Sponsored Content
Top Forums Shell Programming and Scripting Extraction of upstream and downstream regions from long sequence file Post 302951621 by Don Cragun on Saturday 8th of August 2015 02:44:11 AM
Old 08-08-2015
In addition to what Scrutinizer already said, note that the script and both of the input data files must be in UNIX text file format (with a single <newline> character as the line terminator); not Windows format (with <carriage-return> <newline> characters pairs as the line terminator); and not text produced by some text formatting tool like Microsoft word.
 

10 More Discussions You Might Find Interesting

1. Programming

selecting rows with specific IDs for downstream analysis

Hi, I'm working hard on SQL and I came across a hurdle I'm hoping you can help me out with. I have two tables table1 headers: chrom start end name score strand 11 9720685 9720721 U0 0 + 21 9721043 9721079 U0 0 - 1 9721093 9721129 U0 0 + 20 ... (2 Replies)
Discussion started by: labrazil
2 Replies

2. Shell Programming and Scripting

awk: union regions

Hi all, I have difficulty to solve the followign problem. mydata: StartPoint EndPoint 22 55 2222 2230 33 66 44 58 222 240 11 25 22 60 33 45 The union of above... (2 Replies)
Discussion started by: phoeberunner
2 Replies

3. UNIX for Dummies Questions & Answers

fast sequence extraction

Hi everyone, I have a large text file containing DNA sequences in fasta format as follows: >someseq GAACTTGAGATCCGGGGAGCAGTGGATCTC CACCAGCGGCCAGAACTGGTGCACCTCCAG GCCAGCCTCGTCCTGCGTGTC >another seq GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT GACATTTTCATTACTACCATTTTGGAGTACA >seq3450... (4 Replies)
Discussion started by: Fahmida
4 Replies

4. UNIX for Dummies Questions & Answers

extract regions of file based on start and end position

Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2. Based on a post elsewhere, I found the code: awk... (2 Replies)
Discussion started by: pathunkathunk
2 Replies

5. Shell Programming and Scripting

find common entries and match the number with long sequence and cut that sequence in output

Hi all, I have a file like this ID 3BP5L_HUMAN Reviewed; 393 AA. AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3; DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot. DT 05-JUL-2004, sequence version 1. DT 05-SEP-2012, entry version 71. FT COILED 59 140 ... (1 Reply)
Discussion started by: manigrover
1 Replies

6. Shell Programming and Scripting

FILE_ID extraction from file name and save it in CSV file after looping through each folders

FILE_ID extraction from file name and save it in CSV file after looping through each folders My files are located in UNIX Server, i want to extract file_id and file_name from each file .and save it in a CSV file. How do I do that? I have folders in unix environment, directory structure is... (15 Replies)
Discussion started by: princetd001
15 Replies

7. Shell Programming and Scripting

Obtain the names of the flanking regions

Hi I have 2 files; usually the end position in the file1 is the start position in the file2 and the end position in file2 will be the start position in file1 (flanks) file1 Id start end aaa1 0 3000070 aaa1 3095270 3095341 aaa1 3100822 3100894 aaa1 ... (1 Reply)
Discussion started by: anurupa777
1 Replies

8. IP Networking

Newbie BIND DNS question: resolving upstream hosts?

Old skool UNIX and Linux geek here, but newbie to the world of DNS and bind. I've recently been tasked with replacing our DNS infrastructure, currently on Windows, with a RHEL based solution. And I assume that means using bind, which I've not used before. Here's my question: Suppose our company... (3 Replies)
Discussion started by: lupin..the..3rd
3 Replies

9. Shell Programming and Scripting

Parsing and masking regions from a single fasta file with subsequence

HI, I have a Complete genome fasta file and I have list of sub sequence regions in the format as : 4353..5633 6795..9354 1034..14456 I want a script which can mask these region in a single complete genome fasta file with the alphabet N kindly help (2 Replies)
Discussion started by: margarita
2 Replies

10. Shell Programming and Scripting

Sequence extraction

i want to extract specific region of interest from big file. i have only start position, end position and seq id, see my query is: I have file1 is this >GL3482.1 GAACTTGAGATCCGGGGA GCAGTGGATCTCCACCAG CGGCCAGAACTGGTGCAC CTCCAGGCCAGCCTCGTC CTGCGTGTC >GL3550.1... (14 Replies)
Discussion started by: harpreetmanku04
14 Replies
XmTextGetSubstringWcs(library call)									       XmTextGetSubstringWcs(library call)

NAME
XmTextGetSubstringWcs -- A Text function that retrieves a portion of a wide character internal text buffer SYNOPSIS
#include <Xm/Text.h> int XmTextGetSubstringWcs( Widget widget, XmTextPosition start, int num_chars, int buffer_size, wchar_t *buffer); DESCRIPTION
XmTextGetSubstringWcs retrieves a copy of a portion of the internal text buffer of a Text widget that is stored in a wide character format. The function copies a specified number of characters from a given start position in the internal text buffer into a buffer provided by the application. A NULL terminator is placed at the end of the copied data. widget Specifies the Text widget ID. start Specifies the beginning character position from which the data will be retrieved. This is an integer number of characters from the beginning of the text buffer. The first character position is 0 (zero). num_chars Specifies the number of wchar_t characters to be copied into the provided buffer. buffer_size Specifies the size of the supplied buffer as a number of wchar_t storage locations. The minimum size is num_chars + 1. buffer Specifies the wide character buffer into which the internal text buffer will be copied. For a complete definition of Text and its associated resources, see XmText(3). RETURN
XmCOPY_SUCCEEDED The function was successful. XmCOPY_FAILED The function failed because it was unable to copy the specified number of characters into the buffer provided. The buffer size may be insufficient. The contents of buffer are undefined. XmCOPY_TRUNCATED The requested number of characters extended beyond the internal buffer. The function copied characters between start and the end of the widget's buffer and terminated the string with a NULL terminator; fewer than num_chars characters were copied. RELATED
XmText(3) and XmTextGetSubstring(3). XmTextGetSubstringWcs(library call)
All times are GMT -4. The time now is 12:55 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy