Retrieving sequences corresponding to start and end position


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Retrieving sequences corresponding to start and end position
# 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?
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Splitting week start date and end date based on custom period start dates

Below are my custom period start and end dates based on a calender, these dates are placed in a file, for each period i need to split into three weeks for each period row, example is given below. Could you please help out to achieve solution through shell script.. File content: ... (2 Replies)
Discussion started by: nani2019
2 Replies

2. Shell Programming and Scripting

Remove lines between the start string and end string including start and end string Python

Hi, I am trying to remove lines once a string is found till another string is found including the start string and end string. I want to basically grab all the lines starting with color (closing bracket). PS: The line after the closing bracket for color could be anything (currently 'more').... (1 Reply)
Discussion started by: Dabheeruz
1 Replies

3. UNIX for Dummies Questions & Answers

extract regions of file based on start and end position

Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2. Based on a post elsewhere, I found the code: awk... (2 Replies)
Discussion started by: pathunkathunk
2 Replies

4. Shell Programming and Scripting

Calculating start and end of UK summertime

I have a need to calculate when British Summer Time starts and ends. After messing around, the following seems to work in Bash. echo `date +%Y`-03-`cal 3 \`date +%Y\` | grep -oE "^]{2}" | tail -1`T01:00:00Zand echo `date +%Y`-03-`cal 10 \`date +%Y\` | grep -oE "^]{2}" | tail ... (10 Replies)
Discussion started by: esb4me
10 Replies

5. Shell Programming and Scripting

Remove the spaces at the end of a line starting from a fixed position

I want to remove the trailing spaces at the end of each line starting from a particular position(using ksh script). For example, in the attached file, I want to remove all the spaces starting from the position 430 till the end. The space has to be removed only from the 430th position no matter in... (3 Replies)
Discussion started by: Suryaaravindh
3 Replies

6. Shell Programming and Scripting

Subsitute from a position till end of line.

Hi, Having a following file's content, lets say: ABC|ANA|LDJ|||||DKD|||||| AJJ|KKDD||KKDK|||||||||||| KKD||KD|||LLLD||||LLD||||| Problem: Need to replace pipes from 8th occurrence of pipe till end. so the result should be: ABC|ANA|LDJ|||||DKD AJJ|KKDD||KKDK|||| ------- ------- ... (12 Replies)
Discussion started by: _Noprofi
12 Replies

7. UNIX for Dummies Questions & Answers

find if a position is between a given start and end position

Hi, I am a newbie in unix programming so maybe this is a simple question. I would like to know how can I make a script that outputs only the values that are not between any given start and end positions Example file1: 2 30 40 80 82 100 file2: ID1 1 ID2 35 ID3 80 ID4 81 ID6... (9 Replies)
Discussion started by: fadista
9 Replies

8. Shell Programming and Scripting

Add 'ENDEND' on end of each record at position is 14-20

I have file format like below and I'm trying to modify this file. I need to add 'ENDEND' end of each record. 01 ASH01 1CTCTL EDPPOO STAND 01 ASH08 0020 A1TH 101 01 ASH09 0022 A1TH 102 01 ASH09 0022 A1TH 103 01 ASH02 2CTCTL ... (5 Replies)
Discussion started by: naveenkcl
5 Replies

9. Shell Programming and Scripting

check position of end of line(URGENT PLS)

I Have to check in a file that all the lines are ending at same posiotin. Ex : line 1 is ending at position 88 line 2 should at same position i.e 88 Thanks in advance (6 Replies)
Discussion started by: evvander
6 Replies

10. Shell Programming and Scripting

check position of end of line for some specific lines

-------------------------------------------------------------------------------- Have to check in a file that the lines starting with 620 and 705 are ending at same posiotin. 82012345 62023232323 70523949558 62023255454 9999 In the above lines, i have to check the lines starting... (1 Reply)
Discussion started by: senthil_is
1 Replies
Login or Register to Ask a Question