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Shell Programming and Scripting
Trimming sequences based on Reference
Post 302433902 by Xterra on Wednesday 30th of June 2010 11:56:15 PM
07-01-2010
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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
2 Replies
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)
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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
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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)
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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)
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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
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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
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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
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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 MOJAVE
platform::shell
platform::shell(n) Tcl Bundled Packages platform::shell(n) __________________________________________________________________________________________________________________________________________________ NAME
platform::shell - System identification support code and utilities SYNOPSIS
package require platform::shell ?1.1.4? platform::shell::generic shell platform::shell::identify shell platform::shell::platform shell _________________________________________________________________ DESCRIPTION
The platform::shell package provides several utility commands useful for the identification of the architecture of a specific Tcl shell. This package allows the identification of the architecture of a specific Tcl shell different from the shell running the package. The only requirement is that the other shell (identified by its path), is actually executable on the current machine. While for most platform this means that the architecture of the interrogated shell is identical to the architecture of the running shell this is not generally true. A counter example are all platforms which have 32 and 64 bit variants and where a 64bit system is able to run 32bit code. For these running and interrogated shell may have different 32/64 bit settings and thus different identifiers. For applications like a code repository it is important to identify the architecture of the shell which will actually run the installed packages, versus the architecture of the shell running the repository software. COMMANDS
platform::shell::identify shell This command does the same identification as platform::identify, for the specified Tcl shell, in contrast to the running shell. platform::shell::generic shell This command does the same identification as platform::generic, for the specified Tcl shell, in contrast to the running shell. platform::shell::platform shell This command returns the contents of tcl_platform(platform) for the specified Tcl shell. KEYWORDS
operating system, cpu architecture, platform, architecture platform::shell 1.1.4 platform::shell(n)