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Top Forums Shell Programming and Scripting Retrieving sequences corresponding to start and end position Post 303023854 by Ibk on Monday 24th of September 2018 05:23:14 PM
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!
 

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SEQ(1)							    BSD General Commands Manual 						    SEQ(1)

NAME
seq -- print sequences of numbers SYNOPSIS
seq [-w] [-f format] [-s string] [-t string] [first [incr]] last DESCRIPTION
The seq utility prints a sequence of numbers, one per line (default), from first (default 1), to near last as possible, in increments of incr (default 1). When first is larger than last the default incr is -1. All numbers are interpreted as floating point. Normally integer values are printed as decimal integers. The seq utility accepts the following options: -f format Use a printf(3) style format to print each number. Only the E, e, f, G, g, and % conversion characters are valid, along with any optional flags and an optional numeric minimum field width or precision. The format can contain character escape sequences in backslash notation as defined in ANSI X3.159-1989 (``ANSI C89''). The default is %g. -s string Use string to separate numbers. The string can contain character escape sequences in backslash notation as defined in ANSI X3.159-1989 (``ANSI C89''). The default is . -t string Use string to terminate sequence of numbers. The string can contain character escape sequences in backslash notation as defined in ANSI X3.159-1989 (``ANSI C89''). This option is useful when the default separator does not contain a . -w Equalize the widths of all numbers by padding with zeros as necessary. This option has no effect with the -f option. If any sequence numbers will be printed in exponential notation, the default conversion is changed to %e. The seq utility exits 0 on success and non-zero if an error occurs. EXAMPLES
# seq 1 3 1 2 3 # seq 3 1 3 2 1 # seq -w 0 .05 .1 0.00 0.05 0.10 SEE ALSO
jot(1), printf(1), printf(3) HISTORY
The seq command first appeared in Plan 9 from Bell Labs. A seq command appeared in NetBSD 3.0, and ported to FreeBSD 9.0. This command was based on the command of the same name in Plan 9 from Bell Labs and the GNU core utilities. The GNU seq command first appeared in the 1.13 shell utilities release. BUGS
The -w option does not handle the transition from pure floating point to exponent representation very well. The seq command is not bug for bug compatible with the Plan 9 from Bell Labs or GNU versions of seq. BSD
February 19, 2010 BSD
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