Note that the following awk code produces both output files you want in one invocation (with pairs with 2nd lines longer than 15 characters in a file name long and pairs with 2nd lines shorter than 16 characters in a file named short):
If you want to try this on a Solaris/SunOS system, change awk to nawk or /usr/xpg4/bin/awk.
These 3 Users Gave Thanks to Don Cragun For This Post:
Hi ,
I have a peculiar case, where my sed command is working on a file which contains lines of small length.
sed "s/XYZ:1/XYZ:3/g" abc.txt > xyz.txt
when abc.txt contains lines of small length(currently around 80 chars) , this sed command is working fine.
when abc.txt contains lines of... (3 Replies)
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)
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)
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)
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)
I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
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)
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)
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)
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
LEARN ABOUT DEBIAN
x2sys_solve
X2SYS_SOLVE(1gmt) Generic Mapping Tools X2SYS_SOLVE(1gmt)NAME
x2sys_solve - Determine systematic corrections from crossovers
SYNOPSIS
x2sys_solve -Ccolumn -TTAG -Emode [ COE_list.d ] [ -V ] [ -W ] [ -Z ] [ -bi[s|S|d|D[ncol]|c[var1/...]] ]
DESCRIPTION
x2sys_solve will use the supplied crossover information to solve for systematic corrections that can then be applied per track to improve
data quality. Several systematic corrections can be solved for using a least-squares approach. Note: Only one data column can be processed
at the time.
-T Specify the x2sys TAG which tracks the attributes of this data type.
-C Specify which data column you want to process. Needed for proper formatting of the output correction table and must match the same
option used in x2sys_list when preparing the input data.
-E The correction type you wish to model. Choose among the following functions f(p), where p are the m parameters per track that we
will fit simultaneously using a least squares approach:
c will fit f(p) = a (a constant offset); records must contain cruise ID1, ID2, COE.
d will fit f(p) = a + b * d (linear drift; d is distance; records must contain cruise ID1, ID2, d1, d2, COE.
g will fit f(p) = a + b sin(y)^2 (1980-1930 gravity correction); records must contain cruise ID1, ID2, latitude y, COE.
h will fit f(p) = a + b cos(H) + c cos(2H) + d sin(H) + e sin(2H) (magnetic heading correction); records must contain cruise ID1,
ID2, heading H, COE.
s will fit f(p) = a * z (a unit scale correction); records must contain cruise ID1, ID2, z1, z2.
t will fit f(p) = a + b * (t - t0) (linear drift; t0 is the start time of the track); records must contain cruise ID1, ID2, t1-t0,
t2-t0, COE.
OPTIONS
No space between the option flag and the associated arguments.
COE_list.d
Name of file with the required crossover columns as produced by x2sys_list. NOTE: If -bi is used then the first two columns are
expected to hold the integer track IDs; otherwise we expect those columns to hold the text string names of the two tracks.
-V Selects verbose mode, which will send progress reports to stderr [Default runs "silently"].
-W Means that each input records has an extra column with the composite weight for each crossover record. These are used to obtain a
weighted least squares solution [no weights].
-Z For -Ed and -Et, determine the earliest time or shortest distance for each track, then use these values as the local origin for time
duration or distance calculations. The local origin is then included in the correction table [Default uses 0].
-bi Selects binary input. Append s for single precision [Default is d (double)]. Uppercase S or D will force byte-swapping. Option-
ally, append ncol, the number of columns in your binary input file if it exceeds the columns needed by the program. Or append c if
the input file is netCDF. Optionally, append var1/var2/... to specify the variables to be read.
EXAMPLES
To fit a simple bias offset to faa for all tracks under the MGD77 tag, try
x2sys_list COE_data.txt -V -TMGD77 -Cfaa -Fnc > faa_coe.txt
x2sys_solve faa_coe.txt -V -TMGD77 -Cfaa -Ec > coe_table.txt
To fit a faa linear drift with time instead, try
x2sys_list COE_data.txt -V -TMGD77 -Cfaa -FnTc > faa_coe.txt
x2sys_solve faa_coe.txt -V -TMGD77 -Cfaa -Et > coe_table.txt
To estimate heading corrections based on magnetic crossovers associated with the tag MGD77 from the file COE_data.txt, try
x2sys_list COE_data.txt -V -TMGD77 -Cmag -Fnhc > mag_coe.txt
x2sys_solve mag_coe.txt -V -TMGD77 -Cmag -Eh > coe_table.txt
To estimate unit scale corrections based on bathymetry crossovers, try
x2sys_list COE_data.txt -V -TMGD77 -Cdepth -Fnz > depth_coe.txt
x2sys_solve depth_coe.txt -V -TMGD77 -Cdepth -Es > coe_table.txt
SEE ALSO x2sys_binlist(1), x2sys_cross(1), x2sys_datalist(1), x2sys_get(1), x2sys_init(1), x2sys_list(1), x2sys_put(1), x2sys_report(1)GMT 4.5.7 15 Jul 2011 X2SYS_SOLVE(1gmt)