Sponsored Content
Top Forums Shell Programming and Scripting Parsing a fasta sequence with start and end coordinates Post 302514158 by michaelrozar17 on Friday 15th of April 2011 01:50:14 AM
Old 04-15-2011
Using cut command
Code:
cut -c2-10 inputfile

 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Help Parsing Sequence File

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)
Discussion started by: Fahmida
8 Replies

2. UNIX for Dummies Questions & Answers

How to change sequence name in along fasta file?

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)
Discussion started by: baika
2 Replies

3. Shell Programming and Scripting

Remove lines between the start string and end string including start and end string Python

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)
Discussion started by: Dabheeruz
1 Replies

4. UNIX for Dummies Questions & Answers

Change sequence names in fasta file

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)
Discussion started by: tyrianthinae
2 Replies

5. Shell Programming and Scripting

Extract sequence from fasta file

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)
Discussion started by: ritakadm
2 Replies

6. Shell Programming and Scripting

Count and search by sequence in multiple fasta file

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)
Discussion started by: empyrean
5 Replies

7. Shell Programming and Scripting

Parsing and masking regions from a single fasta file with subsequence

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)
Discussion started by: margarita
2 Replies

8. Shell Programming and Scripting

Command Line Perl for parsing fasta file

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)
Discussion started by: jdilts
2 Replies

9. UNIX for Beginners Questions & Answers

How to find a specific sequence pattern in a fasta file?

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)
Discussion started by: dineshkumarsrk
3 Replies

10. UNIX for Beginners Questions & Answers

Splitting week start date and end date based on custom period start dates

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
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)
All times are GMT -4. The time now is 05:54 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy