10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
and use command line perl to move the all sample gt 8 in length to a new file. the result would be
>0001
agttcgaggtcagaatt
>0003
ggtaacctga
cat ${sample}.fasta | perl -lane... (2 Replies)
Discussion started by: jdilts
2 Replies
2. Shell Programming and Scripting
I have a file1 like
ID E2AK1_HUMAN Reviewed; 630 AA.
CC -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000305}.
ID E1A_ADEM1 Reviewed; 200 AA.
ID E1A_ADES7 Reviewed; 266 AA.
CC -!- SUBCELLULAR LOCATION: Host nucleus... (8 Replies)
Discussion started by: sammy777
8 Replies
3. Shell Programming and Scripting
Hi all
I need to put a command line parser together to parse numeric fields and ranges passed to a script. I'm looking for a bash function that is as elegant and simple as possible.
So the input would be of the following form -
1,2,8-12
This would return -
1,2,8,9,10,11,12
Input can... (7 Replies)
Discussion started by: steadyonabix
7 Replies
4. UNIX for Dummies Questions & Answers
So, the beginning of my script will cat & grep a file with the output directed to a new file. The data I have in this file needs to be parsed, read and evaluated.
Basically, I need to identify the latest date/time stamp and then calculate whether or not it is within 15 minutes of the current... (1 Reply)
Discussion started by: hynesward
1 Replies
5. UNIX for Dummies Questions & Answers
Hey everyone,
I'm having trouble figuring out how to reformat the following (large) file:
>Cluster 1
0 563nt, >FX2FH6V05GB01A... *
1 405nt, >FX2FH6V05F7LOL... at +/98%
>Cluster 2
0 551nt, >FX2FH6V05FTLO0... at +/98%
1 561nt, >FX2FH6V05F5F1E... *
2 343nt, >FX2FH6V05GBHRK... at +/98%
I... (2 Replies)
Discussion started by: mycoguy
2 Replies
6. Shell Programming and Scripting
Hey guys,
I have this file generated by me... i want to create some HTML output from it.
The problem is that i am really confused about how do I go about reading the file.
The file is in the following format:
TID1 Name1 ATime=xx AResult=yyy AExpected=yyy BTime=xx BResult=yyy... (8 Replies)
Discussion started by: umar.shaikh
8 Replies
7. Shell Programming and Scripting
I'm trying to make a script that will read variables line by line from a flatfile
i.e.
$ cat testfile
dbfoo sfoo prifoo poofoo bfoo osfoo
dbfoo2 sfoo2 prifoo2 poofoo2 bfoo2 osfoo2
$
The first pass of the script through the flatfile I want:
$1=dbfoo $2=sfoo... (6 Replies)
Discussion started by: loadnabox
6 Replies
8. Shell Programming and Scripting
Hello,
Im very new to PERL and as a project to work on developing my skills at PERL Im trying to parse poker hands.
Ive tried many methods however I cant get the last step.
$yourfile= 'FILENAME';#poker hands to parse
open (FILE, "$yourfile") or die $!;
@lines = <FILE>;
for (@lines) ... (1 Reply)
Discussion started by: Ek0
1 Replies
9. Shell Programming and Scripting
I am VERY new to unix scripting. I am having trouble parsing a line into fields for further processing.
I have this script:
#bin/sh
cat ztest2.txt | while read line
do
zvar1=`echo $line | cut -f6`
echo "zvar1 is " $zvar1
done
********************
ztest2.txt looks like:
1 ... (2 Replies)
Discussion started by: rlwilli
2 Replies
10. Shell Programming and Scripting
I have a text file of lines like:
A=5|B=7|G=4|C=3|P=4|...
In other words, each line is a pipe-delimited set of pairs of strings of the form "X=Y".
What I want to do is find the token starting with "C", and print it and its value (so I'd want to print "C=3" in the example above).
I'm... (11 Replies)
Discussion started by: monkeys
11 Replies