thank you so much it works..
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genious.kalia.141198 •
How can I add an incremented value just after Accession no. ?
I have a large csv file (1.7GB) containing sequences, and i have to provide a header to each sequence, so i did some thing like this with bash to do same:
*#/bin/bash
cat con_test.csv > out.out
for file in out.out; do
sed -e 's/^/>NZ_CP00000.1 volvox complete genome\n/' -i "$file" done*
my input files:
AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA
CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG
TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA
AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG
my output file after running this script. (NZ_CP00000.1)
NZ_CP00000.1 volvox complete genome AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
NZ_CP00000.1 volvox complete genome GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA
NZ_CP00000.1 volvox complete genome CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG
NZ_CP00000.1 volvox complete genome TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA
NZ_CP00000.1 volvox complete genome AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG
Now i want to assign a different or unique value with the accession no. to all my sequences, so that the description line looks something like this: ( NZ_CP00000.1_000000001) and the unique value incremented for every time
>NZ_CP00000.1_000000001 volvox complete genome AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
>NZ_CP00000.1_000000002 volvox complete genome GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA
>NZ_CP00000.1_000000003 volvox complete genome CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG
>NZ_CP00000.1_000000004 volvox complete genome TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA
>NZ_CP00000.1_000000005 volvox complete genome AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG
how can i achieve this?
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cpad0112
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genious.kalia.141198 •
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genious.kalia.141198 •
3 answers
awk '/^>/ {$1=sprintf("%s_%010d",$1,++N);} {print;}' input.fa
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Pierre Lindenbaum
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Pierre Lindenbaum
$ seqkit replace -p '^(.+?) (.+)' -r '${1}_{nr} $2' --nr-width 9 -w 0 seq.fa
>NZ_CP00000.1_000000001 volvox complete genome
AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
>NZ_CP00000.1_000000002 volvox complete genome
GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA
>NZ_CP00000.1_000000003 volvox complete genome
CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG
>NZ_CP00000.1_000000004 volvox complete genome
TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA
>NZ_CP00000.1_000000005 volvox complete genome
AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTA
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shenwei356
i think seqkit is not installed thats why generating error. command not found.
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genious.kalia.141198 •
oh, you can google it
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shenwei356
nl -nrz -bp">" test.fa | sed "/>/ s/^\([0-9]\+\).*\(>\w\+\.[0-9]\)\(.*\)/\2_\1\3/g;s/^\s\+//g"
>NZ_CP00000.1_000001 volvox complete genome
AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
>NZ_CP00000.1_000002 volvox complete genome
GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA
>NZ_CP00000.1_000003 volvox complete genome
CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG
>NZ_CP00000.1_000004 volvox complete genome
TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA
>NZ_CP00000.1_000005 volvox complete genome
AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG
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