTTTTCT
TTTTTTTTTTTTGCTTATTCTTCCTTATCACTTTTTTTTTTCTACTCTATGCTTCCTGTCTGTCTCGTTT
CTGCCTCGTTGGTTTATTTTTCCTGCCTCTTTCTTTTTTT
>M01015:63:000000000-D2M18:1:1101:16505:1648
GCCTCTAGCACGCGTCTAACTAATCACTCTCTTCCTTTTCTTTTCTTTTGCCTTGTCTCTTCTTCCCCTC
TCTTGCTTCCCTCTACTTCTTTTTTTTTTTTTTCTTCCGTCTCCTTCTTTTTTTCTTCTCTACTTTTTTT
TCTTCTTTTTTTTTCTTTCTCTTTTTTTCTTTCTTTTTTCTTTCTTTTTCTTCTTCTTTTTTTCTATTTT
CTTCTCTTCTACTCTCTTTTCTTTTTTCTTCTTTTTCTTT
>M01015:63:000000000-D2M18:1:1101:17397:1654
GGCACTCGTATCGATGCGGCCGCGGGTGATGTGATTAGTTATACGCGTGCTAGTGGC
>M01015:63:000000000-D2M18:1:1101:17397:1654
TCCTCTAGCACGCGTCTAACTAATCACATCACCCGCGGCCGCATCGATACGAGTGCC
I want to extract only sequences(With headers) contains "ggcactcgtatcgatgcggccgcg" sequnces at the beginning and "gtgattagttagacgcgtgctagaggc" at the end. like this
M01015:63:000000000-D2M18:1:1101:17421:1643 GGCACTCGTATCGATGCGGCCGCGGTGATGTTAGTCGCGTGCCGTGTTTTGTTACACGCGTGCCAGTGAT TAGTTAGACGCGTGCTAGAGGC
Thanks for the reply cpad0112. I have made few changes in the question, so will you help with that?
Please do not do this. It is bad practice/forum etiquette to change the question. I can tell from these answers, and the current state of your question that the content has been changed significantly, which makes these answers no longer informative.
Please make sure you ask good questions in the first instance. If you need something new, ask a new question.
@ k.kathirvel93 ! As Joe said please do not edit OP after a possible solution is furnished.
Try this for modified query:
$ seqkit grep -srip ^ggcactcgtatcgatgcggccgcg test.fa | seqkit grep -srip gtgattagttagacgcgtgctagaggc$
>M01015:63:000000000-D2M18:1:1101:17421:1643
GGCACTCGTATCGATGCGGCCGCGGTGATGTTAGTCGCGTGCCGTGTTTTGTTACACGCG
TGCCAGTGATTAGTTAGACGCGTGCTAGAGGC
Thanks for the reply genomax. I have made few changes in the question, so will you help with that?
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How to extract pattern matching sequences from a fasta file?
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k.kathirvel93 : Don't delete questions after they have received an answer.