I have a text file, input.fasta contains some protein sequences. input.fasta is shown below.
I would like to extract the parts of the above sequences based on another file ids.txt . It is shown below.
For example, From the sequence P02649, I need to extract the positions from 3rd character to 23rd character. The output would be
I tried the following python code.
Hi,
I want to extract a part of filename and pass it as a parameter to one of the scripts. Could someone help.
File name:-
NLL_NAM_XXXXX.XXXXXXX_1_1.txt.
Here i have to extract only XXXXX.XXXXXXX and the position will be constant. that means that i have to extract some n characters from... (6 Replies)
Hi there,
I'm having some problem with UNIX scripting (ksh), perhaps somebody can help me out?
For example:
------------
Sample content of my log file (text file):
--------------------------------------
File1: ....
info_1 ...
info_2 ...
info_3 ...
File2: ....
info_1 ...
info_2 ...... (10 Replies)
I need to extract the following lines from this text and put it in different files.
From xxxx@gmail.com Thu Jun 10 21:15:46 2010
Return-Path: <xxxxx@gmail.com>
X-Original-To: xxx@localhost
Delivered-To:xxxx@localhost
Received: from ubuntu (localhost )
by ubuntu (Postfix) with ESMTP... (11 Replies)
Hi,
I have a file with more than 28000 records and it looks like below..
>mm10_refflat_ABCD range=chr1:1234567-2345678
tgtgcacactacacatgactagtacatgactagac....so on
>mm10_refflat_BCD range=chr1:3234567-4545678...
tgtgcacactacacatgactagtatgtgcacactacacatgactagta
.
.
.
.
.
so on
... (2 Replies)
I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
Hello All,
I need to extract part of a file into a new file
My file is
Define schema xxxxxx
Insert into table
(
a
,b
,c
,d
)
values
(
1,
2,
3, (15 Replies)
Hello to all,
I would like to search sequences of bytes inside big binary file.
The bin file contains blocks of information, each block begins is estructured as follow:
1- Each block begins with the hex 32 (1 byte) and ends with FF. After the FF of the last block, it follows 33.
2- Next... (59 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 need to save part of a file to a different one, start and end offset bytes are provided by two counters in long format. If the difference is big, how should I do it to prevent buffer overflow in java? (7 Replies)
I have a variable and assigned the following values
***XYZ_201519_20150929140642_20150929140644_211_0_0_211
I need to read this variable from backward and stop read when I get first underscore (_)
In this scenario I should get 211
Thanks
Kris (3 Replies)
Discussion started by: mkris
3 Replies
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viewperl
VIEWPERL(1) User Commands VIEWPERL(1)NAME
viewperl - quickly view syntax highlighted Perl code
SYNOPSIS
viewperl [OPTION]... FILE...
DESCRIPTION
View a Perl source code file, syntax highlighted.
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hide POD documentation (line numbers still increment)
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reset formatting and line numbers each file (default)
-R, --no-reset
supress resetting of formatting and line numbers
-s, --shift=WIDTH
set tab width (default is 4)
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translate tabs into spaces (default)
-T, --no-tabs
supress translating of tabs into spaces
--help display this help and exit
Note that module names should be given as they would appear after a Perl `use' or `require' statement. `Getopt::Long', for example.
Each string given using -c is considered a different file, so line number and formatting resets will apply.
View a Perl source code file, syntax highlighted.
-c, --code=CODE
view CODE, syntax highlighted
-l, --lines
display line numbers
-L, --no-lines
supress display of line numbers (default)
-m, --module=FILE
consider FILE the name of a module, not a file name
-n, --name
display the name of each file (default)
-N, --no-name
supress display of file names (implied by --no-reset)
-p, --pod
display inline POD documentation (default)
-P, --no-pod
hide POD documentation (line numbers still increment)
-r, --reset
reset formatting and line numbers each file (default)
-R, --no-reset
supress resetting of formatting and line numbers
-s, --shift=WIDTH
set tab width (default is 4)
-t, --tabs
translate tabs into spaces (default)
-T, --no-tabs
supress translating of tabs into spaces
--help display this help and exit
Note that module names should be given as they would appear after a Perl `use' or `require' statement. `Getopt::Long', for example.
Each string given using -c is considered a different file, so line number and formatting resets will apply.
viewperl August 2007 VIEWPERL(1)