Sponsored Content
Top Forums Shell Programming and Scripting Extract specific content from data and rename its header problem asking Post 302406475 by patrick87 on Tuesday 23rd of March 2010 05:05:10 AM
Old 03-23-2010
Extract specific content from data and rename its header problem asking

Input file 1:
Code:
>pattern_5
GAATTCGTTCATGTAGGTTGASDASFGDSGRTYRYGHDGSDFGSDGGDSGSDGSDFGSDF
ATTTAATTATGATTCATACGTCATATGTTATTATTCAATCGTATAAAATTATGTGACCTT
SDFSDGSDFKSDAFLKJASLFJASKLFSJAKJFHASJKFHASJKFHASJKFHSJAKFHAW
>pattern_1
AAGTCTTAAGATATCACCGTCGATTAGGTTTATACAGCTTTTGTGTTATTTAAATTTGAC
ASDASRFSARFASFEDEGSDGHSDHWDYTQATWQRQOPTPEOTPWRIYRHIRGOPEIWRA
.
.

Input file 2:
Code:
pattern_5    5   15
pattern_5    18  25 
pattern_1    10  19
pattern_1    22  27
.
.

Desired output:
Code:
>pattern_5_0.01
TCGTTCATGTA
>pattern_5_0.02
TTGASDAS
>pattern_1_0.01
GATATCACCG
>pattern_1_0.02
GATTAG
.
.

I got a long list of input file 1 and input file 2. Input file 1 is the raw data while input file 2 is the range of input file 1 data that I'm interested to extract and generate the output result file. The column 2 and column 3 of input file 2 is the position that I interested to extract from the data of input file 1. The output file I will rename with the header like "pattern_*_0.0*"
It seems like awk or perl scripts able to archive these goal.
Thanks a lot for any advice.

Last edited by patrick87; 03-23-2010 at 06:31 AM.. Reason: further explaining of my question
 

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
COLUMN(1)						    BSD General Commands Manual 						 COLUMN(1)

NAME
column -- columnate lists SYNOPSIS
column [-tx] [-c columns] [-s sep] [file ...] DESCRIPTION
The column utility formats its input into multiple columns. Rows are filled before columns. Input is taken from file operands, or, by default, from the standard input. Empty lines are ignored. The options are as follows: -c Output is formatted for a display columns wide. -s Specify a set of characters to be used to delimit columns for the -t option. -t Determine the number of columns the input contains and create a table. Columns are delimited with whitespace, by default, or with the characters supplied using the -s option. Useful for pretty-printing displays. -x Fill columns before filling rows. ENVIRONMENT
The COLUMNS, LANG, LC_ALL and LC_CTYPE environment variables affect the execution of column as described in environ(7). EXIT STATUS
The column utility exits 0 on success, and >0 if an error occurs. EXAMPLES
(printf "PERM LINKS OWNER GROUP SIZE MONTH DAY " ; printf "HH:MM/YEAR NAME " ; ls -l | sed 1d) | column -t SEE ALSO
colrm(1), ls(1), paste(1), sort(1) HISTORY
The column command appeared in 4.3BSD-Reno. BUGS
Input lines are limited to LINE_MAX (2048) bytes in length. BSD
July 29, 2004 BSD
All times are GMT -4. The time now is 05:41 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy