Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to find a specific sequence pattern in a fasta file? Post 303041622 by Scrutinizer on Friday 29th of November 2019 01:38:20 PM
Old 11-29-2019
Can it occur only once per sequence? If not what should happen with multiple matches per sequence?
 

9 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

cmd sequence to find & cut out a specific string

A developer of mine has this requirement - I couldn't tell her quickly how to do it with UNIX commands or a quick script so she's writing a quick program to do it - but that got my curiousity up and thought I'd ask here for advice. In a text file, there are some records (about half of them)... (4 Replies)
Discussion started by: LisaS
4 Replies

2. Shell Programming and Scripting

Parsing a fasta sequence with start and end coordinates

Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this? For Example Chr 1 is in following format I need regions from 2 - 10 should give me AATTCCAAA and in a similar way 15- 25 should give... (8 Replies)
Discussion started by: empyrean
8 Replies

3. UNIX for Dummies Questions & Answers

Find & Replace command - Fasta file

Hi all ! I have a fasta file that looks like that: >Sequence1 RTYIPLCASQHKLCPITFLAVK (it's just an example, obviously in reality I have several pairs of lines like that) Using UNIX command(s), would it be possible to replace all the characters except the "C" of the second line only by... (7 Replies)
Discussion started by: Cevin21
7 Replies

4. 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

5. 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

6. Shell Programming and Scripting

How to find a file with a specific pattern for current sysdate & upon find email the details?

I need assistance with following requirement, I am new to Unix. I want to do the following task but stuck with file creation date(sysdate) Following is the requirement I need to create a script that will read the abc/xyz/klm folder and look for *.err files for that day’s date and then send an... (4 Replies)
Discussion started by: PreetArul
4 Replies

7. 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

8. 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

9. Shell Programming and Scripting

Extract specific line in an html file starting and ending with specific pattern to a text file

Hi This is my first post and I'm just a beginner. So please be nice to me. I have a couple of html files where a pattern beginning with "http://www.site.com" and ending with "/resource.dat" is present on every 241st line. How do I extract this to a new text file? I have tried sed -n 241,241p... (13 Replies)
Discussion started by: dejavo
13 Replies
FLIST(1)                                                             [nmh-1.5]                                                            FLIST(1)

NAME
flist, flists - list the number of messages in given sequence(s) SYNOPSIS
flist [+folder1 [+folder2 ...]] [-sequence name1 [-sequence name2 ...]] [-all | -noall] [-showzero | -noshowzero] [-recurse | -norecurse] [-fast | -nofast] [-alpha | -noalpha] [-version] [-help] flists is equivalent to flist -all DESCRIPTION
Flist is used to search a list of folders and display the number of messages in these folders that are in a given sequence or set of sequences (for example the "unseen" sequence). This is especially useful if you use some mechanism such as slocal or procmail (typically in conjunction with rcvstore) to pre-sort your mail into different folders before you view it. By default, the command flist will search the current folder for the given sequence or sequences (usually "unseen"). If (possibly multi- ple) folders are specified on the command line with +folder, then all these folders are searched for the given sequence(s). Flist will display for each folder searched, the number of messages in each of the specified sequences, and the total number of messages. The option -sequence is used to specify the name of a sequence in which to search for. This option may be used multiple times to specify multiple sequences. If this is not given, then the default is to search for all the sequences specified by the "Unseen-Sequence" profile component. For more details about sequences, read the mh-sequence(5) man page. Typically, flist will produce a line for each sequence, for every folder that is searched, even those which do not contain any messages in the given sequence. Specifying -noshowzero will cause flist to print only those folder/sequence combinations such the folder has a non- zero number of messages in the given specified sequence. If -recurse is given, then for each folder that is search, flist will also recursively descend into those folders to search subfolders for the given sequence. If -fast is given, only the names of the folders searched will be displayed, and flist will suppress all other output. If this option is used in conjunction with -noshowzero, then flist will only print the names of those folders searched that contain messages in in at least one of the specified sequences. Multiple Folders If the option -all is given (and no folders are specified with +folder), then flist will search all the folders in the top level of the users nmh directory. These folders are all preceded by the read-only folders, which occur as "atr-cur-" entries in the user's nmh context. An example of the output of flist -all is: /work/Mail has 5 in sequence unseen (private); out of 46 inbox+ has 10 in sequence unseen ; out of 153 junklist has 0 in sequence unseen ; out of 63 postmaster has 1 in sequence unseen ; out of 3 The "+" after inbox indicates that it is the current folder. The "private" flag indicates that the given sequence for that folder is private. See the mh-sequence(5) man page for details about private sequences. If the option -all and +folder are both specified, then flist will search this folder, and all its first level subfolders for the given sequence. You may specify multiple folders in this way. If flist is invoked by a name ending with "s" (e.g. flists), then the switch -all is assumed by default. The sorting order for the listing is alphabetical (with -alpha), or in a priority order defined by the "Flist-Order" profile entry (with -noalpha). Each item in the "Flist-Order" is a folder name or a folder name pattern that uses * to match zero or more characters. Longer matching patterns have precedence over shorter matching patterns. For example: Flist-Order: personal petproject mh* * admin *junk This order puts a few interesting folders first, such as those with mail addressed to you personally, those about a pet project, and those about mh-related things. It places uninteresting folders at the end, and it puts everything else in the middle in alphabetical order. FILES
$HOME/.mh_profile The user profile PROFILE COMPONENTS
Path: To determine the user's nmh directory mh-sequences: File that contains public sequences Unseen-Sequence: The name of the unseen message sequence Flist-Order: To sort folders by priority SEE ALSO
folder(1), rcvstore(1), slocal(1), mh-sequence(5) DEFAULTS
`-sequence' defaults to Unseen-Sequence profile entry `-showzero' `-noall' `-norecurse' `-noalpha' `-nofast' CONTEXT
If +folder is given, it will become the current folder. If multiple folders are given, the last one specified will become the current folder. MH.6.8 11 June 2012 FLIST(1)
All times are GMT -4. The time now is 02:03 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy