01-28-2009
It can either be not installed or not in the path. I don't know your OS, but maybe a search with it's package manager for gsed could help.
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1. UNIX for Dummies Questions & Answers
I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this:
> Seq I
ACGACTAGACGATAGACGATAGA
> Seq 2
ACGATGACGTAGCAGT
> Seq 3
ACGATACGAT
I know I can extract the IDs alone with the following code
grep... (3 Replies)
Discussion started by: Xterra
3 Replies
2. Shell Programming and Scripting
I really need some help with this task. I have a bunch of FASTA files with hundreds of DNA sequences that look like this:
>SeqID1
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
TGACAGGTTCAAAGGCTGCAGTGCAGTGACGTGACGATTT
>Sequence 22... (13 Replies)
Discussion started by: Xterra
13 Replies
3. UNIX for Dummies Questions & Answers
I have a fasta file that looks like this:
>Noname
ACCAAAATAATTCATGATATACTCAGATCCATCTGAGGGTTTCACCACTTGTAGAGCTAT
CAGAAGAATGTCAATCAACTGTCCGAGAAAAAAGAATCCCAGG
>Noname
ACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAAACTAGCACTAGCCTG
ACCTTTAGCCAGACTTCTCACTCTTAATGCTGCGGACAAACAGA
...
I want to... (2 Replies)
Discussion started by: Oyster
2 Replies
4. UNIX for Dummies Questions & Answers
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Discussion started by: baika
2 Replies
5. Shell Programming and Scripting
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
Discussion started by: ritakadm
2 Replies
6. UNIX for Dummies Questions & Answers
Hi,
I need some help with modifying fasta headers.
I have a fasta file with thousands of contigs and I need to modify their headers with the information obtained from a second file.
File 1 contains the fasta sequences:
>contig0001 length=11115 numreads=10777
agatgtagatctct... (6 Replies)
Discussion started by: Lokaps
6 Replies
7. UNIX for Dummies Questions & Answers
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
Discussion started by: Xterra
2 Replies
8. Shell Programming and Scripting
Input File:
>Seq1
ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD
>Seq2
SDASDAQEQWEQeqAdfaasd
>Seq3
ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG
......
Desired Output File
>Seq1
ASDADAFASF
ASFADGSDGF
SDFSDFSDFS
DFSDFSDFSD
FSDFSDFSDF
SD
>Seq2 (4 Replies)
Discussion started by: patrick87
4 Replies
9. UNIX for Beginners Questions & Answers
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
Discussion started by: dineshkumarsrk
14 Replies
10. UNIX for Beginners Questions & Answers
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
11 Replies
LEARN ABOUT MINIX
dh_installwm
DH_INSTALLWM(1) Debhelper DH_INSTALLWM(1)
NAME
dh_installwm - register a window manager
SYNOPSIS
dh_installwm [debhelperoptions] [-n] [--priority=n] [wm...]
DESCRIPTION
dh_installwm is a debhelper program that is responsible for generating the postinst and prerm commands that register a window manager with
update-alternatives(8). The window manager's man page is also registered as a slave symlink (in v6 mode and up). It must be installed in
usr/share/man/man1/ in the package build directory prior to calling dh_installwm. In compat 9 and earlier, the manpage was optional.
FILES
debian/package.wm
List window manager programs to register.
OPTIONS
--priority=n
Set the priority of the window manager. Default is 20, which is too low for most window managers; see the Debian Policy document for
instructions on calculating the correct value.
-n, --no-scripts
Do not modify postinst/prerm scripts. Turns this command into a no-op.
wm ...
Window manager programs to register.
NOTES
Note that this command is not idempotent. dh_prep(1) should be called between invocations of this command. Otherwise, it may cause multiple
instances of the same text to be added to maintainer scripts.
SEE ALSO
debhelper(7)
This program is a part of debhelper.
AUTHOR
Joey Hess <joeyh@debian.org>
11.1.6ubuntu2 2018-05-10 DH_INSTALLWM(1)