Rename FASTA headers based on filename
Hi
FASTA header looks like:
>1570-13.segment.flu1_PB2
>1570-13.segment.flu2_PB1
>1570-13.segment.flu3_PA
etc
Filenames looks like:
201301234.fasta
I want to have FASTA headers that looks like:
>201301234_PB2
>201301234_PB1
>201301234_PA
I have seen this answer: Change header of a Fasta file according to the file name How can I modify this to preserve the _PB2...?
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AK
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SaltedPork
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SaltedPork
3 answers
Hi SaltedPork,
Try:
for i in $(ls *.fasta); do fname=$(basename ${i} .fasta); perl -pe "s/^>.+_/>${fname}_/g" ${fname}.fasta > reID_${fname}.fasta; done
Edited (better use *.fasta, see response from RamRS):
for i in *.fasta; do fname=$(basename ${i} .fasta); perl -pe "s/^>.+_/>${fname}_/g" ${fname}.fasta > reID_${fname}.fasta; done
I have a heavily customized shell. My ls is an example. My LSCOLORS setting interferes with the filename here. See sample output:
➜ for f in $(ls *.gz)
> file $f
hs37d5_GRCm38p6.fasta.gz: cannot open `\033[0m\033[38;5;9mhs37d5_GRCm38p6.fasta.gz\033[0m' (No such file or directory)
hs37d5_GRCm38p6.reheader.fasta.gzip.gz: cannot open `\033[38;5;9mhs37d5_GRCm38p6.reheader.fasta.gzip.gz\033[0m' (No such file or directory)
hs37d5_GRCm38p6.reheader.fasta.gz: cannot open `\033[38;5;9mhs37d5_GRCm38p6.reheader.fasta.gz\033[0m' (No such file or directory)
: cannot open `\033[m' (No such file or directory)
➜ for f in $(/bin/ls *.gz)
> file $f
hs37d5_GRCm38p6.fasta.gz: gzip compressed data, extra field
hs37d5_GRCm38p6.reheader.fasta.gz: gzip compressed data, extra field
hs37d5_GRCm38p6.reheader.fasta.gzip.gz: gzip compressed data, from Unix, last modified: Mon May 6 16:15:43 2019
➜ for f in *.gz
> file $f
hs37d5_GRCm38p6.fasta.gz: gzip compressed data, extra field
hs37d5_GRCm38p6.reheader.fasta.gz: gzip compressed data, extra field
hs37d5_GRCm38p6.reheader.fasta.gzip.gz: gzip compressed data, from Unix, last modified: Mon May 6 16:15:43 2019
With respect to filenames causing a problem, if filenames contained white spaces, $(ls) would pass that as separate inputs whereas * would glob it as one with the spaces escaped. See below:
➜ touch a "b c"
➜ for f in $(/bin/ls *)
> file $f
a: empty
b: cannot open `b' (No such file or directory)
c: cannot open `c' (No such file or directory)
➜ for f in *
> file $f
a: empty
b c: empty
Just using bash:
for i in *fasta; do n="${i%.fasta}"; sed -i.bak "s/>[^_]\+/>$n/" $i; done
This loops over all files in the current directory that end with "fasta". For each file:
n="${i%.fasta}"removes the .fasta file extension (can be generalized to any extension by usingn="${i%.*}")sed "s/>[^_]\+/>$n/"matches a string in the file that starts with ">" and is followed by any character that's not an underscore, and replaces it with the filename minus extension found in the previous step. Depending on your requirements, you may want to tighten up this regex.- The
-i.bakpart just tells sed to replace the string in the original file, but make a backup called <originalname>.bak.
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Using seqkit : replace
seqkit replace -p '.segment.flu1' -r '' <your_fasta_file>
Explanation
replace = name/sequence by regular expression.
-p, --pattern string search regular expression
-r, --replacement string replacement. supporting capture variables
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