Hi Everyone,
I am new in the world of UNIX and Shell scripting.
I am working with a sequence file that looks like this:
>contig00001 length=128 numreads=2
aTGTGCTGGgTGGGTGCCTGTTgCCccATGCTCCAGTtCAGGATTtCAGGCAttCTCATG
TCCAGCATTTCTATTTAATCCTGCTGCTGGACTTGGGTGGtCTCAGTCtGGGAAGTGAGC
tGTCTGTG... (8 Replies)
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)
Hi,
I am trying to remove lines once a string is found till another string is found including the start string and end string. I want to basically grab all the lines starting with color (closing bracket). PS: The line after the closing bracket for color could be anything (currently 'more').... (1 Reply)
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
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)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
HI,
I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456
I want a script which can mask these region in a single complete genome fasta file with the alphabet N
kindly help (2 Replies)
I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
and use command line perl to move the all sample gt 8 in length to a new file. the result would be
>0001
agttcgaggtcagaatt
>0003
ggtaacctga
cat ${sample}.fasta | perl -lane... (2 Replies)
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Below are my custom period start and end dates based on a calender, these dates are placed in a file, for each period i need to split into three weeks for each period row, example is given below.
Could you please help out to achieve solution through shell script..
File content:
... (2 Replies)
Discussion started by: nani2019
2 Replies
LEARN ABOUT DEBIAN
oggcut
OGGCUT(1) User Manuals OGGCUT(1)NAME
oggCut - extracts parts of an ogg file (.ogv, .ogg and .oga)
SYNOPSIS
oggCut [options] inputfile outputfile
DESCRIPTION
oggCut creates a new ogg file named outputfile as a subpart of the original file named inputfile
oggCut is able to cut video (theora) only files, audio (vorbis) only files or files with both video and audio streams.
The start and end time for the cut area must be given in milliseconds with the options -s and -e.
As a video stream consists of I-frames (which are full pictures) and P-frames (which are delta pictures to the leading I-frame) the oggCut
algorithm searches for the first I-frame. If a video file would start with a p-frame, the player is not able to interpret this picture, as
the leading I-frame (on where it is based) is not available. oggCut starts the I-frame search at the start time given by the -s option. So
expect a shorter video time than the calculated seconds for the new file.
oggCut does not do any reencoding, therefore the output quality is completely the same as from the input file.
For those involved into the ogg container format: The file is cut on packet basis, not on page basis.
There is another tool called oggCut out in the internet with a different synopis. This one has not been written by the author of this tool
you are actually using.
OPTIONS -s Cut start position in ms. If the input file is a video file, the cut area starts with the next keyframe found. Default: 0
Example: -s 5000
-l Length of the cut area in ms. If -e is also given, the length is ignored.
Example: -l 10000
-e Cut end position in ms. If -l is also used, the end position is prefered. If the end position is set to -1, the end of the stream is
assumed.
Default: -1
Example: -e 20000
EXAMPLE
oggCut -s 1000 -e 21000 myVideo.ogv myOutput.ogv
Creates a new video called myOutput.ogv from the video myVideo.ogv starting after 1 second ending after 21 seconds
AUTHOR
Joern Seger <yorn at gmx dot net>
SEE ALSO oggCat(1), oggJoin(1), oggSplit(1), oggTranscode(1), oggSlideshow(1), oggThumb(1), oggSilence(1)Linux JAN 2010 OGGCUT(1)