Match patterns between two files and extract certain range of strings Post: 303041969

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Top Forums UNIX for Beginners Questions & Answers Match patterns between two files and extract certain range of strings Post 303041969 by bunny_merah19 on Monday 9th of December 2019 10:43:59 PM

12-09-2019

Registered User

Quote:

Originally Posted by vgersh99

a bit verbose, but a possible starter.
awk -f bunny.awk inputfile2.txt inputfile1.fa where bunny.awk is:

Code:

function printRec() {
   #print a[f], s[f], e[f]
   for ( i in s) {
      split(i,t, OFS)
      if (f == ">" t[1])
        print ">" i ORS substr(a[f],s[i],e[i]-s[i]+1)
   }
   f=""
   split("",a)
}
FNR==NR {
   idx=$1 OFS $2 OFS $3
   s[idx]=$2
   e[idx]=$3
   next
}
/>/ && f {
   printRec()
}
f { a[f]=(f in a)?a[f] $1:$1 }
/^>/ { f=$1 }
END { printRec() }

results in:

Code:

>l-WR24-1:1 1 71
GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGGGGCGGAGGGCG
>l-ZF385A-2:1 33 105
TGAGCTTCGGGTCACCGCCCCTCCAGAGGCTGAGTACTCAGGACTCGTCAGACACCCAGGGGTGAGATGAGAC
>l-YJC-1:1 1 161
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCA
>l-YJC-1:1 1 165
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCAGGCA

Hi vgersh99,

Your codes work like charm. Thanks a million. Smilie

--- Post updated at 03:59 AM ---

Quote:

Originally Posted by RudiC

Try also

Code:

awk '
NR==FNR         {PAT[$1,$2,$3]
                 next
                }
                {IX  = $1
                 L1  = length ($1) + 1
                 $1 = $1 "|"
                 $0 = $0
                 for (p in PAT) {split (p, T)
                                 if (IX == T[1]) print RS p ORS substr ($0, T[2]+L1, T[3]-T[2]+1)
                                }
                }
' SUBSEP="\t" inputfile2.txt   RS=">"  OFS="" inputfile1.fa

>l-WR24-1:1    1    71
GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGGGGCGGAGGGCG
>l-ZF385A-2:1    33    105
TGAGCTTCGGGTCACCGCCCCTCCAGAGGCTGAGTACTCAGGACTCGTCAGACACCCAGGGGTGAGATGAGAC
>l-YJC-1:1    1    161
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCA
 >l-YJC-1:1    1    165
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCAGGCA

If you really really need the output lines 60 chars in length, use

Code:

                 if (IX == T[1])    {print RS p
                                     TMP = substr ($0, T[2]+L1, T[3]-T[2]+1)
                                     PTR = 1
                                     while (PTR < length (TMP))    {print substr (TMP, PTR, 60)
                                                                    PTR += 60
                                                                   }
                                    }

Hi RudiC,

Your codes work great on my real data too. Thanks a million Smilie

--- Post updated at 04:43 AM ---

Quote:

Originally Posted by vgersh99

if you need to "fold" the lines at 60 char width, pipe the output to fold:

Code:

awk .... | fold -w 60

Ok, got it... thanks Smilie

bunny_merah19

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