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
pynast
VERSION:(1) User Commands VERSION:(1)NAME
PyNAST - alignment of short DNA sequences
SYNOPSIS
pynast [options] {-i input_fp -t template_fp}
DESCRIPTION
[] indicates optional input (order unimportant) {} indicates required input (order unimportant)
Example usage:
pynast -i my_input.fasta -t my_template.fasta
OPTIONS --version
show program's version number and exit
-h, --help
show this help message and exit
-t TEMPLATE_FP, --template_fp=TEMPLATE_FP
path to template alignment file [REQUIRED]
-i INPUT_FP, --input_fp=INPUT_FP
path to input fasta file [REQUIRED]
-v, --verbose
Print status and other information during execution [default: False]
-p MIN_PCT_ID, --min_pct_id=MIN_PCT_ID
minimum percent sequence identity to consider a sequence a match [default: 75.0]
-l MIN_LEN, --min_len=MIN_LEN
minimum sequence length to include in NAST alignment [default: 1000]
-m PAIRWISE_ALIGNMENT_METHOD, --pairwise_alignment_method=PAIRWISE_ALIGNMENT_METHOD
method for performing pairwise alignment [default: uclust]
-a FASTA_OUT_FP, --fasta_out_fp=FASTA_OUT_FP
path to store resulting alignment file [default: derived from input filepath]
-g LOG_FP, --log_fp=LOG_FP
path to store log file [default: derived from input filepath]
-f FAILURE_FP, --failure_fp=FAILURE_FP
path to store file of seqs which fail to align [default: derived from input filepath]
-e MAX_E_VALUE, --max_e_value=MAX_E_VALUE
Depreciated. Will be removed in PyNAST 1.2
-d BLAST_DB, --blast_db=BLAST_DB
Depreciated. Will be removed in PyNAST 1.2
SEE ALSO
http://pynast.sourceforge.net
Version: pynast 1.1 August 2011 VERSION:(1)