12-30-2013
Shell script for changing the accession number of DNA sequences in a FASTA file
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 "mydesired_name_45" replacing serially 46,47, 48 with my desired name as static next to each of the > symbol.
kindly help me with the script
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NEW(1) [nmh-1.5] NEW(1)
NAME
new - report on folders with new messages
fnext - set current folder to next folder with new messages
fprev - set current folder to previous folder with new messages
unseen - scan new messages in all folders with new messages
SYNOPSIS
new [sequences] [-mode mode] [-folders foldersfile] [-version] [-help]
fnext is equivalent to new -mode fnext
fprev is equivalent to new -mode fprev
unseen is equivalent to new -mode unseen
DESCRIPTION
New in its default mode produces a one-line-per-folder listing of all folders containing messages in the listed sequences or in the
sequences listed in the profile entry "Unseen-Sequence". Each line contains the folder, the number of messages in the desired sequences,
and the message lists from the .mh_sequences file. For example:
foo 11.* 40-50
bar 380. 760-772 824-828
total 391.
The `*' on foo indicates that it is the current folder. The last line shows the total number of messages in the desired sequences.
New crawls the folder hierarchy recursively to find all folders, and prints them in lexicographic order. Override this behavior by provid-
ing foldersfile containing the pre-sorted list of folders new should check, one per line.
In fnext and fprev modes, new instead changes to the next or previous matching folder, respectively.
In unseen mode, new executes scan sequences for each matching folder.
FILES
$HOME/.mh_profile The user profile
PROFILE COMPONENTS
Path: To determine the user's nmh directory
Current-Folder: To find the default current folder
Unseen-Sequence: The name of the unseen message sequence
SEE ALSO
scan(1), mh-format(5)
HISTORY
Based on Luke Mewburn's new (http://www.mewburn.net/luke/src/new).
MH.6.8 11 June 2012 NEW(1)