Thank you! This works perfectly and all ordered correctly.
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Collapse multifasta file by specific chromosome names
I have a multicast file with unique identifiers ('SUBJECT.1', 'SUBJECT.2' etc) like this:
>SUBJECT.1.1:1203-2742(+)
AAATTT
>SUBJECT.1:354-700(+)
CCCGGG
>SUBJECT.2:789-2000(+)
GGGCCC
>SUBJECT.2:2012-2742(+)
TTTAAA
how would I extract every line that's associated to each unique identifier and concatenate them together to form an output file that looks like
>SUBJECT.1
AAATTTCCCGGG
>SUBJECT.2
GGGCCCTTTAAA
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1 answer
Then use awk:
cut -d':' -f1 input.fa > output.fa
awk '/>/ { id = $0 } !/>/ { seq[id] = seq[id] $0 } END { for (id in seq) print id "\n" seq[id] }' output.fa > output_collapsed.fa
In this example I have assumed that the IDs you want to collapse are those before :, please adapt the code to your desired IDs as you consider. And as i said, remember the order of the sequences.
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Maybe something along these lines?:
1) Simplify headers:
2) Concat entries with same IDs using seqkit, specifically,
seqkit concatI'd make 100% sure that the entries in the fasta file are ordered properly before merging, and that you don't have duplicated ids.
seqkit only works when merging two file, this is a single file.