Sponsored Content
Full Discussion: Fasta header modification
Top Forums UNIX for Dummies Questions & Answers Fasta header modification Post 302923148 by Lokaps on Thursday 30th of October 2014 05:27:50 PM
Old 10-30-2014
Hi,

Thanks for the replies. Unfortunately it doesn't seem to work Smilie

In the case of Singh and Akshay, the output is just like file 1 and with Don's code, the output is >--[cov=]

Does it matter if file is a tsv file and not separated by space?

Thanks
 

9 More Discussions You Might Find Interesting

1. Linux

Reading the header of a tar file(posix header)

say i have these many file in a directory named exam. 1)/exam/newfolder/link.txt. 2)/exam/newfolder1/ and i create a tar say exam.tar well the problem is, when i read the tar file i dont find any metadata about the directories,as you cannot create a tar containig empty directories. on the... (2 Replies)
Discussion started by: Tanvirk
2 Replies

2. Shell Programming and Scripting

Renaming all header to specific header pattern

Input #HAC0253 EFVHIJHIJEFVTHIJOPKOPKTEFVEFVEFVOPKHIJOPKOPKHIJTTEFVEFVTEFV #BASFS12 EFVEFVHIJEFVEFVTOPKEFVOPKTHIJTTHIJOPK #ACG5115 TEFVEFVOIJEFVHIJHIJOPKOPKHIJHIJTTEFVEFVOPKTTEFVEFVOPKHIJOPKOPKOPK #ECG5114 IJTOPKHIJEFVOEFVEFVOPKTTEFVEFVOPKHIJOPKOPKOPK . . Output (5 Replies)
Discussion started by: patrick87
5 Replies

3. UNIX for Dummies Questions & Answers

Merge all csv files in one folder considering only 1 header row and ignoring header of all others

Friends, I need help with the following in UNIX. Merge all csv files in one folder considering only 1 header row and ignoring header of all other files. FYI - All files are in same format and contains same headers. Thank you (4 Replies)
Discussion started by: Shiny_Roy
4 Replies

4. Shell Programming and Scripting

Add column header and row header

Hi, I have an input like this 1 2 3 4 2 3 4 5 4 5 6 7 I would like to count the no. of columns and print a header with a prefix "Col". I would also like to count the no. of rows and print as first column with each line number with a prefix "Row" So, my output would be ... (2 Replies)
Discussion started by: jacobs.smith
2 Replies

5. Shell Programming and Scripting

Manipulate all rows except header, but header should be output as well

Hello There... I have a sample input file .. number:department:amount 125:Market:125.23 126:Hardware store:434.95 127:Video store:7.45 128:Book store:14.32 129:Gasolline:16.10 I will be doing some manipulations on all the records except the header, but the header should always be... (2 Replies)
Discussion started by: juzz4fun
2 Replies

6. Shell Programming and Scripting

Shorten header of protein sequences in fasta file

I have a fasta file as follows >sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM KGVTSTRVYERA >sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Discussion started by: alexypaul
3 Replies

7. Shell Programming and Scripting

Help with reformat single-line multi-fasta into multi-line multi-fasta

Input File: >Seq1 ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD >Seq2 SDASDAQEQWEQeqAdfaasd >Seq3 ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG ...... Desired Output File >Seq1 ASDADAFASF ASFADGSDGF SDFSDFSDFS DFSDFSDFSD FSDFSDFSDF SD >Seq2 (4 Replies)
Discussion started by: patrick87
4 Replies

8. Shell Programming and Scripting

Find header in a text file and prepend it to all lines until another header is found

I've been struggling with this one for quite a while and cannot seem to find a solution for this find/replace scenario. Perhaps I'm getting rusty. I have a file that contains a number of metrics (exactly 3 fields per line) from a few appliances that are collected in parallel. To identify the... (3 Replies)
Discussion started by: verdepollo
3 Replies

9. Shell Programming and Scripting

Shorten header of protein sequences in fasta file to only organism name

I have a fasta file as follows >sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3 MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Discussion started by: jerrild
3 Replies
FLIPDIFF(1)							     Man pages							       FLIPDIFF(1)

NAME
flipdiff - exchange the order of two incremental patches SYNOPSIS
flipdiff [[-p n] | [--strip-match=n]] [[-U n] | [--unified=n]] [[-d PAT] | [--drop-context=PAT]] [[-q] | [--quiet]] [[-z] | [--decompress]] [[-b] | [--ignore-space-change]] [[-B] | [--ignore-blank-lines]] [[-i] | [--ignore-case]] [[-w] | [--ignore-all-space]] [--in-place] diff1 diff2 flipdiff {[--help] | [--version]} DESCRIPTION
flipdiff exchanges the order of two patch files that apply one after the other. The patches must be "clean": the context lines must match and there should be no mis-matched offsets. The swapped patches are sent to standard output, with a marker line ("=== 8< === cut here === 8< ===") between them, unless the --in-place option is passed. In that case, the output is written back to the original input files. OPTIONS
-p n, --strip-match=n When comparing filenames, ignore the first n pathname components from both patches. (This is similar to the -p option to GNU patch(1).) -q, --quiet Quieter output. Don't emit rationale lines at the beginning of each patch. -U n, --unified=n Attempt to display n lines of context (requires at least n lines of context in both input files). (This is similar to the -U option to GNU diff(1).) -d pattern, --drop-context=PATTERN Don't display any context on files that match the shell wildcard pattern. This option can be given multiple times. Note that the interpretation of the shell wildcard pattern does not count slash characters or periods as special (in other words, no flags are given to fnmatch). This is so that "*/basename"-type patterns can be given without limiting the number of pathname components. -i, --ignore-case Consider upper- and lower-case to be the same. -w, --ignore-all-space Ignore whitespace changes in patches. -b, --ignore-space-change Ignore changes in the amount of whitespace. -B, --ignore-blank-lines Ignore changes whose lines are all blank. -z, --decompress Decompress files with extensions .gz and .bz2. --in-place Write output to the original input files. --help Display a short usage message. --version Display the version number of flipdiff. LIMITATIONS
This is only been very lightly tested, and may not even work. Using --in-place is not recommended at the moment. There are some cases in which it is not possible to meaningfully flip patches without understanding the semantics of the content. This program only uses complete lines that appear at some stage during the application of the two patches, and never composes a line from parts. Because of this, it is generally a good idea to read through the output to check that it makes sense. AUTHOR
Tim Waugh <twaugh@redhat.com> Package maintainer patchutils 23 January 2009 FLIPDIFF(1)
All times are GMT -4. The time now is 10:54 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy