Hi all,
I need to replace automatically all special characters of one filename with some corresponding characters
For example >
ö --> oe
ä --> ae
....
If the special character comes more than one time, then all the coccuerences have to be replaced.
I would like to have a... (6 Replies)
Hello,
I have some files in a directory like:
01_07_2010_aa.txt
01_07_2010_bb.txt
01_07_2010_cc.txt
01_07_2010_dd.txt
01_07_2010_ee.txt
01_07_2010_ff.txt
I want to change their names to :
3nm_aa.txt
3nm_bb.txt
3nm_cc.txt
3nm_dd.txt
3nm_ee.txt
3nm_ff.txt (8 Replies)
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)
Hi is it possible to change multiple files (~10k) names with out disturbing the data in it. ?
input
Hynda|cgr10(+):100027702-1000312480|.txt
Hynda|cgr10(+):100027702-1000312483|.txt
Hynda|cgr10(+):100027702-1000312484|.txt
Hynda|cgr10(+):100027702-1000312482|.txt
output... (4 Replies)
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)
Hi,
How can I change following file name in a bash script?
From file names: myfile-module-1.0-3.0.el6.x86_64.package
To file names: myfile-module1_0-1.0-3.0.el6.x86_64.package
^ ^ ^ ^ ^ ^ ^ ^
Basically, the digit 1.0 is a version number, the digit 3.0 is... (11 Replies)
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)
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)
I have a landing directory on my unix (solaris) server, that receives the following files:
MLH4301I AAOT-hhslog.610.20150805.txt
MLH4301I AAOT-hhslog.611.20150805.txt
MLH4301I AAOT-hhslog.612.20150805.txt
MLH4301I AAOT-hhslog.613.20150805.txt
and I need to add to this files the number 10000... (6 Replies)
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
LEARN ABOUT DEBIAN
cdhit
CD-HIT(1) User Commands CD-HIT(1)NAME
cdhit - quickly group sequences
SYNOPSIS
cdhit [Options]
DESCRIPTION
====== CD-HIT version 4.6 (built on Apr 26 2012) ======
Options
-i input filename in fasta format, required
-o output filename, required
-c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical
amino acids in alignment divided by the full length of the shorter sequence
-G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino
acids in alignment divided by the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see
options -aL, -AL, -aS, -AS
-b band_width of alignment, default 20
-M memory limit (in MB) for the program, default 800; 0 for unlimitted;
-T number of threads, default 1; with 0, all CPUs will be used
-n word_length, default 5, see user's guide for choosing it
-l length of throw_away_sequences, default 10
-t tolerance for redundance, default 2
-d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space
-s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of
the cluster
-S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the
representative of the cluster can not be bigger than 60
-aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences
-uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing
gaps) must not be more than 10% of the sequence
-uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tail-
ing gaps) must not be more than 10% of the sequence
-U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more
than 10 bases
-B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use
-B 1 for huge databases
-p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
-g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast clus-
ter). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but
either 1 or 0 won't change the representatives of final clusters
-bak write backup cluster file (1 or 0, default 0)
-h print this help
Questions, bugs, contact Limin Fu at l2fu@ucsd.edu, or Weizhong Li at liwz@sdsc.edu For updated versions and information, please
visit: http://cd-hit.org
cd-hit web server is also available from http://cd-hit.org
If you find cd-hit useful, please kindly cite:
"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam
Godzik. Bioinformatics, (2001) 17:282-283 "Tolerating some redundancy significantly speeds up clustering of large protein data-
bases", Weizhong Li, Lukasz Jaroszewski & Adam Godzik. Bioinformatics, (2002) 18:77-82
cd-hit 4.6-2012-04-25 April 2012 CD-HIT(1)