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Full Discussion: how to fetch substring from records into another file
Top Forums Shell Programming and Scripting how to fetch substring from records into another file Post 302220690 by aigles on Friday 1st of August 2008 11:57:08 AM
Old 08-01-2008
The order of the output correspond to the order of headers in file1.
The logic is :
For each record in file 1
Proceed extractions specified in file 2 relative to this record
The script:
Code:
awk '

NR==FNR {
   if (NR==1)
      Key_len = length($1) + 1;
   k = ">" substr($0,1, Key_len-1);
   n = ++Keys[k];
   From[k,n] = $2;
     To[k,n] = $3;
    Len[k,n] = $3 - $2;
   next;
}

function print_selected(    i,k,p,str) {
   if (selected) {
      k = substr(Header, 1, Key_len);
      for (i=1; i<=Keys[k]; i++) {
         printf("%s (%s-%s)\n", Header, From[k,i], To[k,i]);
         str = substr(Alphabets, From[k,i], Len[k,i]);
         p = 1
         while (p<=Len[k,i]) {
            print substr(str, p, 70);
            p += 70;
         }
      }
   }
}

/^>/ {
   print_selected();
   selected  = (substr($0, 1, Key_len) in Keys);
   Header    = $0;
   Alphabets = "";
   next;
}

selected {
   Alphabets = Alphabets $0;
}

END {
   print_selected();
}
' sm2.dat sm1.dat

Input file 1 (sm1.dat):
Code:
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra]
MRVIAAAMLYLYIVVLAICSVGIQGIDYPSVSFNLAGAKSATWDFLRMPHDLVGEDNKYNDGEPITGNII
GRDGLCVDVRNGYDTDGTPLQLWPCGTQRNQQWTFYTDDTIRSMGKCMTANGLSNGSNIMIFNCSTAVEN
AIKWEVTIDGSIINPSSG
>bi|21083|em|CAA26939.1| precursor [Ricinus communis]
MKPGGNTIVIWMYAVATWLCFGSTSGWSFTLEDNNIFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTG
ADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAIT
HLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTL
>bi|19526601|geb|AAL87006.1| chain A [Viscum album]
YERLRLRVTHQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSTIPVSDAQRFVLVELTNEGGDSITAAI
DVTNLYVVAYQAGDQSYFLRDAPRGAETHLFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVT
ALRFPGGNTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVY

Input file 2 (sm2.dat) :
Code:
bi|2138271|geb|AAC15885 92      110
bi|19526601|geb|AAL8700 74      92
bi|2138271|geb|AAC15885 20      132
bi|21083|em|CAA26939.1| 19      37
bi|21083|em|CAA26939.1| 52      70
bi|2138271|geb|AAC15885 26      38

Output :
Code:
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra] (92-110)
LWPCGTQRNQQWTFYTDD
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra] (20-132)
SVGIQGIDYPSVSFNLAGAKSATWDFLRMPHDLVGEDNKYNDGEPITGNIIGRDGLCVDVRNGYDTDGTP
LQLWPCGTQRNQQWTFYTDDTIRSMGKCMTANGLSNGSNIMI
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra] (26-38)
IDYPSVSFNLAG
>bi|21083|em|CAA26939.1| precursor [Ricinus communis] (19-37)
LCFGSTSGWSFTLEDNNI
>bi|21083|em|CAA26939.1| precursor [Ricinus communis] (52-70)
TVQSYTNFIRAVRGRLTT
>bi|19526601|geb|AAL87006.1| chain A [Viscum album] (74-92)
NLYVVAYQAGDQSYFLRD

Jean-Pierre.
 

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LEARN ABOUT PHP

iconv_substr

ICONV_SUBSTR(3) 							 1							   ICONV_SUBSTR(3)

iconv_substr - Cut out part of a string

SYNOPSIS

       string  iconv_substr  (string  $str, int  $offset, [int	$length = iconv_strlen($str, $charset)], [string  $charset = ini_get("iconv.inter-
       nal_encoding")])

DESCRIPTION

	Cuts a portion of $str specified by the $offset and $length parameters.

PARAMETERS

	      o $str
		- The original string.

	      o $offset
		- If $offset is non-negative, iconv_substr(3) cuts the portion out of $str beginning at $offset'th character, counting from  zero.
		If  $offset  is  negative, iconv_substr(3) cuts out the portion beginning at the position, $offset characters away from the end of
		$str.

	      o $length
		- If $length is given and is positive, the return value will contain at most $length characters of  the  portion  that	begins	at
		$offset  (depending  on  the length of $string).  If negative $length is passed, iconv_substr(3) cuts the portion out of $str from
		the $offset'th character up to the character that is $length characters away from the end of the string. In case $offset  is  also
		negative, the start position is calculated beforehand according to the rule explained above.

	      o $charset
		-  If  $charset parameter is omitted, $string are assumed to be encoded in iconv.internal_encoding.  Note that $offset and $length
		parameters are always deemed to represent offsets that are calculated on the basis of the character set  determined  by  $charset,
		whilst the counterpart substr(3) always takes these for byte offsets.

RETURN VALUES

	Returns the portion of $str specified by the $offset and $length parameters.

	If $str is shorter than $offset characters long, FALSE will be returned.

SEE ALSO

       substr(3), mb_substr(3), mb_strcut(3).

PHP Documentation Group 													   ICONV_SUBSTR(3)
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