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Retrieving sequences corresponding to start and end position

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# 1  
Old 09-21-2018
Retrieving sequences corresponding to start and end position
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

Code:
>my_ref_seq
GCCCTATAAGGGCAGAAGCTTGTCCTTCTTGTGCCAGTTATGACGTTTGTCCTAACTGCACATCTGGTAG
CATCCCCGATGATGGGTCTTCCAAAGGACAGATCCCCTCCTGGGAAGATGTTACAAAAACTTCTACCTAC
TCTCTCTTGTTGTCTGAGGACACATCCGACGAACTGCACCCTGACGACCTGGTTAACGTTGCTGCTCATA
TCCGAAAGGCCTTGTCCACTCAGTCTCACCCGGCAAATGTTGATATGTGCAAAGAACAGCTCACATCTCT
GTTGGTTATGGCTGAAGCAATGCTACCCCAACGCTCTAGGTCGACACTCCCACTACACCAAAAATATGTG

position.txt
Code:
my_ref_seq    1550   1590    
my_ref_seq    2399   2429    
my_ref_seq    3008   3038

expected result
Code:
seq_id            Start   End     sequence
my_ref_seq    1550   1590    TCCGAAAGGCCTTGTCCACTCAGTCTCACC
my_ref_seq    2399   2429    TCTCTCTTGTTGTCTGAGGACACATCCGAC
my_ref_seq    3008   3038    GAACTGTCCGAAAGGCCTTGTCCACTCAAA

Thank you for the help.
Last edited by Scrutinizer; 09-21-2018 at 05:09 PM.. Reason: code tags
# 2  
Old 09-21-2018
Unfortunately, this can't be tested with the data given. Howsoever, try
Code:
awk '
NR == 1         {print "seq_id            Start   End     sequence"
                 next}
NR == FNR       {SEQ = SEQ $0
                 next
                }
                {print $0, substr (SEQ, $2, $3-$2+1)
                }
' fastafile position.txt

# 3  
Old 09-22-2018
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 updated 09-22-18 at 04:21 AM ------

Thank you Rudic

Fixed it
# 4  
Old 09-24-2018
Hi,

After trying to retrieve the sequence using

Code:
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, substr (SEQ, $2, $3-$2+1)}' my_seq.fasta file_2.txt > output.txt

I have a sequence NC_004064.1 (from NCBI) in a file and another file with Query ID, start position and end position

Code:
>my_querry_seq.fasta 
GTGATTTAATTATAGAGAGATAGTGACTTTCACTTTTCTTTCTTTGCATTTCGCTGGACTCAAACTGTTC
CATAATGGCTCCAGTTGTTTCCAGAGATCAATGTAAACCTAAAACACCAAAGCCCCACCGACCAGCCCCT
CCCCACAGGTGCACTACCAGGTGCCCTGAGGATTGTGGGTGGTACGTGGGTCGCTGCTCCTGCCCCAACG
TCTGCCAACGCGAGGGTTGGGACGACTTCTTCGTAGCTGACAAGGTGAAGCCTCCTAGCTACGTCGCCTC
AAAGACCTCGGTCGCAGATGTTGTCGACTGGCTACTTGAAGAAGACCCTGCTACGGACGGCCCCTCGGAA
TTTGACCTCACGCAATTTTTCCAGGCTTACACGGACAAGTCCCACCAGATCCACCGTGACTATGCCCCGG
ACCAGCTTGCTCAGGCCCTTGACATGGCTTACATACTATCGGTGGACCCCCCGGACATCAAGCTCCCAGA
GTATGAGGCAACTAGGTTCACCCATGACACCTCCTACAAGGGCAAACTGCCTAAGTGGCTGCGTGTGTAT
GGCATCAAGTCCCGAGAGCTAGCGAAGAAGGCTGTAACCAACATTCGGGGTGGAGCCCATTGGGCCAAGG
GGCTGTTCAAGCAAATGTGGGACTCGTTGCCTGGTTGGAGTGAGGTGGAGGCGTACTTCAAAGCTTTCTT
CGCTGGCATCATCACCGGTGTTGAGGACGCGCTGTCGAAGTCTCCGTCATCGGTGTGGACCTCACTCAAG
CTCACGCCGTTGCTATACATATGGCGCAACATCAACGAGTGCTCTGATATTGCTGTGATACTAGGAGCCT
TCTGGGCGACACTGGAACTTTACAACATCCCATCCAAAGTGTACGACCTGGTGTCAACTGCACTTGGCCC


file_2.txt

Code:
ID start end
my_seq 10 40
my_seq 35 65
my_seq 50 20
my_seq 76 96


I want to use the second file to retrieve the sequence from the start to end position printed in front of each

Note that in line 3 the start (50) position is greater than the end (20) but want this to print from 50 to 20

I want the sequence printed in front in this format

Expected Output
ID Start End Sequence


I will really appreciate your help.

Thanks
Last edited by vgersh99; 09-24-2018 at 06:51 PM.. Reason: please start using code tags!
# 5  
Old 09-25-2018
I can't immediately see an error, so - where are you stuck, what doesn't work? Error messages?
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