CODEWITHSUNDEEP
awkfasta
user2993059
user2993059

Reputation: 55

Use AWK to search through fasta file, given a second file containing sequence names

I have a 2 files. One is a fasta file contain multiple fasta sequences, while another file includes the names of candidate sequences I want to search (file Example below).

seq.fasta

>Clone_18
GTTACGGGGGACACATTTTCCCTTCCAATGCTGCTTTCAGTGATAAATTGAGCATGATGGATGCTGATAATATCATTCCCGTGT
>Clone_23
GTTACGGGGGGCCGAAAAACACCCAATCTCTCTCTCGCTGAAACCCTACCTGTAATTTGCCTCCGATAGCCTTCCCCGGTGA
>Clone_27-1
GTTACGGGGACCACACCCTCACACATACAAACACAAACACTTCAAGTGACTTAGTGTGTTTCAGCAAAACATGGCTTC
>Clone_27-2
GTTACGGGGACCACACCCTCACACATACAAACACAAACACTTCAAGTGACTTAGTGTGTTTCAGCAAAACATGGCTTCGTTTTGTTCTAGATTAACTATCAGTTTGGTTCTGTTTGTCCTCGTACTGGGTTGTGTCAATGCACAACTT
>Clone_34-1
GTTACGGGGGAATAACAAAACTCACCAACTAACAACTAACTACTACTTCACTTTTCAACTACTTTACTACAATACTAAGAATGAAAACCATTCTCCTCATTATCTTTGCTCTCGCTCTTTTCACAAGAGCTCAAGTCCCTGGCTACCAAGCCATCG
>Clone_34-3
GTTACGGGGGAATAACAAAACTCACCAACTAACAACTAACTACTACTTCACTTTTCAACTACTTTACTACAATACTAAGAATGAAAACCATTCTCCTCATTATCTTTGCTCTCGCTCTTTTCACAAGAGCTCAAGTCCCTGGCTACCAAGCCATCGATATCGCTGAAGCCCAATC
>Clone_44-1
GTTACGGGGGAATCCGAATTCACAGATTCAATTACACCCTAAAATCTATCTTCTCTACTTTCCCTCTCTCCATTCTCTCTCACACACTGTCACACACATCC
>Clone_44-3
GTTACGGGGGAATCCGAATTCACAGATTCAATTACACCCTAAAATCTATCTTCTCTACTTTCCCTCTCTCCATTCTCTCTCACACACTGTCACACACATCCCGGCAGCGCAGCCGTCGTCTCTACCCTTCACCAGGAATAAGTTTATTTTTCTACTTAC

name.txt

Clone_23
Clone_27-1

I want to use AWK to search through the fasta file, and obtain all the fasta sequences for given candidates whose names were saved in another file.

awk 'NR==FNR{a[$1]=$1} BEGIN{RS="\n>"; FS="\n"} NR>FNR {if (match($1,">")) {sub(">","",$1)} for (p in a) {if ($1==p) print ">"$0}}' name.txt seq.fasta

The problem is that I can only extract the sequence of first candidate in name.txt, like this

>Clone_23
GTTACGGGGGGCCGAAAAACACCCAATCTCTCTCTCGCTGAAACCCTACCTGTAATTTGCCTCCGATAGCCTTCCCCGGTGA

Can anyone help to fix one-line awk command above?

Upvotes: 0

Views: 1668

Answers (2)

hek2mgl
hek2mgl

Reputation: 157992

If it is ok or even desired to print the name as well, you can simply use grep:

grep -Ff name.txt -A1 a.fasta
  • -f name.txt picks patterns from name.txt
  • -F treats them as literal strings rather than regular expressions
  • A1 prints the matching line plus the subsequent line

If the names are not desired in output I would simply pipe to another grep:

above_command | grep -v '>'

An awk solution can look like this:

awk 'NR==FNR{n[$0];next} substr($0,2) in n && getline' name.txt a.fasta

Better explained in a multiline version:

# True as long as we are reading the first file, name.txt
NR==FNR {
    # Store the names in the array 'n'
    n[$0]
    next
}

# I use substr() to remove the leading `>` and check if the remaining
# string which is the name is a key of `n`. getline retrieves the next line
# If it succeeds the condition becomes true and awk will print that line
substr($0,2) in n && getline

Upvotes: 2

Ed Morton
Ed Morton

Reputation: 203522

$ awk 'NR==FNR{n[">"$0];next} f{print f ORS $0;f=""} $0 in n{f=$0}' name.txt seq.fasta
>Clone_23
GTTACGGGGGGCCGAAAAACACCCAATCTCTCTCTCGCTGAAACCCTACCTGTAATTTGCCTCCGATAGCCTTCCCCGGTGA
>Clone_27-1
GTTACGGGGACCACACCCTCACACATACAAACACAAACACTTCAAGTGACTTAGTGTGTTTCAGCAAAACATGGCTTC

Upvotes: 2

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