Hi All,
Below is my requirement. Whatever coming in between ' ', needs to delete.
Input File Contents:
==============
This is nice 'boy'
This 'is
bad
boy.' Got it
Expected Output
===========
This is nice
This
Got it (4 Replies)
Hi guys,
i have the follow problem i need to delete 10 row before the pattern and 1 after and the pattern row itself.
file looks like:
frect 9.8438 25.8681 10.625 25
. dynprop \
(# \
(call fox_execute(__self))) \
(FOX_VAR_29 \
... (4 Replies)
Hello sed gurus. I am using ksh on Sun and have a file created by concatenating several other files. All files contain header rows. I just need to keep the first occurrence and remove all other header rows.
header for file
1111
2222
3333
header for file
1111
2222
3333
header for file... (8 Replies)
i have a file sample.txt containing
i want to delete lines starting with 123 neglecting spaces and tabs.
but not lines containing 123. i.e.
i want files sample.txt as
help me
thanxx (4 Replies)
Hi friends,
I am looking for sed command/script that would search for a given fixed pattern on odd lines and then if it matches, prints the matching pattern and the next line. For example, in the example below, i am looking for pattern 0 and 1011 on odd lines.
########## start of example file... (10 Replies)
Hello,
I am having hard time figuring out how to print/delete the lines between two pattern. Here is the part of the file nastran1.bdf:
RBE3 48729 32232 123456 0.30000 123 59786 59787
60114
RBE3 48732 1330 123 0.30000 123 10107... (4 Replies)
The intended result should be :
PDF converters
'empty line'
gpdftext and pdftotext?xml version="1.0"?>
xml:space="preserve"><note-content version="0.1" xmlns:/tomboy/link" xmlns:size="http://beatniksoftware.com/tomboy/size">PDF converters
gpdftext and pdftotext</note-content>... (9 Replies)
Hi
I need to delete duplicate like pattern lines from a text file containing 2 duplicates only (one being subset of the other) using sed or awk preferably.
Input:
FM:Chicago:Development
FM:Chicago:Development:Score
SR:Cary:Testing:Testcases
PM:Newyork:Scripting
PM:Newyork:Scripting:Audit... (6 Replies)
I have a file
Line 1 a
Line 22
Line 33
Line 1 b
Line 22
Line 1 c
Line 4
Line 5
I want to delete all lines before last occurrence of a line which contains something which is defined in a variable. Say a variable var contains 'Line 1', then I need the following in the output.
... (21 Replies)
In the awk piped to sed below I am trying to format file by removing the odd xxxx_digits and whitespace after, then move the even xxxx_digit to the line above it and add a space between them. There may be multiple lines in file but they are in the same format. The Filename_ID line is the last line... (4 Replies)
Discussion started by: cmccabe
4 Replies
LEARN ABOUT DEBIAN
srf2fastq
srf2fastq(1) Staden io_lib srf2fastq(1)NAME
srf2fastq - Converts SRF files to Sanger fastq format
SYNOPSIS
srf2fastq [options] srf_archive ...
DESCRIPTION
srf2fastq extracts sequences and qualities from one or more SRF archives and writes them in Sanger fastq format to stdout.
Note that Illumina also have a fastq format (used in the GERALD directories) which differs slightly in the use of log-odds scores for the
quality values. The format described here is using the traditional Phred style of quality encoding.
OPTIONS -c Outputs calibrated confidence values using the ZTR CNF1 chunk type for a single quality per base. Without this use the original
Illumina _prb.txt files consisting of four quality values per base, stored in the ZTR CNF4 chunks.
-C Masks out sequences tagged as bad quality.
-s root
Generates files on disk with filenames starting root, one file per non-explicit element in the SRF/ZTR region (REGN) chunk. Typi-
cally this results in two files for paired end runs. The filename suffixes come from the names listed in the SRF region chunks.
This option conflicts with the -S parameter.
-S Splits sequences into regions, but sequentially lists each sequence region to stdout instead of splitting to separate files on disk.
This option conflicts with the -s parameter.
-n When using -s the filename suffixes are simply numbered (starting with 1) instead of using the names listed in the SRF region
chunks.
-a Appends region index to the sequence names. Ie generate "name/1" and "name/2" for a paired read.
-e Include any explicit sequence (ZTR region chunk of type 'E') in the sequence output. The explicit sequence is also included in the
quality line too. Currently this is utilised by ABI SOLiD to store the last base of the primer.
-r region list
Reverse complements the sequence and reverses the quality values for all regions in the region list. This is a comma separated list
of integer values enumerating the regions, starting from 1. Note that this option only works when either -s or -S are specified.
EXAMPLES
To extract only the good quality sequences from all srf files in the current directory using calibrated confidence values (if available).
srf2fastq -c -C *.srf > runX.fastq
To extract a paired end run into two separate files with sequences named name/1 and name/2.
srf2fastq -s runX -a -n runX.srf
To extract a paired end run as a single file, alternating forward and reverse sequences, with the second read being reverse complemented.
srf2fastq -S -r 2 runX.srf > runX.fastq
AUTHOR
James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
December 10 srf2fastq(1)