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Thanks Yoda. Woks perfectly

The code did no give any output

I tried this but does not give me the desired result awk '{if (NR==FNR) {l[NR]=$0;a[NR]=$2;b[NR]=$3} else if (a[FNR]>=$4 && b[FNR]<=$5) {print l[FNR],$0}}' file1 file2 . file3

Hi,

I have a tab delimited file1:
NC_013499.1 3180 3269 GQ342961.1
NC_030295.1 5925 6014 FN398100.2
NC_007915.1 6307 6396 KU529284.1
NC_013499.1...

Thank you Rudic, I have tried the code but did not give me the required output. The input files are separate files as well as the expected output.

These are examples of the input sequence. Just one long sequence per file. thanks
>File_1.fa
TTGAAAGGGGGCCCGGGGGATCTCCCCCGCGGTAACTGGTCACAGTTGCCGCGGACGGAGATCATCCCCC...

I want to add the sequence length of File_1.fa and File _2.fa to form the form the fifth column in File_1_pos.txt and File_2_poa.txt respectively using awk and bash. Can anyone help me? Thanks
...

Thanks,

The pattern is also in other positions, I need to get all the positions the pattern matches to.

>my_file
GTGTGTCATTTTAGCCCGTTGGGTTTCATTAAGGTGTGTCACCAGGTGGGTGGTACCTGGAGGTTATTCT
ATTGGGATAACGAGAGGAGGAGGGGCTAGAGGTCCGCGAGATTTGGGGTAGGCGGAGCCTCAGGAGGGTC...

Hi,

Am trying to print all sequence that matches this pattern CGTTGggtTTCATT and their positions in my file but "ggt" can be any nucleotide. The sequence in big letters must match.

I used awk...

Hi,

After trying to retrieve the sequence using

awk 'NR == 1 {print "seq_id Start End Nul_Seq"} NR == FNR {SEQ = SEQ $0;next}{if ($2>$3) print $0, substr (SEQ, $3, $2-$3+1); else print $0,...

Thank you Rudic,

The code is almost perfect but returns the input fasta file as header before the expected output.
I don't want the input fasta file added to the output.

Thanks

------ Post...

Hi all,

I have a fasta file of a reference sequnce, I will like to retrieve sequences corresponding to a list of start and end position in another file

>my_ref_seq...

Thanks vgersh99. Code worked perfectly

Hi,

I have a fasta file with multiple sequences. How can i get only unique sequences from the file.

For example
my_file.fasta

>seq1...