Hi All,
I have a file of 100 lines of each having 1000 columns. I need to find the difference of each column against each other. That means, Col1-Col1; Col1-Col2; Col1-Col3;......Col1-Col1000; Col2-Col1; Col2-Col2; Col2-Col3;.... and so on ....up to Col1000-Col1000.
Lets say the file is... (6 Replies)
Hello everybody,
I have a text file containing 10,000 rows and 5000 columns. The values are separated by a tab.
Ex.
file_ex.ped
1 mike 0 0 2 1 A A G G C T A G
1 jack 0 0 2 2 T A G T C A A C
1 Mary 0 0 1 2 A T G C A T G C
...
I would like a out put file
1 mike 0 0 2 1 AA GG CT AG
1... (7 Replies)
Hello everybody,
I have some large files containing statistical data. The data is stored in the following generic format:
>cat my_file
1, 2, 3
1, 2, 3
1, 2, 3
>
The values of columns no.2 and 3 are expressed in bytes. I would like to transform them in Megabytes, by dividing them with... (3 Replies)
Hi All,
I have two sets of files.
Set 1: 100 text files with extension .txt with names like 1.txt, 2.txt, 3.txt until 100.txt
Set 2: One big file with extension .dat
The text files have some records in columns like this:
0.7316431 82628
0.7248189 82577
0.7248182 81369
0.7222999... (1 Reply)
I have a text file that has three columns. But at the end of the text file, there are trailing lines that have missing second and third columns:
4 0.04972604 KLHL28
4 0.0497332 CSTB
4 0.04979822 AIF1
4 0.04983331 DECR2
4 0.04990344 KATNB1
4
4
4
4
How can I remove the trailing... (3 Replies)
Hi everyone, I had a similar question a couple days ago but my problem has gotten significantly (to me anyway) more complex.
I have two files:
File 1:
0808 166 166 62 9 0
1000fights 1 1 2 1 0
100places2visit 2 2 2 2 0
10veronica91 167 167 3 1 0
11thgorgeous 346 346 3806 1461 122... (2 Replies)
Legends,
Please help me in , how do i subtract the variable values listed like below.
the first value of orig should be subtracted from first value of prev and so on.
san> echo $orig
346 316 340 239 410 107 291 139 128 230 167 147 159 159 172 116 110 260 177 0 177 169 168 186 165 366 195... (15 Replies)
Hi Folks,
I have a file with 2 columns TAB delimited and I want to add '1' to the first column and subtract '-1' from the second column.
What I have tried so far is;
awk -F"\t" '{ $1-=1;$2+=1}1' OFS='\t' file
File
0623 0623
0624 0624
0643 0643
1059 1037
1037 1037
1038 1038... (2 Replies)
Columns 4 and 5 are X and Y coordinates, column 6 is the elevation
I would like to add 2 new columns at the end of the file with values
the distance between first(X)(Y) and last location (X)(Y), based in 2 rows
the difference in elevation = ($6-prev6)
How to calculate the requested values... (6 Replies)
Discussion started by: jiam912
6 Replies
LEARN ABOUT DEBIAN
2ndscore
2NDSCORE(1) User Contributed Documentation 2NDSCORE(1)NAME
2ndscore - find the best hairpin anchored at each position.
SYNOPSIS
2ndscore in.fasta > out.hairpins
DESCRIPTION
For every position in the sequence this will output a line:
-0.6 52 .. 62 TTCCTAAAGGTTCCA GCG CAAAA TGC CATAAGCACCACATT
(score) (start .. end) (left context) (hairpin) (right contenxt)
For positions near the ends of the sequences, the context may be padded with 'x' characters. If no hairpin can be found, the score will be
'None'.
Multiple fasta files can be given and multiple sequences can be in each fasta file. The output for each sequence will be separated by a
line starting with '>' and containing the FASTA description of the sequence.
Because the hairpin scores of the plus-strand and minus-strand may differ (due to GU binding in RNA), by default 2ndscore outputs two sets
of hairpins for every sequence: the FORWARD hairpins and the REVERSE hairpins. All the forward hairpins are output first, and are
identified by having the word 'FORWARD' at the end of the '>' line preceding them. Similarly, the REVERSE hairpins are listed after a '>'
line ending with 'REVERSE'. If you want to search only one or the other strand, you can use:
--no-fwd Don't print the FORWARD hairpins
--no-rvs Don't print the REVERSE hairpins
You can set the energy function used, just as with transterm with the --gc, --au, --gu, --mm, --gap options. The --min-loop, --max-loop,
and --max-len options are also supported.
FORMAT OF THE .BAG FILES
The columns for the .bag files are, in order:
1. gene_name
2. terminator_start
3. terminator_end
4. hairpin_score
5. tail_score
6. terminator_sequence
7. terminator_confidence: a combination of the hairpin and tail score that
takes into account how likely such scores are in a random sequence. This
is the main "score" for the terminator and is computed as described in
the paper.
8. APPROXIMATE_distance_from_end_of_gene: The *approximate* number of base
pairs between the end of the gene and the start of the terminator. This
is approximate in several ways: First, (and most important) TransTermHP
doesn't always use the real gene ends. Depending on the options you give
it may trim some off the ends of genes to handle terminators that
partially overlap with genes. Second, where the terminator "begins"
isn't that well defined. This field is intended only for a sanity check
(terminators reported to be the best near the ends of genes shouldn't be
_too far_ from the end of the gene).
USING TRANSTERM WITHOUT GENOME ANNOTATIONS
TransTermHP uses known gene information for only 3 things: (1) tagging the putative terminators as either "inside genes" or "intergenic,"
(2) choosing the background GC-content percentage to compute the scores, because genes often have different GC content than the intergenic
regions, and (3) producing slightly more readable output. Items (1) and (3) are not really necessary, and (2) has no effect if your genes
have about the same GC-content as your intergenic regions.
Unfortunately, TransTermHP doesn't yet have a simple option to run without an annotation file (either .ptt or .coords), and requires at
least 2 genes to be present. The solution is to create fake, small genes that flank each chromosome. To do this, make a fake.coords file
that contains only these two lines:
fakegene1 1 2 chome_id
fakegene2 L-1 L chrom_id
where L is the length of the input sequence and L-1 is 1 less than the length of the input sequence. "chrom_id" should be the word directly
following the ">" in the .fasta file containing your sequence. (If, for example, your .fasta file began with ">seq1", then chrom_id =
seq1).
This creates a "fake" annotation with two 1-base-long genes flanking the sequence in a tail-to-tail arrangement: --> <--. TransTermHP can
then be run with:
transterm -p expterm.dat sequence.fasta fake.coords
If the G/C content of your intergenic regions is about the same as your genes, then this won't have too much of an effect on the scores
terminators receive. On the other hand, this use of TransTermHP hasn't been tested much at all, so it's hard to vouch for its accuracy.
SEE ALSO transterm(1)AUTHOR
Alex Mestiashvili <alex@biotec.tu-dresden.de>
2011-02-19 2NDSCORE(1)