trimming of fasta file

Question

[harry]

As I have multiple fasta sequences like see below:

>read1
CAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCG
>read2
CATCTGCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGTGGTGAGGTCGACTTGAGAAAGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCCT
>read3
TTGAGGTGGGAGGATCGCTTCAGCCTGGAAGGTTGAGGCTGCAGTCAGCTGCGATAGCACTACTACACTCCAGCCTTGGACAACAGAGGGAGACCTTTCGCTGTCACCCCTCTAGAATCCACGTATACGAAAATTCCAAATGTTAGTTGGGCATAGTGGCAAGCACCTGTAGTCTCAGCCACGTGGGAGG

These are in different lengths so I want to isolate the middle sequence of all the fasta_sequence_reads. It is better if all are 150-160bp in sequences. Is there is a way to do this? Thanks in advance. for example, I have 1 read like below which contain 247 nucleotides: read2:

CATCTGCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGTGGTGAGGTCGACTTGAGAAAGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCCT

so after trimming from both sides the middle part is remaining 153bp:

TTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGTGGTGAGGTCGACTTGAGAAAGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATT

Like this, I want to do for my whole fasta sequence by using one command. So please can you tell me how to get a middle sequence of fasta files. thanks in advance.

[Pierre Lindenbaum]

how is it different from your previous question ? Script for making exon file

[harry]

In previous questions, I asked about how to cut a sequence and rejoin. means cut in 2 equal parts and join the downstream region to the upstream region. in this question I want to isolate the sequence from the middle part which overhangs from both sides of the middle part. Thanks

[Pierre Lindenbaum]

. in this question I want to isolate the sequence from the middle part which overhangs from both sides of the middle part.

it's the very same kind of operation.

[harry]

Can you please tell me how is it I doing this because I want a 150 bp sequence from the middle? 75bp upstream and 75bp downstream from the middle. Thanks

[Pierre Lindenbaum]

https://thomas-cokelaer.info/blog/2011/05/awk-the-substr-command-to-select-a-substring/

[Mark]

This is essentially alignment with trimming. You can do this with a GUI application like ugene, or geneious or bioedit. You can also see this answer: Most efficient way to trim overhanging bases after alignment

[Pierre Lindenbaum]

God kills a kitten every time you use a gui.

[Mark]

I disagree! Sometimes it's easier to just use a gui and get the job done. This is a good example where such usage is perfect. I do this regularly for trimming large MSA aligned to a reference.

[rpolicastro]

The problem with GUI applications is that they are often not easily reproducible and scalable in workflows. It's better in the long term to use CLI unless absolutely necessary.

Answer 1

[cpad0112]

$ awk -v OFS="\n" '/^>/ {getline seq}{print $0,substr(seq,length(seq)/2-75,150)}' test.fa 

>read1
CAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCG
>read2
TTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGTGGTGAGGTCGACTTGAGAAAGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCC
>read3
TCAGCCTGGAAGGTTGAGGCTGCAGTCAGCTGCGATAGCACTACTACACTCCAGCCTTGGACAACAGAGGGAGACCTTTCGCTGTCACCCCTCTAGAATCCACGTATACGAAAATTCCAAATGTTAGTTGGGCATAGTGGCAAGCACCTG