Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Extract specific content from data and rename its header problem asking
Top Forums Shell Programming and Scripting Extract specific content from data and rename its header problem asking Post 302406848 by alister on Wednesday 24th of March 2010 04:22:33 AM
Old 03-24-2010
Hi, patrick87:
Code:
awk 'FNR==NR {if (/^>/) p=substr($0,2); else a[p]=a[p] $0; next} {printf(">%s_0.%02u\n%s\n", $1, ++i[$1], substr(a[$1], $2, $3-$2+1))}' f1 f2

While processing the first file (FNR==NR), if a line begins with ">", grab everything that follows it and store it in p, the pattern name. If a line does not begin with a ">", then it is data for the current pattern, p; append the line to a[p], that pattern's entry in array a. Repeat until done with the first file.

For the second file, we use the pattern name in the first field and the index values in the second and third fields to extract the required substring from a[$1], while incrementing a counter for each pattern name seen, in the i array, i[$1].

Cheers,
Alister
Last edited by alister; 03-24-2010 at 05:31 AM..
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Extract specific content from a file

My input file: >sequence_1 ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC ASDSFDFFDFDFFWERERERERFSDFESFSFD >sequence_2 ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS >sequence_3 VEDFGSDGSDGSDGSDGSDGSDGSDG dDFSDFSDFSDFSDFSDFSDFSDFSDF SDGFDGSFDGSGSDGSDGSDGSDGSDG My... (22 Replies)
Discussion started by: patrick87
22 Replies

2. Shell Programming and Scripting

Extract all the content after a specific data

My input: >seq_1 DSASSTRRARRRRTPRTPSLRSRRSDVTCS >seq_3 RMRLRRWRKSCSERS*RRSN >seq_8 RTTGLSERPRLPTTASRSISSRWTR >seq_10 NELPLEKGSLDSISIE >seq_9 PNQGDAREPQAHLPRRQGPRDRPLQAYA+ QVQHRRHDHSRTQH*LCRRRQREDCDRLHR >seq_4 DRGKGQAGCRRPQEGEALVRRCS>seq_6 FA*GLAAQDGEA*SGRG My output: Extract all... (22 Replies)
Discussion started by: patrick87
22 Replies

3. Shell Programming and Scripting

Extract specific data content from a long list of data

My input: Data name: ABC001 Data length: 1000 Detail info Data Direction Start_time End_time Length 1 forward 10 100 90 1 forward 15 200 185 2 reverse 50 500 450 Data name: XFG110 Data length: 100 Detail info Data Direction Start_time End_time Length 1 forward 50 100 50 ... (11 Replies)
Discussion started by: patrick87
11 Replies

4. Shell Programming and Scripting

Remove specific pattern header and its content problem facing

Input file: >TRACK: Position: 1 TYPE: 1 Pos: SVAVPQRHHPGGTVFREPIIIPAIPRLVPGWNKPIIIGRHAFGDQYRATDRVIPGPGKLE LVYTPVNGEPETVKVYDFQGGGIAQTQYNTDESIRGFAHASFQMALLKGLPLYMSTKNTI LKRYDGRFKDIFQEIYESTYQKDFEAKNLWYEHRLIDDMVAQMIKSEGGFVMALKNYDGD >TRACK: Position: 1 TYPE: 2 Pos: FAHASFQMALLKGLPLYMS... (8 Replies)
Discussion started by: patrick87
8 Replies

5. Shell Programming and Scripting

Way to extract detail and its content above specific value problem asking

Input file: >position_10 sample:68711 coords:5453-8666 number:3 type:complete len:344 MSINQYSSDFHYHSLMWQQQQQQQQHQNDVVEEKEALFEKPLTPSDVGKLNRLVIPKQHA ERYFPLAAAAADAVEKGLLLCFEDEEGKPWRFRYSYWNSSQSYVLTKGWSRYVKEKHLDA NRTS* >position_4 sample:68711 coords:553-866 number:4 type:partial len:483... (7 Replies)
Discussion started by: patrick87
7 Replies

