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Full Discussion: extract regions of file based on start and end position
Top Forums UNIX for Dummies Questions & Answers extract regions of file based on start and end position Post 302694999 by pathunkathunk on Saturday 1st of September 2012 12:45:47 AM
Old 09-01-2012
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:
Code:
awk 'NR==FNR{if($0~/^>/){i=substr($0,2);getline};a[i]=a[i] $0;next}{print ">" $1 ORS substr(a[$1], $2, $3-$2+1)}' file1 FS=\\t file2

But with the files I have, regions are extracted from only a subset of the specified sequences.

file1 (my real file is much longer, >47000 lines, and each sequence is much longer too):
Code:
>GL349621.1TTTACAATTGCTATTGTAACAATATATCAGGAGCCTTGTATTAAATTTTCACGCATTTTTACCAAACAAA
>GL3422.1
TTACCGGCACTTCATTCACTTTTAAATACCCGTGTTTCGATTTTGTTGTTTTAGCCCCGCGTAAAGCAAA
>GL3423.1
104-151:aphid_project aman$ head -10 Ap_assembly2_scaffolds_corrected.fasta 
>GL3421.1
TTTACAATTGCTATTGTAACAATATATCAGGAGCCTTGTATTAAATTTTCACGCATTTTTACCAAACAAA
>GL3422.1
TTACCGGCACTTCATTCACTTTTAAATACCCGTGTTTCGATTTTGTTGTTTTAGCCCCGCGTAAAGCAAA[/QUOTE]file2: 



Quote:



    
    
GL3550.1    61498    52100
GL3465.1    293074    297989
GL3567.1    234944    236074
GL3482.1    323100    323743
GL3550.1    41911    40888
GL3472.1    274408    272617
GL3550.1    75587    73909
GL3465.1    869051    867919
GL3472.1    294812    289561
GL3567.1    238848    236284

    




