Shell Programming and Scripting

I have an input file in this format (shown below). I have to select the lines which doesnt followed by 'miR-" and to save such lines into an output file. For easy identification they are shown here in blue color. They have to be selected. Pls. help me to write a shell script to select those lines which doesnt followed by miR- and have to write them in a file.
KINDLY DO THE HELP

>sample1:1:1:1056:8164#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1057:7503#0 0 0
>sample1:1:1:1057:18666#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1057:1725#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1057:12664#0 0 0
>sample1:1:1:1057:18537#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1058:8130#0 1 1
miR-2396;Chr26:42482649-42482717 -1 2
>sample1:1:1:1058:19619#0 1 1
miR-184;Chr21:25913771-25913853 +52 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
miR-16-1;Chr12:19596200-19596290 -52 2
>sample1:1:1:1060:13498#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1060:11510#0 0 0
>sample1:1:1:1060:2691#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1060:5177#0 0 0
>sample1:1:1:1060:13599#0 1 1
miR-16-1;Chr12:19596200-19596290 -52 2
>sample1:1:1:1060:12022#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1061:8105#0 0 0
>sample1:1:1:1062:4635#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1062:2052#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1062:17129#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1063:6105#0 0 0
>sample1:1:1:1064:11266#0 0 0
>sample1:1:1:1065:5224#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1065:14605#0 1 1
miR-152;Chr19:39081165-39081250 +53 2
>sample1:1:1:1066:5654#0 0 0
>sample1:1:1:1066:10310#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1067:3521#0 1 1
miR-184;Chr21:25913771-25913853 +52 2
>sample1:1:1:1067:1055#0 1 1

You posted the input data, but it would be kind to post us the expected result/output.

Regards

That's because your problem statement is quite vague. A "read" operation does not "have" a format, which is why "read" cannot "be" in any format.

Your input data in a file or from a pipe "has" or "is in" some particular format. So, I'll assume that this -

Code:

Chr18:4000-4010
Chr20:393939-400303
Chr30:38838-30020

is the format of your input data. Again, I'll assume that this data is in a file, as opposed to a pipe stream.

In the shell, you'd read a file like so -

Code:

$
$ # display the content of the file. My file is called "f32", yours may be different.
$ cat f32
Chr18:4000-4010
Chr20:393939-400303
Chr30:38838-30020
$
$ # read data from input file "f32"
$ while read LINE; do   echo "Oh my! I've now read this line => $LINE"; done < f32
Oh my! I've now read this line => Chr18:4000-4010
Oh my! I've now read this line => Chr20:393939-400303
Oh my! I've now read this line => Chr30:38838-30020
$
$

HTH,
tyler_durden

My input file (data1) is like this
Chr8:4000-4500
Chr10:4000-4600

I written a shell program like this.
while read LINE;
do echo "$LINE";
samtools faidx Bos_taurusUMD3.fa "$line";
done < data1


It has to read a line like Chr8:4000-4500 from input file and that line has to be executed in a command like 'samtools faidx Bos_taurusUMD3.fa Chr8:4000-4500'. Then I will get the sequence like this.
>Chr8:4000-4500
TAATTCGTTTTTCTTTTTTCCTCTCTGACTCATTTATTTGTACCATTCTATCTTCTAATT
CACTAATCTTATCTTCTGCCTCTGTTATTCTACTATTTGTCGCCTCCAGAGTGTTTTTGA
TCTCATTTATTGCATTATTCATTATATATTGACTCTTTTTTATGTCTTCTAGGTCCTTGT
TAAACCTTTCTTGCATCTTCTCAATCCTTGTCTCCAGGTTATTTATCTGTGATTCCATTT
TGATTTCAAGATTTTGGATCAATTTCACTATCATTATTCAGAATTCTTTATCAGGTAGAT
TCCTTATCTCTTCCTCTTTTGTTTTGTTTGGTGGGCATTTATCCTGTTCCTTTACCTGCT
GGGTATTCCTCTGTCTCTTCATCTTGTTTATATTGCTGAGTTTGGGGTGTCCTTTCTGTA
TTCTGGCAGTTTGTGGAGTTCTCTTTATTGTGGAGTTTCCTCGCTGTGTATGGGTTTGTA
CAGGTGGCTTGTCAAGGTTTC

but when I execute the shell it is displaying the output like this

Chr8:4000-4500
>
Chr10:4000-4600
>
but not displaying the sequence.but I execute the command at $ prompt like
$samtools faidx Bos_taurusUMD3.fa Chr8:4000-4500
it is running and displaying the sequence.

How to execute it in my shell by reading each line from input line, execute it in command and display the sequences.
KINDLY HELP ME

try like this

Code:

samtools faidx Bos_taurusUMD3.fa "$line"

Thank u very much for your reply. I used as u specified "$line" in samtools command like samtools faidx Bos_taurusUMD3.fa "$line";

It is giving out like this. Sequence was not given. it displays it as > only.

Chr8:86884850-86884997
>
ChrX:96383583-96383703
>
Chr15:33347613-33347720
>
~
Kindly help me how to execute that to generate the sequence.