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Top Forums UNIX for Beginners Questions & Answers Match patterns between two files and extract certain range of strings Post 303041964 by vgersh99 on Monday 9th of December 2019 11:44:45 AM
Old 12-09-2019
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


Last edited by vgersh99; 12-09-2019 at 12:51 PM..
This User Gave Thanks to vgersh99 For This Post:
 

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strmerge(1)						      General Commands Manual						       strmerge(1)

NAME
strmerge - batch string replacement SYNOPSIS
strmerge [-m prefix] [-p patternfile] [-s string] source-program... OPTIONS
Add prefix to message numbers in the output source program and source message catalog. You can use this prefix as a mnemonic. You must process source message catalogs that contain number prefixes using the mkcatdefs command. Message numbers will be in the form: <prefix><msg_num> Set numbers will be in the form: S_<prefix><set_num> If you process your input source program with the mkcatdefs command, the resulting source program and source message catalog might not be portable. For more information, see the Writing Software for the International Market. Use patternfile to match strings in the input source program. By default, the command searches for the pattern file in the current directory, your home directory and finally /usr/lib/nls. If you omit the -p option, the strmerge command uses a default patterns file that is stored in /usr/lib/nls/patterns. Write string at the top of the source message catalog. If you omit the -s option, strmerge uses the string specified in the $CATHEAD section of the patterns file. DESCRIPTION
The strmerge command reads the strings specified in the message file produced by strextract and replaces those strings with calls to the message file in the source program to create a new source program. The new version of source program has the same name as the input source program, with the prefix nl_. For example, if the input source program is named prog.c, the output source program is named nl_prog.c. You use this command to replace hard-coded messages (text strings identified by the strextract command) with calls to the catgets function and to create a source message catalog file. The source message catalog contains the text for each message extracted from your input source program. The strmerge command names the file by appending to the name of the input source program. For example, the source message catalog for the prog.c program is named prog.msg. You can use the source message catalog as input to the gencat command. At run time, the program reads the message text from the message catalog. By storing messages in a message catalog, instead of your pro- gram, you allow the text of messages to be translated to a new language or modified without the source program being changed. In the source-program argument, you name one or more source programs for which you want strings replaced. The strmerge command does not replace messages for source programs included using the #include directive. Therefore, you might want a source program and all the source programs it includes on a single strmerge command line. You can create a patterns file (as specified by patternfile ) to control how the strmerge command replaces text. The patterns file is divided into several sections, each of which is identified by a keyword. The keyword must start at the beginning of a new line, and its first character must be a dollar sign ($). Following the identifier, you specify a number of patterns. Each pattern begins on a new line and follows the regular expression syntax you use in the ed editor. For more information on the patterns file, see the patterns(4) refer- ence page. RESTRICTIONS
You can specify only one rewrite string for all classes of pattern matches. The strmerge command does not verify if the message text file matches the source file being rewritten. The strmerge command does not replace strings to files included with #include directive. You must run the strmerge command on these files separately. EXAMPLES
The following produces a message file prog.cat for a program called prog.c. % strextract -p c_patterns prog.c prog2.c % vi prog.str % strmerge -p c_patterns prog.c prog2.c % gencat prog.cat prog.msg prog2.msg % vi nl_prog.c % vi nl_prog2.c % cc nl_prog.c nl_prog2.c In this example, the strextract command uses the c_patterns file to determine which strings to match. The input source programs are named prog.c and prog2.c. If you need to remove any of the messages or extract one of the created strings, edit the resulting message file, prog.str. Under no condi- tions should you add to this file. Doing so could result in unpredictable behavior. You issue the strmerge command to replace the extracted strings with calls to the message catalog. In response to this command, strmerge creates the source message catalogs, prog.msg and prog2.msg, and the output source programs, nl_prog.c and nl_prog2.c. Before compiling the source programs, you must edit nl_prog.c and nl_prog2.c to include the appropriate catopen and catclose function calls. The gencat command creates a message catalog and the cc command creates an executable program. SEE ALSO
extract(1), gencat(1), strextract(1), trans(1), regexp(3), catopen(3), catgets(3), patterns(4) Writing Software for the International Market strmerge(1)
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