05-26-2013
10 More Discussions You Might Find Interesting
1. 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
2. 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
9 Replies
3. Shell Programming and Scripting
My file looks something like this
Wnat I need is to look for the Reference sequence (">Reference1") and based on the length of that sequence trim all the entries in that file. So, the rersulting file will contain all sequences with the same length, like this
Thus, all sequences will keep... (5 Replies)
Discussion started by: Xterra
5 Replies
4. Shell Programming and Scripting
I have a large numbers of files containing data that look like this:
(ID31:0.01682,(ID-123:0.00000,(ID_24:0.00000,ID&890:0.00000):0.00000):0.00000,ID12876:0.00000);
(ID_24:-0.00052,(ID31:0.01697,(ID-123:-0.00059,ID&890:0.03528):0.00037):0.00027,ID12876:0.03484);
I need to find ":" anywhere... (6 Replies)
Discussion started by: Xterra
6 Replies
5. 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
6. 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
7. UNIX for Dummies Questions & Answers
I have posted this before but did not get much feedback. So I will try again. I need to remove sequences from a file based on values listed on a second file.
The sequences file looks like this:
Sequences.txt
>Sample1 Freq 59
ggatatgatgatgaactggt
>Sample1 Freq 54
ggatatgatgttgaactggt... (4 Replies)
Discussion started by: Xterra
4 Replies
8. Shell Programming and Scripting
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 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
hwloc_distances_s
hwloc_distances_s(3) Hardware Locality (hwloc) hwloc_distances_s(3)
NAME
hwloc_distances_s -
SYNOPSIS
#include <hwloc.h>
Data Fields
unsigned relative_depth
unsigned nbobjs
float * latency
float latency_max
float latency_base
Detailed Description
Distances between objects.
One object may contain a distance structure describing distances between all its descendants at a given relative depth. If the containing
object is the root object of the topology, then the distances are available for all objects in the machine.
If the latency pointer is not NULL, the pointed array contains memory latencies (non-zero values), as defined by the ACPI SLIT
specification.
In the future, some other types of distances may be considered. In these cases, latency may be NULL.
Field Documentation
float* hwloc_distances_s::latency
Matrix of latencies between objects, stored as a one-dimension array. May be NULL if the distances considered here are not latencies.
Values are normalized to get 1.0 as the minimal value in the matrix. Latency from i-th to j-th object is stored in slot i*nbobjs+j.
float hwloc_distances_s::latency_base
The multiplier that should be applied to latency matrix to retrieve the original OS-provided latencies. Usually 10 on Linux since ACPI SLIT
uses 10 for local latency.
float hwloc_distances_s::latency_max
The maximal value in the latency matrix.
unsigned hwloc_distances_s::nbobjs
Number of objects considered in the matrix. It is the number of descendant objects at relative_depth below the containing object. It
corresponds to the result of hwloc_get_nbobjs_inside_cpuset_by_depth.
unsigned hwloc_distances_s::relative_depth
Relative depth of the considered objects below the object containing this distance information.
Author
Generated automatically by Doxygen for Hardware Locality (hwloc) from the source code.
Version 1.4.1 Mon Feb 27 2012 hwloc_distances_s(3)