Hopefully someone here can point me in the correct direction.
I'm working on a username migration and am trying to map my users ols usernames to the new ones.
Right now every user has a username of firstname.lastname i.e. john.doe
I'm trying to create a bash or python script that will take... (3 Replies)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Hi,
I need some help with modifying fasta headers.
I have a fasta file with thousands of contigs and I need to modify their headers with the information obtained from a second file.
File 1 contains the fasta sequences:
>contig0001 length=11115 numreads=10777
agatgtagatctct... (6 Replies)
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)
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)
I've been struggling with this one for quite a while and cannot seem to find a solution for this find/replace scenario. Perhaps I'm getting rusty.
I have a file that contains a number of metrics (exactly 3 fields per line) from a few appliances that are collected in parallel. To identify the... (3 Replies)
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT DEBIAN
colors
COLORS(3) libbash colors Library Manual COLORS(3)NAME
colors -- libbash library for setting tty colors.
SYNOPSIS
colorSet <color>
colorReset
colorPrint [<indent>] <color> <text>
colorPrintN [<indent>] <color> <text>
DESCRIPTION
General
colors is a collection of functions that make it very easy to put colored text on tty.
The function list:
colorSet Sets the color of the prints to the tty to COLOR
colorReset Resets current tty color back to normal
colorPrint Prints TEXT in the color COLOR indented by INDENT (without adding a newline)
colorPrintN The same as colorPrint, but trailing newline is added
Detailed interface description follows.
Available colors:
Green
Red
Yellow
White
The color parameter is non-case-sensitive (i.e. RED, red, ReD, and all the other forms are valid and are the same as Red).
FUNCTIONS DESCRIPTIONS
colorSet <color>
Sets the current printing color to color.
colorReset
Resets current tty color back to normal.
colorPrint [<indent>] <color>
Prints text using the color color indented by indent (without adding a newline).
Parameters:
<indent>
The column to move to before start printing. This parameter is optional. If ommitted - start output from current cursor position.
<color>
The color to use.
<color>
The text to print.
colorPrintN [<indent>] <color>
The same as colorPrint, except a trailing newline is added.
EXAMPLES
Printing a green 'Hello World' with a newline:
Using colorSet:
$ colorSet green
$ echo 'Hello World'
$ colorReset
Using colorPrint:
$ colorPrint 'Hello World'; echo
Using colorPrintN:
$ colorPrintN 'Hello World'
AUTHORS
Hai Zaar <haizaar@haizaar.com>
Gil Ran <gil@ran4.net>
SEE ALSO ldbash(1), libbash(1)Linux Epoch Linux