07-01-2010
My bad!
Thanks alot! It worked like a charm!
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
My file looks like this:
But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ)
Would it be possible to use awk to perform this task? (2 Replies)
Discussion started by: Xterra
2 Replies
2. Shell Programming and Scripting
My files look like this
And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted.
The expected result should look like this
Thus, all the sequences would end with AGCCCTA... (2 Replies)
Discussion started by: Xterra
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3. Shell Programming and Scripting
This is what I would like to accomplish, I have an input file (file A) that consist of thousands of sequence elements with the same number of characters (length), each headed by a free text header starting with the chevron ‘>' character followed by the ID (all different IDs with different lenghts)... (9 Replies)
Discussion started by: Xterra
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4. Shell Programming and Scripting
I got two files right now, input file (target file), reference file 1 (query file)
reference file 1 (long list of data)
KOLOPWMOPOPO
ADASDASD
ADSASDASDAD
.
.
target file (one long liner content)
ADASDASDTYUKOKOLOPWMOPOPOOPLUAADSASDASDADPOPOUYADADASDASD
desired output file content
... (1 Reply)
Discussion started by: patrick87
1 Replies
5. UNIX for Dummies Questions & Answers
Hi,
I have a string say "whateverCluster".
I need everthing apart from the string "Cluster"
Input:
whateverCluster
Desired output:
whatever (5 Replies)
Discussion started by: mohtashims
5 Replies
6. Shell Programming and Scripting
Hi,
I have a file with more than 28000 records and it looks like below..
>mm10_refflat_ABCD range=chr1:1234567-2345678
tgtgcacactacacatgactagtacatgactagac....so on
>mm10_refflat_BCD range=chr1:3234567-4545678...
tgtgcacactacacatgactagtatgtgcacactacacatgactagta
.
.
.
.
.
so on
... (2 Replies)
Discussion started by: Diya123
2 Replies
7. Shell Programming and Scripting
I have two files with thousands of sequences of different lengths. infile1 contains the actual sequences and infile2 the scores for each A, T, G and C in infile1. Something like this:
infile1:
>HZVJKYI01ECH5R
TTGATGTGCCAGCTGCCGTTGGTGTGCCAA
>HZVJKYI01AQWJ8
GGATATGATGATGAACTGGTTTGGCACACC... (4 Replies)
Discussion started by: Xterra
4 Replies
8. Shell Programming and Scripting
I have to remove sequences from a file based on the distance value. I am attaching the file containing the distances (Distance.xls)
The second file looks something like this:
Sequences.txt
>Sample1 Freq 59
ggatatgatgatgaactggt
>Sample1 Freq 54
ggatatgatgttgaactggt
>Sample1 Freq 44... (2 Replies)
Discussion started by: Xterra
2 Replies
9. Shell Programming and Scripting
I have a list of IDs in file1 and a list of sequences in file2. I can print sequences from file2, but I'm asking for help in printing the sequences in the same order as the IDs appear in file1.
file1:
EN_comp12952_c0_seq3:367-1668
ES_comp17168_c1_seq6:1-864
EN_comp13395_c3_seq14:231-1088... (5 Replies)
Discussion started by: pathunkathunk
5 Replies
10. Shell Programming and Scripting
I have this file:
>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC
Add I am trying to use this script to output sequences longer than 15 characters:
sed -r '/^>/N;{/^.{,15}$/d}'
The desire output would be this:
>ID4... (8 Replies)
Discussion started by: Xterra
8 Replies
LEARN ABOUT DEBIAN
checkbashisms
CHECKBASHISMS(1) General Commands Manual CHECKBASHISMS(1)
NAME
checkbashisms - check for bashisms in /bin/sh scripts
SYNOPSIS
checkbashisms script ...
checkbashisms --help|--version
DESCRIPTION
checkbashisms, based on one of the checks from the lintian system, performs basic checks on /bin/sh shell scripts for the possible presence
of bashisms. It takes the names of the shell scripts on the command line, and outputs warnings if possible bashisms are detected.
Note that the definition of a bashism in this context roughly equates to "a shell feature that is not required to be supported by POSIX";
this means that some issues flagged may be permitted under optional sections of POSIX, such as XSI or User Portability.
In cases where POSIX and Debian Policy disagree, checkbashisms by default allows extensions permitted by Policy but may also provide
options for stricter checking.
OPTIONS
--help, -h
Show a summary of options.
--newline, -n
Check for "echo -n" usage (non POSIX but required by Debian Policy 10.4.)
--posix, -p
Check for issues which are non POSIX but required to be supported by Debian Policy 10.4 (implies -n).
--force, -f
Force each script to be checked, even if it would normally not be (for instance, it has a bash or non POSIX shell shebang or appears
to be a shell wrapper).
--extra, -x
Highlight lines which, whilst they do not contain bashisms, may be useful in determining whether a particular issue is a false posi-
tive which may be ignored. For example, the use of "$BASH_ENV" may be preceded by checking whether "$BASH" is set.
--version, -v
Show version and copyright information.
EXIT VALUES
The exit value will be 0 if no possible bashisms or other problems were detected. Otherwise it will be the sum of the following error val-
ues:
1 A possible bashism was detected.
2 A file was skipped for some reason, for example, because it was unreadable or not found. The warning message will give details.
SEE ALSO
lintian(1).
AUTHOR
checkbashisms was originally written as a shell script by Yann Dirson <dirson@debian.org> and rewritten in Perl with many more features by
Julian Gilbey <jdg@debian.org>.
DEBIAN
Debian Utilities CHECKBASHISMS(1)