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Shell scripting for this sequence to compare

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# 1  
Old 10-08-2010
Question Shell scripting for this sequence to compare
I have two input files (given below) and to compare each line of the File1 with each line of File2 starts with '>sample1'. If a match occurs and that matched line in the File2 contains another line or sequence of lines starting with "Chr" they have to be displayed in output file with that sample. If a match occurs and the matched line in File2 does not contain a 'Chr' line(s) it has be omitted or not taken into consideration for output file. For easy understanding, I marked the matched lines in file1 and file2 with blue color which are taken into consideration for final output. I maked the matched lines in file1 with file2 (which doesnt contain 'Chr' lines) in red color which are not taken into account for output. The final output to be selected also given below. PLS. KINDLY HELP ME FOR THE SHELL SCRIPTING OF THIS. [/COLOR



File1:
[COLOR="Blue"]>sample1:1:1:1057:7503#0 0 0
>sample1:1:1:1057:12664#0 0 0
>sample1:1:1058:8130#0 5 830
>sample1:1:1:1059:6357#0 0 0
>sample1:1:1:1059:10418#0 0 0
>sample1:1:1:1059:12084#0 1 1
>sample1:1:1:1060:11510#0 0 0
>sample1:1:1:1060:5177#0 0 0
>sample1:1:1:1061:8105#0 0 0
>sample1:1:1:1063:6105#0 0 0
>sample1:1:1:1064:11266#0 0 0
>sample1:1:1:1066:5654#0 0 0
>sample1:1:1:1067:10266#0 0 0
>sample1:1:1:1068:2100#0 0 0
>sample1:1:1:1069:3450#0 0 0
>sample1:1:1:1070:7530#0 0 0
>sample1:1:1:1071:8627#0 0 0
>sample1:1:1:1071:8552#0 0 0
>sample1:1:1:1072:7060#0 0 0
>sample1:1:1:1073:7329#0 0 0
>sample1:1:1:1073:20394#0 0 0
>sample1:1:1:1074:7081#0 0 0
>sample1:1:1:1076:1654#0 0 0
>sample1:1:1:1077:15575#0 0 0
>sample1:1:1:1077:15683#0 0 0

File2:
>sample1:1:1:1056:8164#0 1 1
Chr21 +25913822 2
>sample1:1:1:1057:7503#0 0 0
>sample1:1:1:1057:18666#0 1 1
Chr21 +25913822 2
>sample1:1:1:1057:1725#0 1 1
Chr21 +25913822 2
>sample1:1:1:1057:12664#0 0 0
>sample1:1:1:1057:18537#0 1 1
Chr21 +25913822 2
>sample1:1:1:1058:8130#0 5 830
Chr19 +52245923 1
Chr17 +69679873 1
Chr23 +52121254 1
Chr11 +100949523 1
Chr8 +28333267 1
>sample1:1:1:1058:19619#0 1 1
Chr21 +25913822 2
>sample1:1:1:1059:6357#0 0 0
>sample1:1:1:1059:10418#0 0 0
>sample1:1:1:1059:12084#0 1 1
Chr12 -19596251 2
>sample1:1:1:1060:13498#0 1 1

Output:
sample1:1:1:1058:8130#0 5 830
Chr19 +52245923 1
Chr17 +69679873 1
Chr23 +52121254 1
Chr11 +100949523 1
Chr8 +28333267 1
sample1:1:1:1059:12084#0 1 1
Chr12 -19596251
# 2  
Old 10-08-2010
Code:
awk 'BEGIN{FS=RS;RS=">"}NR==FNR{a[$1]=$0}/Chr/ && a[$1]{printf}'  file1 file2

This User Gave Thanks to danmero For This Post:
hravisankar
# 3  
Old 10-08-2010
MySQL
Code:
sed "" File1 | while read -r l ; do sed -n "/$l/,/>sample1/p" File2 | sed -e 'N;' -e '/>sample1.*\n>sample1/d' | 
sed -e '/Chr.*/N;' -e 's/\(Chr.*\)\n>sample1.*/\1/' ; done
>sample1:1:1:1058:8130#0 5 830
Chr19 +52245923 1
Chr17 +69679873 1
Chr23 +52121254 1
Chr11 +100949523 1
Chr8 +28333267 1
>sample1:1:1:1059:12084#0 1 1
Chr12 -19596251 2

# 4  
Old 10-08-2010
Problem in reading largers sequences
Thanks a lot for this script. It worked well with small data file. My datafiles file1 and file2 contains minimum 370MB. when I execute this command, after 5 minutes i am getting $ prompt without any result. If possible, can u help me anything to add for executing more data.

Quote:
Originally Posted by danmero
Code:
awk 'BEGIN{FS=RS;RS=">"}NR==FNR{a[$1]=$0}/Chr/ && a[$1]{printf}'  file1 file2

# 5  
Old 10-08-2010
Quote:
Originally Posted by hravisankar
Thanks a lot for this script. It worked well with small data file. My datafiles file1 and file2 contains minimum 370MB.
Before asking for a solution you should bring up-front all variables as: file(s) size, system specs, your own knowledge, etc...
This User Gave Thanks to danmero For This Post:
hravisankar
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