Result after using awk command above:
[QUOTE]>GL350250.1

>GL3465.1
ATGGTCTCAAAGCCGTTTGTTTTCGTGTTTGTGCTCATGTCCGTGGTCGGTGTGTCGTTCTCCGTGACCGAAGAAAACGATGGTACAAAGGTCGTGGACAAGGAAGAGGACCATCATCAGAACATCCAAGAGGAACTCAAGAAATTTTTGTCGACGTTAGAGAAAATCGACATAGACCAGATATTGAACAACCACAGGTTGATGTCGAACAACGTCAAATGTTTTCTGAACGAAGGACCGTGTACGGCACAACTGAGGGAAATGAAAAGTAAGAGTGTGTGCGACACGTAATATTACTGATTGTACGATGACTTCGCTAAATACTATTTGGTTGAAATATATTATTATGCCTAAATTACTGTAAATCATGTATTTAATAATTTACTAGTACCTATAATATATTATTTTGATAAATTTATATTTCATGTTTAGTAGTTATTTAGTACAACGTACGAGTATTAATAATTTGAATAAATTATGTAAAGCCATTTTGTAAGCATAGCCAATACATATTTCAATATATTGACATTTTCGTCATCAATCATTATAGTTTGCTGTAAAAATAATATTATTTAAATTCGACAATTTGTATTGACAAGATAATCAAAACACCAAATATTTTAGTAAAATTTAATAAATCAAGTTATTATAATATGCCAATTTAGTAACATTTTAAAAAGAATAATACCAAAAGGTCATCGCGTACTCCTCGAATCAGCCACTACTTAGTACTTTCTACGTAGTACTTACAAGCAAAAACACTTATAAAGTTATAAATTATATATCTATTTAAAGAAAAGCCAATTCCAAATTGTTTGTTTTTTAAACCCAGCAACATCATAATAAAAACCTACATTTTAAATATAGTTGAGAACAGAGTAGTTCTGACTAAGGAGAAAAAATATAATAATAACAACCAAAAGGTTCTATTTGAAGAACAAAGACGATCTTGGTTCTAAACGGAATTTTTTCGAAACTATTATTTTCTTTTTATTTTAAGTTAATATTTTCTAAGAACAAAACACAAATGTCAAAGTTTAATGCAAAACAACACTTTGATAATTTTTAGATTCAACAAACCGTTCTATATGAAAGAAGATATTACAGTATGAAGTTTAAAATGTTT
>GL3567.1
ATGGCTCATCTTAACTTATTTGTTGTTCTGGTCGCGTCGCTTGTGTGCTTCACGTTGGCCGAAGAAAAATACACAACTAAATTCGACAACTTCGACGTGGACAAGGTGTTGAACAACGACAGAATTTTAACCAGTTACATCAAGTGTTTGCTGGACCAGGGAAATTGCACCAATGAAGGCCGAGAATTGAAGAGTAAGTCATATAAGAACAAACGTATATTATATTTTAGTATTTCAATTTTCAAGTATGTTATACAATTAAAATTATAATGACATTGATTTAACTATCGGTACATTTTTAAAAATTGTAATATCTATATACTTCTGGGGTATACTATAATCTATACTCTATAACAACTTCTATATATATATATATAATATATATTATATAAGTATCAAAAAATTACCAATATAAAAAAAAAAACCATAACATATATATTTAATATTGTACCTACTTTATAAAATGCTTTAAGTTCGTCAGCATAATATAATTTTATTTATCTGACAATCGTACTAAATTATCATCTTGAGTACATATCGATATAACAATAATACATACCGTATTATAATGTTATACTTAACCAAGTTACCGTAAACGATAAATAAGAACAACACTAACAATTATAATTTTATTTGTATTCTTAAGATTACGGTTTTCACTTTCACATTAAACATAATATTATATCGACAAGACCTTGCTTACTCAGTCAGACTCACTTTCACCGGGTGTTGTAATTATTTTTCATCTGAGCCGAATTACCGTGTATAGTATTTAGAAAGAAACAAAGTCGATACGTAAAATGTGTGGTTAATCCTTAAATTTTTCCTTGCTATATTAAAATGTTTATTAATAATTGTTTTTAAACTTCTTTTTCACAATAATGTACATGTGTTATAATTATATTTTCTTGTCTGATTAAATTTGCAGAAGTTTTACCAGACGCATTGAAAACTGACTGCAGCAAATGTACAGCTGTACAAAAAGACAGATCAGAAAAAGTAATCAAGTTTTTGATCAAAAACCGTTCTAAAGACTTTGATAATTTGACCGCCAAATACGACCCATCAGGCGAATACAAAAAGAAGATCGAAAAATTCGACGCGGAAAGGGCTGCGGCTGCTAAACATTAA
>GL3482.1
ATGGTGCATCTTAACTTATTTGTTGTTGTGGTCGCGTCACTGGTGTGCTTCACATTGGCTCAAGAAAAGTACTCAACTAAATACGAAAACTTTGACGAGGACAAGGTGTTAAACAACGACAGCCTTTTAACCAGCTACATCAATTGTTTGCTCGACGAGGGAAATTGTACCGAGGAAGGCCAAGCGTTGAAAAGTAAATCACAATAACAAATGTATTATATTTTAGTATTTTAACTTTCAAGTATATTATACAATTAAAATCATAATGACATTGATTTAACTATCGGTACATTTTTAAAAAAATGGATATCTAATATCTATACTATACTTTTGGGGTATACTAGCTATAGTCTAAACTCTAAAACAACTACTAGGTACATTATATGTATCAAATAAATATCAACAAACTTCCATTTGGCATAGGTGTAATAATTATATTAATTTCATATCTAATTAAATGTACAGGAATTTTACCAGACGCATTAAAAACTAACTGTGGAAAATGTACGGATGCACAAAAATTGAAAATAGAAAAAATAATGAAATTTTTGATCAAGAACCGTTCTATTGACTTTGATCGTTTGACCGCCAAATACGACCCATCGGGAGAATACAAGAAAAAGCTCGAAAAATTCTCCGCTTAA
>GL3550.1

>GL3472.1

>GL3550.1

>GL3465.1

>GL3472.1

>GL3567.1

So the specified region is only extracted for 3 out of 10 queries. I have checked and all headers that appear in file2 are also represented in file1. The sequences are long enough to contain all of the beginning and end points. Any ideas on what's going wrong?
 

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