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Full Discussion: Matching string and assembling
Top Forums UNIX for Dummies Questions & Answers Matching string and assembling Post 302969911 by RudiC on Wednesday 30th of March 2016 01:57:44 AM
Old 03-30-2016
T'was too late last night - sorry. Try
Code:
awk '
BEGIN           {for (i = split ("A C G T", Y); i>0; i--) R[Y[i]] = Y[5-i]
                }

function MM(CR) {for (i=0; i<length (CR); i++)  {X = substr (CR, 1, i) "." substr (CR, i+2)
                                                 for (j=i; j<length (CR); j++)  {T = substr (X,  1, j) "." substr (X,  j+2)
                                                                                 if (match (REF, T))  return 1
                                                                                }
                                                }
                 return 0
                }
/^>/            {SN = $0
                 next
                }
                {RV = ""
                 for (i = split ($0, A, ""); i>0; i--) RV = RV R[A[i]]
                 }
match (REF, $0) ||
MM($0)          {print SN ORS $0
                }
match (REF, RV) ||
MM(RV)          {print SN ORS RV
                }
' REF="AGAGAGACCTGGAGAGAGAGTGACGATGAGCAGTGACGATGACGTACGATAGCAGTAGACGCA" file
>read1 ori 498
AGAGAGACCTGGAGAGAGAGT
>read2 ori-rep 500
AGAGAGACCTGGAGAGAGAGT
>read3 1-misma 456
GGAGAGACCTGGAGAGAGAGT
>read4 2-misma 456
TGAGAGACCTGGAGAGAGAGA
>read5 ori-rev 532
AGAGAGACCTGGAGAGAGAGT
>read6 ori-rev-1-misma 499
GGAGAGACCTGGAGAGAGAGT
>read7 medium 512
AGAGAGAGTGACGATGAGCAG
>read8 last 488
AGTGACGATGACGTACGATAGCAGTAGACGCA
>read9 last rep 488
AGTGACGATGACGTACGATAGCAGTAGACGCA
>read10 last gap 488
AGTGACGATGACGTACGATAGCAGTAGACGA

This User Gave Thanks to RudiC For This Post:
Xterra
 

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LEARN ABOUT MOJAVE

git-symbolic-ref

GIT-SYMBOLIC-REF(1)                                                 Git Manual                                                 GIT-SYMBOLIC-REF(1)

NAME

       git-symbolic-ref - Read, modify and delete symbolic refs

SYNOPSIS

       git symbolic-ref [-m <reason>] <name> <ref>
       git symbolic-ref [-q] [--short] <name>
       git symbolic-ref --delete [-q] <name>

DESCRIPTION

       Given one argument, reads which branch head the given symbolic ref refers to and outputs its path, relative to the .git/ directory.
       Typically you would give HEAD as the <name> argument to see which branch your working tree is on.

       Given two arguments, creates or updates a symbolic ref <name> to point at the given branch <ref>.

       Given --delete and an additional argument, deletes the given symbolic ref.

       A symbolic ref is a regular file that stores a string that begins with ref: refs/. For example, your .git/HEAD is a regular file whose
       contents is ref: refs/heads/master.

OPTIONS

       -d, --delete
           Delete the symbolic ref <name>.

       -q, --quiet
           Do not issue an error message if the <name> is not a symbolic ref but a detached HEAD; instead exit with non-zero status silently.

       --short
           When showing the value of <name> as a symbolic ref, try to shorten the value, e.g. from refs/heads/master to master.

       -m
           Update the reflog for <name> with <reason>. This is valid only when creating or updating a symbolic ref.

NOTES

       In the past, .git/HEAD was a symbolic link pointing at refs/heads/master. When we wanted to switch to another branch, we did ln -sf
       refs/heads/newbranch .git/HEAD, and when we wanted to find out which branch we are on, we did readlink .git/HEAD. But symbolic links are
       not entirely portable, so they are now deprecated and symbolic refs (as described above) are used by default.

       git symbolic-ref will exit with status 0 if the contents of the symbolic ref were printed correctly, with status 1 if the requested name is
       not a symbolic ref, or 128 if another error occurs.

GIT

       Part of the git(1) suite

Git 2.17.1                                                          10/05/2018                                                 GIT-SYMBOLIC-REF(1)
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