03-10-2014
Post example input and example output of what you want.
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Please advice how can we search for a string say (abc) in multiple files and to get total occurrence of that searched string. (Need number of records that exits in period of time).
File look like this (read as filename.yyyymmdd)
a.20100101
b.20100108
c.20100115
d.20100122
e.20100129... (2 Replies)
Discussion started by: zooby
2 Replies
2. Shell Programming and Scripting
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
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
Discussion started by: Ann Mc Cartney
1 Replies
4. UNIX for Dummies Questions & Answers
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
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
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
7. Shell Programming and Scripting
Hi,
I want to search only duplicate sequence number in file e.g
4757610
4757610
should display only duplicate sequence number in file.
file contain is:
4757610 6zE:EXPNL ORDER_PRIORITY='30600022004757610' ORDER_IDENTIFIER='4257771056' MM_ASK_VOLUME='273' MM_ASK_PRICE='1033.0000' m='GBX'... (5 Replies)
Discussion started by: ashfaque
5 Replies
8. Shell Programming and Scripting
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
Discussion started by: Ibk
3 Replies
9. UNIX for Beginners Questions & Answers
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
Discussion started by: dineshkumarsrk
14 Replies
10. UNIX for Beginners Questions & Answers
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
FLAME(1) General Commands Manual FLAME(1)
NAME
flame -- reply to Usenet News posting automatically
SYNOPSIS
flame [options] [filename]
DESCRIPTION
Flame is a AI tool providing an automated method for replying to articles posted to Usenet News. Special care is paid to allow the user to
specify the type of reply he desires. The following options are supported by flame:
-- Take input from stdin.
-x regexp
Crosspost to all newsgroups matching regexp.
-n number
Post this reply number times.
-b Reply in BIFF MODE.
-d Delay response until original posting expires.
-m Misdirect to a random Author.
-r ROT13 quotes from original posting.
-g regexp
Reply to all messages in newsgroups matching regexp.
-A Call the Author Assh*le in 12 languages.
-B Bait the Author.
-C Accuse the Author of communist leanings.
-D Denigrate the Author.
-E Picks apart the Author's educational background.
-F Accuse the Author of fascist leanings.
-G Post using Greek insult module.
-H Accuse the Author of homophobic leanings.
-I Question the Author's intelligence.
-J Accuse the Author of purchasing Japanese imports.
-K Accuse the Author of working for the KGB, MOSSAD, CIA, or MI5 as appropriate.
-L Post using Latin insult module.
-M Insult the Author's mother.
-N Accuse the Author of Neo-Nazi leanings.
-O Quote obscure references proving falsehood of the posting.
-P Question the Author's parentage.
-Q Accuse the Author of deviant sexual practices.
-R Accuse the Author of racist leaning.
-S Accuse the Author of sexist leanings.
-T Accuse the Author of cross dressing.
-U State that the Author just doesn't understand anything.
-V Pretend sympathy for Author's virgin sensibilities.
-W Accuse the Author of voting for George Bush.
-X Prepend obscene adjectives wherever syntactically correct.
-Y Accuse the Author of PLO membership.
-Z Accuse the Author of Zionist leanings.
ENVIRONMENT
The environment variable FLAME_TYPE can be set to any combination of the above parameters, and will be used as the default flame type to
generate.
The environment variable OBSCENE points to a file containing miscellaneous obscene adjectives for the -X option above.
MACROS
Macro Support will be added to the next release of flame.
AUTHOR
Unknown
FILES
.lastflame
This file contains the number of the last article flamed. Used when flameing an entire newsgroup.
.prefflame
This file contains the user's preferred flames.
.altflame
This file contains alternate phrasing of some of the more standard flames. Used to keep the program from flaming itself.
SEE ALSO
rn(1), more(1), newsrc(5), readnews(1), Pnews(1), Rnmail(1)
DIAGNOSTICS
Self Documenting.
BUGS
Occasionally, flame will turn on the user, and flame all outgoing postings. When this happens, the best thing to do reinstall your news
software and flame.
FLAME(1)