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Full Discussion: Match patterns between two files and extract certain range of strings
Top Forums UNIX for Beginners Questions & Answers Match patterns between two files and extract certain range of strings Post 303041961 by bunny_merah19 on Monday 9th of December 2019 09:44:58 AM
Old 12-09-2019
Match patterns between two files and extract certain range of strings
Hi,

I need help to match patterns from between two different files and extract region of strings.

inputfile1.fa
Code:
>l-WR24-1:1
GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGG
GGCGGAGGGCGACGGCGGGTGGTGAGCGGCCCGGGAGGGGCCGGGCGGTGGGGTCACGTG
CGGCGGGCGGGGCGCGGGCTGACCCAGCTGTGCCCGCAGGCGCCCGGGCGGGCCGGGGGC
CGTGGCGGAGGAGGAGCGCTGCACGGTGGAGCGTCGGGCCGACCTCACCTACGCGGAGTT
CTACCACAAAGTGGACTTGCCCTTCCAGGAGTATGTGGAGCAGCTGCTGCACCCCCAGGA
CCCCACCTCCCTGGGCAATGACACCCTGTACTTCTTCGGGGACAACAACTTCACCGAGTG
GGCCTCTCTCTTTCGGCACTACTCCCCACCCCCATTTGGCCTGCTGGGAACCGCTCCAG
>l-ZF385A-2:1
CAGAATGTGGGTGAGGGTGGCGCCTATGAGGCTGAGCTTCGGGTCACCGCCCCTCCAGAG
GCTGAGTACTCAGGACTCGTCAGACACCCAGGGGTGAGATGAGACTCTCGAGTGGGATTT
GGGAGGATACCCCTCTAGAGGGGACACCAAAACCTGACCAGTGCCCACCCCATCTCCAGA
ACTTCTCCAGCCTGAGCTGTGACTACTTTGCCGTGAACCAGAGCCGCCTGCTGGTGTGTG
ACCTGGGCAACCCCATGAAGGCAGGAGCCAGTCTGTGGGGTGGCCTTCGGTTTACAGTCC
CTCATCTCCGGGACACTAAGAAAACCATCCAGTTTGACTTCCAGATCCTCAGGTAGGGAG
TGAGTGTGTCTAGGCTGGGGCTGAGCTGGGGACGGAAGGGAGGGCTGGGCGCCATTCTCA
CTGGCTGCACTCCAGCACCTCAGTCTTGCCTCCATCCCACAGCAAGAATCTCAACAACTC
GCAAAGCGACGTGGTTTCCTTTCGGCTCTCCGTGGAGGCTCAGGCCCAGGTCACCCTGAA
CGGGTCAGTGCCAGGCAAAATGGGGTCT
>l-YJC-1:1
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACG
CGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGT
CAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCAGGCACAGCATCCCCACGGG
CCTCCACGCCAACCTGTCCGAGGGCCGCCCCGTGGGTCCGGCCCGCCGTGGCGCCTCATC
GCTGCTCGGCCCGG

inputfile2.txt
Code:
l-WR24-1:1	1	71
l-WR73-7:4	28	506
l-WR86-1:1	140	138
l-YJC-1:1	1	161
l-YJC-1:1	1	165
l-ZFP57-11:1	1	991
l-ZF320-1:5	5	6031
l-ZMYND10-2:1	5	253
l-ZF329-4:1	151	5704
l-ZF708-1:1	195	3744
l-ZF843-3:1	14	1053
l-ZF385A-2:1	33	105
l-ZF843-3:2	4	235

The output file as below. It should contain the strings extracted from inputfile1.fa according to start and stop numbers (in blue) indicated in inputfile2.txt as shown above.


Code:
>l-WR24-1:1	1	71
GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGG
GGCGGAGGGCG
>l-ZF385A-2:1	33	105
TGAGCTTCGGGTCACCGCCCCTCCAGAGGCTGAGTACTCAGGACTCGTCAGACACCCAGG
GGTGAGATGAGAC
>l-YJC-1:1	1	161
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACG
CGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGT
CAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCA
>l-YJC-1:1	1	165
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACG
CGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGT
CAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCAGGCA

I have tried to match these two files using bioinformatics tools like seqtk and bedtools but they did not give me what I want and some of their data requirements just don't fit mine. I am still learning awk and I want to do this in awk. Below are one of the codes that I did to match the two files but failed and I do not know how to extract certain regions of characters.

Code:
awk 'FNR == NR{A[$1]; next}/^\>/{f = (substr($1,2) in A) ? 1 : 0}f' inputfile2.txt inputfile1.fa

Would appreciate your kind help. thanks
Last edited by bunny_merah19; 12-09-2019 at 10:57 AM..
 

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