Finding specific text from a file that is within specific symbols

netpumber · 06-19-2014, 08:20 AM

Hello. I have a big file that contains DNA sequences like this :

Quote:

>gnl|SRA|SRR035295.82647.2 FIHSSUW02I7CY6.2 length=269
TAGAGACCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTCCGTCCAACATGGAATGATTGG
TACGCATCTGCAAATTCTTTGGATGTCACAAATCTGTATGGTGCGTCTCTTCTCATCCAGTATTGCTCCT
GATCTTTTTTTGAAGTCACTTCTTGTAAGAAATCAGCAACGCCTTTCCTTGCAGGGCATTTAAATCCCAT
TGACTCAAAAAACTCAAGGACGTGTTCACGTGGGCCTTGATATACAATTTTGCCATCAG
>gnl|SRA|SRR035295.4505.2 FIHSSUW02H007H.2 length=250
AAGCAGTGGTATCAACGAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTGA
TGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGTT
ACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGACT
GTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGGCG
>gnl|SRA|SRR035296.68126.2 FIQ4L3X01D8M3K.2 length=259
AAACATAATTATACCCTTGCTGAACTCGGCACCAATACTTTGCTTGATCTTTTCTTGAGACAACCTCTTG
GAGGAAATCGGCAACGCCTTTTCTTTCAGGGCACCTAAAACCAAAACCCTCAAAATACTCTAATACATCA
CTTCTCGGCCCATGATAAATAATGACTCCTTCTGCCATCAACATAATGTCATCAAAGAGATCAAATACTT
CTGGTGCTGGTTGAAGAAGTGAAATGACCACAGAAGCGTCTGTTATATG
>gnl|SRA|SRR035294.13646.2 FIHSSUW01ERMVS.2 length=248
AGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTGA
TGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGTT
ACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGACT
GTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG
>gnl|SRA|SRR035296.38443.2 FIQ4L3X01BO4OB.2 length=249
AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTG
ATGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGT
TACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGAC
TGTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG
>gnl|SRA|SRR035296.36031.2 FIQ4L3X01DKY6J.2 length=249
AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTG
ATGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGT
TACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGAC
TGTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG
>gnl|SRA|SRR035295.53565.2 FIHSSUW02J2P5E.2 length=249
AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTG
ATGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGT
TACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGAC
TGTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG
>gnl|SRA|SRR035294.113925.2 FIHSSUW01BDZ3B.2 length=249
AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTG
ATGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGT
TACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGAC
TGTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG
>gnl|SRA|SRR035294.94312.2 FIHSSUW01EADXQ.2 length=249
AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTG
ATGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGT
TACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGAC
TGTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG
>gnl|SRA|SRR035294.74028.2 FIHSSUW01E2UJV.2 length=249
AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTG
ATGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGT
TACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGAC
TGTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG

and i want to print out e.g the sequence with id = SRR035294.94312.2

As you can see every sequence has an id and each of them start with a > symbol.
So is there anyway to make a cat in the file and print out the text that contains the id and it is between within two > symbols ?

So to get back

Quote:

>gnl|SRA|SRR035294.94312.2 FIHSSUW01EADXQ.2 length=249
AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGGTCCTCCAAGTTCGGGAAAGACAACACTTTTG
ATGGCCTTGGCTGGCACACTTGCAAAAGAGCTTAAGAGTTCGGGTAAAGTAACATATAATGGGCATGAGT
TACATGAGTTTGTACCTGAAAGAACTGCTGCTTATATCAGCCAGAATGATCTCCATATTGGAGAAATGAC
TGTAAGAGAAACATTGGCTTTCTCTGCAAGATGTCAAGG

Thank you.

bigrigdriver · 06-19-2014, 10:11 AM

You should be able to do that with awk. Something along the lines of:

Code:

awk 'BEGIN { RS = ">" } ; $1 ~ /SRR035294.94312.2/ { print $0 }' <your dna file name>

where RS is the record seperator and /SRR035294.94312.2/ is the string to match, and print $0 prints the record which contains the matching string.

Caution: it's been a few years since I did anything with awk. The code above probably needs some correction to make it work.

netpumber · 06-19-2014, 01:05 PM

Ok. Thank you very much. I 'll try it out.

norobro · 06-19-2014, 01:36 PM

If your data is always five lines grep will do what you want:

Code:

grep "SRR035294.94312.2" file.name -A 4

netpumber · 06-19-2014, 02:13 PM

Thank you but there wont be always 5 lines.

As you can see below, i am trying to create a script that will give it the string and the file to search. Also you could execute this from every path where you have your files but it seems that there is a problem with the paths of the files

Code:

#!/bin/bash
STRING=$1
FILE=$(pwd)"/"$2

if [ -z "$FILE" ] && [ -z "$STRING" ]
then
    echo "Usage: fastaFind.sh <query> <fasta file>"
else
    OUTPUT=awk 'BEGIN { RS = ">" } ; $0 ~ /$STRING/ { print $0 }' "$FILE"
fi

echo $OUTPUT

Quote:

% fastaFind.sh SRR035295.53565.2 sra_data-DB.fasta
/home/../../Bioinformatics/fastaFind/fastaFind.sh: line 9: BEGIN { RS = ">" } ; $0 ~ /$STRING/ { print $0 }: No such file or directory

szboardstretcher · 06-19-2014, 02:23 PM

You have to use a command substitution for OUTPUT like this:

Code:

OUTPUT=$(awk 'BEGIN { RS = ">" } ; $0 ~ /$STRING/ { print $0 }' "$FILE")

Not sure that awk will work though...

netpumber · 06-19-2014, 02:41 PM

Hmm doesn't work with awk .

szboardstretcher · 06-19-2014, 03:04 PM

You can look into shell variables in awk to fix that up. I'm not that savvy with awk unfortunately.

netpumber · 06-19-2014, 03:23 PM

It seems that works now with this edit :

Code:

#!/bin/bash
STRING=$1
FILE=$(pwd)"/"$2

if [ -z "$FILE" ] 
then 
    echo "Usage: fastaFind.sh <query> <fasta file>"
else
   awk  'BEGIN { RS = ">" } ; $0 ~ "'$STRING'" { print $0 }' "$FILE"
fi

netpumber · 06-19-2014, 03:23 PM

It seems that works now with this edit :

Code:

#!/bin/bash
STRING=$1
FILE=$(pwd)"/"$2

if [ -z "$FILE" ] 
then 
    echo "Usage: fastaFind.sh <query> <fasta file>"
else
   awk  'BEGIN { RS = ">" } ; $0 ~ "'$STRING'" { print $0 }' "$FILE"
fi