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Full Discussion: Print specific pattern line in c++
Top Forums Programming Print specific pattern line in c++ Post 302536253 by cpp_beginner on Tuesday 5th of July 2011 12:17:49 AM
Old 07-05-2011
Print specific pattern line in c++
Input file:
Code:
@HWI-BRUNOP1_header_1
GACCAATAAGTGATGATTGAATCGCGAGTGCTCGGCAGATTGCGATAAAC
+HWI-BRUNOP1_header_1
TNTTJTTTETceJSP__VRJea`_NfcefbWe[eagggggfgdggBBBBB
@HWI-BRUNOP1_header_2
CAGCAGACGCTTTGATTGCTCGATCTCTTGGTAAATACGGCATCATCTGC
+HWI-BRUNOP1_header_2
TJTTTJFFFFa`TWNMPJGTbZSTPZJHHGT^I^H^SKZeeeeeeb``RT

Desired output file:
Code:
>HWI-BRUNOP1_header_1
GACCAATAAGTGATGATTGAATCGCGAGTGCTCGGCAGATTGCGATAAAC
>HWI-BRUNOP1_header_2
CAGCAGACGCTTTGATTGCTCGATCTCTTGGTAAATACGGCATCATCTGC

Rules to follow when writing c++ program:
1. Print out the line start with "@HWI" and the content below "@HWI";
2. Change the "@HWI" into "#HWI" and save the output result into another file;
Command that I try to deal with 14Gb input file data:
Code:
[home@cpp]time grep -A1 '@HWI' input_file.txt | sed -e 's/--//g' -e 's/@HWI/#HWI/g' | sed '/^$/d' > output_file.txt
real    7m13.413s
user    5m25.382s
sys     1m37.668s
[1]+  Done       time grep -A1 '@HWI' input_file.txt | sed -e 's/--//g' -e 's/@HWI/#HWI/g' | sed '/^$/d' > output_file.txt           
[home@cpp]cat output_file.txt
>HWI-BRUNOP1_header_1
GACCAATAAGTGATGATTGAATCGCGAGTGCTCGGCAGATTGCGATAAAC
>HWI-BRUNOP1_header_2
CAGCAGACGCTTTGATTGCTCGATCTCTTGGTAAATACGGCATCATCTGC

Desired format to run the c++ program:
Code:
cplusplus_program_name input_file_name output_file_name

Thanks for any advice.
 

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LEARN ABOUT DEBIAN

x2sys_merge

X2SYS_MERGE(1gmt)					       Generic Mapping Tools						 X2SYS_MERGE(1gmt)

NAME

       x2sys_merge - Merge an updated COEs tables

SYNOPSIS

       x2sys_merge -Amain_COElist.d -Mnew_COElist.d

DESCRIPTION

       x2sys_merge  will read two crossovers data base and output the contents of the main one updated with the COEs in the second one. The second
       file should only contain updated COEs relatively to the first one.  That is, it MUST NOT contain any new  two  tracks  intersections  (This
       point  is  NOT checked in the code). This program is useful when, for any good reason like file editing NAV correction or whatever, one had
       to recompute only the COEs between the edited files and the rest of the database.

       -A     Specify the file main_COElist.d with the main crossover error data base.

       -M     Specify the file new_COElist.d with the newly computed crossover error data base.

OPTIONS

       No space between the option flag and the associated arguments.

       EXAMPLES
	      To update the main COE_data.txt with the new COEs estimations saved in the smaller COE_fresh.txt, try

	      x2sys_merge -ACOE_data.txt -MCOE_fresh.txt > COE_updated.txt

SEE ALSO

       x2sys_binlist(1), x2sys_cross(1), x2sys_datalist(1), x2sys_get(1), x2sys_init(1), x2sys_list(1), x2sys_put(1), x2sys_report(1)

GMT 4.5.7							    15 Jul 2011 						 X2SYS_MERGE(1gmt)
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