Sponsored Content
Top Forums Shell Programming and Scripting Help with reformat single-line multi-fasta into multi-line multi-fasta Post 303018743 by patrick87 on Thursday 14th of June 2018 04:45:44 AM
Old 06-14-2018
Hi RudiC,

It seems like no work when my data is huge?
eg.
Input file
Code:
cat input_file
>scaffold1|size134247
TCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Output file
Code:
fold -b50 input_file
>scaffold1|size134247
TCTCTGTCTCTCTCTCTCTCTCTCTCTC
TCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Desired Output file
Code:
>scaffold1|size134247
TCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTG
TGTGTGTGTGTGTGTGTGTGTGTGTGTG

I believe fold command will take header into account too?
I wanna split a single-line multi-fasta (exclude >header) into 10 words/symbols per line multi-fasta file.

Thanks for any advice.
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Merge multi-lines into one single line

Hi, Can anyone help me for merge the following multi-line log which beginning with a number and time: into one line. For each line need to delete the return and add a space. Please see the red color line. *****Original Log*****... (4 Replies)
Discussion started by: happyday
4 Replies

2. Shell Programming and Scripting

How to use Perl to merge multi-line into single line

Hi, Can anyone know how to use perl to merge the following multi-line information which beginning with "BAM" into one line. For each line need to delete the return and add a space. Please see the red color line. ******Org. Multi-line) BAM admin 101.203.57.22 ... (3 Replies)
Discussion started by: happyday
3 Replies

3. Shell Programming and Scripting

Help on Merge multi-lines into one single line

Hello, Can anyone let me know how to use Perl script to Merge following multi-lines into one single line... ***** Multi-line***** FILE_Write root OK Tue Jul 01 00:00:00 2008 cl_get_path file descriptor = 1 FILE_Write root OK ... (5 Replies)
Discussion started by: happyday
5 Replies

4. Shell Programming and Scripting

How to use Perl to join multi-line into single line

Hello, Did anyone know how to write a perl script to merge the multi-line into a single line where each line with start at timestamp Input--> timestamp=2009-11-10-04.55.20.829347; a; b; c; timestamp=2009-11-10-04.55.20.829347; aa; bb; cc; (5 Replies)
Discussion started by: happyday
5 Replies

5. Shell Programming and Scripting

Merge multi-line output into a single line

Hello I did do a search and the past threads doesn't really solve my issue. (using various awk commands) I need to combine the output from java -version into 1 line, but I am having difficulties. When you exec java -version, you get: java version "1.5.0_06" Java(TM) 2 Runtime... (5 Replies)
Discussion started by: flagman5
5 Replies

6. Shell Programming and Scripting

Multi lines to single line

HI, My input file contains the data as like below: A1234119993 B6271113 Bghjkjk A1234119992 B6271113hi Bghjkjkmkl the output i require is : A1234119993 B6271113 Bghjkjk A1234119992 B6271113hi Bghjkjkmkl Please help me in this. Thanks (6 Replies)
Discussion started by: pandeesh
6 Replies

7. Shell Programming and Scripting

Joining multi-line output to a single line in a group

Hi, My Oracle query is returing below o/p ---------------------------------------------------------- Ins trnas value a lkp1 x a lkp1 y b lkp1 a b lkp2 x b lkp2 y ... (7 Replies)
Discussion started by: gvk25
7 Replies

8. Shell Programming and Scripting

Multi-line filtering based on multi-line pattern in a file

I have a file with data records separated by multiple equals signs, as below. ========== RECORD 1 ========== RECORD 2 DATA LINE ========== RECORD 3 ========== RECORD 4 DATA LINE ========== RECORD 5 DATA LINE ========== I need to filter out all data from this file where the... (2 Replies)
Discussion started by: Finja
2 Replies

9. UNIX for Dummies Questions & Answers

Remove multi line and single line comments

Hi, I am trying to remove multi line and single line comments like examples below I have tried this pattern. it works fine for single line comments and multi line comments in a single line only. but this fails when the comments are extended in multiple lines as shown in the comment 2 of... (3 Replies)
Discussion started by: ahmedwaseem2000
3 Replies

10. Shell Programming and Scripting

Multi line log files to single line format

I want to read the log file which was generate from other command . And the output was having multi line in log files for job name and server name. But i need to make all the logs on one line Source file 07/15/2018 17:02:00 TRANSLOG_1700 Server0005_SQL ... (2 Replies)
Discussion started by: ranjancom2000
2 Replies
LIPO(1) 						      General Commands Manual							   LIPO(1)

NAME
lipo - create or operate on fat files SYNOPSIS
lipo [-info] [-detailed_info] [-arch arch_type input_file] ... [ input_file] ... [-create] [-thin arch_type] [-replace arch_type file- name] ... [-remove arch_type] ... [-extract arch_type] ... [-extract_family arch_type] ... [-output output_file] [-segalign arch_type value] ... DESCRIPTION
The lipo command creates or operates on ``fat'' (multi-architecture) files. It only ever produces one output file, and never alters the input file. The operations that lipo performs are: listing the architecture types in a fat file; creating a single fat file from one or more input files; thinning out a single fat file to one specified architecture type; and extracting, replacing, and/or removing architec- tures types from the input file to create a single new fat output file. Only one option can be specified, with the exception of -arch, -output, and -segalign, which are used in combination with other options. The input_file argument is required, and only the -create option allows more than one input_file to be specified. The -output flag must be used, except with the -info and -detailed_info flags. The arch_type arguments may be any of the supported architecture names listed in the man page arch(3)exceptforVAXandMips. OPTIONS
-info Briefly list the architecture types in the input fat file (just the names of each architecture). -detailed_info Display a detailed list of the architecture types in the input fat file (all the the information in the fat header, for each archi- tecture in the file). -arch arch_type input_file Tells lipo that input_file contains the specified architecture type. The -arch arch_type specification is unnecessary if input_file is an object file, a fat file, or some other file whose architecture(s) lipo can figure out. -output output_file Specifies its argument to be the output file. -create Take the input files (or file) and create one fat output file from them. -thin arch_type Take one input file and create a thin output file with the specified arch_type. -replace arch_type file_name Take one fat input file; in the output file, replace the arch_type contents of the input file with the contents of the specified file_name. -remove arch_type Take one fat input file and remove the arch_type from that fat file, placing the result in the output file. -extract arch_type Take one fat input file and copy the arch_type from that fat file into a fat output file containing only that architecture. -extract_family arch_type Take one fat input file and copy all of the arch_types for the family that arch_type is in from that fat file into an output file containing only those architectures. The file will be thin if only one architecture is found or fat otherwise. -segalign arch_type value Set the segment alignment of the specified arch_type when creating a fat file containing that architecture. value is a hexadecimal number that must be an integral power of 2. This is only needed when lipo can't figure out the alignment of an input file (cur- rently not an object file), or when it guesses at the alignment too conservatively. The default for files unknown to lipo is 0 (2^0, or an alignment of one byte), and the default alignment for archives is 4 (2^2, or 4-byte alignment). SEE ALSO
arch(3) Apple Computer, Inc. October 23, 1997 LIPO(1)
All times are GMT -4. The time now is 03:00 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy