How to extract and concatenate fasta lines that match substring?

I have a list of unique identifiers

identifiers = ['subject_1', 'subject_2']

and a multi-fasta file containing

>CDS::subject_1::123
AAATTT
>CDS::subject_1::354
CCCGGG
>CDS::subject_2::789
GGGCCC
>CDS::subject_2::765
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

fasta python

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updated 3.8 years ago by rpolicastro

• written 3.8 years ago by YOUSEUFS •

2 answers

seqkit and csvtk answer

seqkit replace -p ".+::(\S+):.+" -r "\$1" test.fasta |
  seqkit fx2tab |
  csvtk fold -tH -f1 -v2 -s"," |
  sed 's/,//g' |
  seqkit tab2fx

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written 3.8 years ago by rpolicastro

cat input.fa  | paste - - | sed 's/>CDS:://;s/::[^\t]*//' | awk '{seq[$1]=sprintf("%s%s",seq[$1],$2);} END{for(n in seq) printf(">%s\n%s\n",n,seq[n]);}'

>subject_1
AAATTTCCCGGG
>subject_2
GGGCCCTTTAAA

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written 3.8 years ago by Pierre Lindenbaum

I'm having trouble getting this to work. Perhaps I should have stated more clearly, the fast-file looks more like

>CDS::NC_005291.1:5877-7537(-)
AAATTT
>CDS::NC_005291.1:7650-7800(-)
CCCGGG
>CDS::NC_007641.1:5877-7537(-)
AAATTT
>CDS::NC_007641.1:7650-7800(-)
CCCGGG

Which I'm trying to turn into

>NC_005291.1
AAATTTCCCGGG
>NC_007641.1
AAATTTCCCGGG

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written 3.8 years ago by YOUSEUFS •

change the sed expression...

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written 3.8 years ago by Pierre Lindenbaum