6. Shell Programming and Scripting

mailx requirement - email body header in bold and data content in normal text

Dear all- I have a requirement to send an email via email with body content which looks something below- Email body contents -------------------- RequestType: Update DateAcctOpened: 1/5/2010 Note that header information and data content should be normal text.. Please advice on... (5 Replies)
Discussion started by: sureshg_sampat
5 Replies

7. Shell Programming and Scripting

Extract all content that match exactly only specific word

Input: 21 templeta parent 35718 36554 . - . ID=parent_cluster_50.21.11; Name=Partial%20parent%20for%20training%20set; 21 templeta kids 35718 36554 . - . ID=_52; Parent=parent_cluster_5085.21.11; 21 templeta ... (7 Replies)
Discussion started by: patrick87
7 Replies

8. Shell Programming and Scripting

Help with rename header content based on reference file problem

I got long list of reference file >data_tmp_number_22 >data_tmp_number_12 >data_tmp_number_20 . . Input file: >sample_data_1 Math, 5, USA, tmp SDFEWRWERWERWRWER FSFDSFSDFSDGSDGSD >sample_data_2 Math, 15, UK, tmp FDSFSDFF >sample_data_3 Math, 50, USA, tmp ARQERREQR . . Desired... (7 Replies)
Discussion started by: perl_beginner
7 Replies

9. Shell Programming and Scripting

extract specific string and rename file

Hi all, I am working on a small prog.. i have a file.txt which contains random data... K LINES V4 ADD CODE `COMPANY` ADD CODE `DISTRIBUTOR` SEQ NAME^K LINES V5 SEQ NAME^K LINES V6 ADD `PACK-LDATE` SEQ NAME^K^KCOMMAND END^KHEADINFO... (1 Reply)
Discussion started by: mukeshguliao
1 Replies

10. Shell Programming and Scripting

Help with rename data content

Input file: data21_result1 data23_result1 data43_result1 data43_result2 data43_result3 data3_result1 . . data9_result1 Desired output data1_result1 data2_result1 data3_result1 data3_result2 data3_result3 data4_result1 (3 Replies)
Discussion started by: perl_beginner
3 Replies

LEARN ABOUT MOJAVE

fc-pattern

FC-PATTERN(1)															     FC-PATTERN(1)

NAME

       fc-pattern - parse and show pattern

SYNOPSIS

       fc-pattern [ -cdVh ]  [ --config ]  [ --default ]  [  [ -f format ]  [ --format format ]  ]  [ --version ]  [ --help ]

	[ pattern  [ element... ]   ]

DESCRIPTION

       fc-pattern  parses  pattern (empty pattern by default) and shows the parsed result.  If --config is given, config substitution is performed
       on the pattern before being displayed.  If --default is given, default substitution is performed on the pattern before being displayed.

       If any elements are specified, only those are printed.

OPTIONS

       This program follows the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is  included
       below.

       -c     Perform config substitution on pattern.

       -d     Perform default substitution on pattern.

       -f     Format output according to the format specifier format.

       -V     Show version of the program and exit.

       -h     Show summary of options.

       pattern
	      Parses and displays pattern (uses empty pattern by default).

       element
	      If set, the element property is displayed for parsed pattern.

SEE ALSO

       FcNameParse(3)  FcConfigSubstitute(3)  FcDefaultSubstitute(3)  FcPatternPrint(3)  FcPatternFormat(3)  fc-cat(1)	fc-cache(1) fc-list(1) fc-
       match(1) fc-query(1) fc-scan(1)

       The fontconfig user's guide, in HTML format: /usr/share/doc/fontconfig/fontconfig-user.html.

AUTHOR

       This manual page was updated by Behdad Esfahbod <behdad@behdad.org>.

								   Apr 20, 2010 						     FC-PATTERN(1)
All times are GMT -4. The time now is 04:35 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy