FASTQ_QUALITY_TRIMMER(1) User Commands FASTQ_QUALITY_TRIMMER(1)NAME
fastq_quality_trimmer - Filters sequences based on quality
DESCRIPTION
usage: fastq_quality_trimmer [-h] [-v] [-t N] [-l N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gor-
don@cshl.edu)
[-h] = This helpful help screen.
[-t N] = Quality threshold - nucleotides with lower
quality will be trimmed (from the end of the sequence).
[-l N] = Minimum length - sequences shorter than this (after trimming)
will be discarded. Default = 0 = no minimum length.
[-z] = Compress output with GZIP.
[-i INFILE]
= FASTQ input file. default is STDIN.
[-o OUTFILE] = FASTQ output file. default is STDOUT. [-v] = Verbose - report number of sequences.
If [-o] is specified,
report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.
SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
to get a better layout as well as an overview about connected FASTX tools.
fastq_quality_trimmer 0.0.13.1 April 2012 FASTQ_QUALITY_TRIMMER(1)
Check Out this Related Man Page
FASTA_FORMATTER(1) User Commands FASTA_FORMATTER(1)NAME
fasta_formatter - changes the width of sequences line in a FASTA file
DESCRIPTION
usage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e] Part of FASTX Toolkit 0.0.13.2 by gordon@cshl.edu
[-h] = This helpful help screen.
[-i INFILE]
= FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA/Q output file. default is STDOUT. [-w N] = max. sequence line width for output FASTA file.
When ZERO (the default), sequence lines will NOT be wrapped - all nucleotides of each sequences will appear on a single line (good
for scripting).
[-t] = Output tabulated format (instead of FASTA format).
Sequence-Identifiers will be on first column, Nucleotides will appear on second column (as single line).
[-e] = Output empty sequences (default is to discard them).
Empty sequences are ones who have only a sequence identifier, but not actual nucleotides.
Input Example:
>MY-ID AAAAAGGGGG CCCCCTTTTT AGCTN
Output example with unlimited line width [-w 0]:
>MY-ID AAAAAGGGGGCCCCCTTTTTAGCTN
Output example with max. line width=7 [-w 7]:
>MY-ID AAAAAGG GGGTTTT TCCCCCA GCTN
Output example with tabular output [-t]:
MY-ID AAAAAGGGGGCCCCCTTTTAGCTN
example of empty sequence: (will be discarded unless [-e] is used)
>REGULAR-SEQUENCE-1 AAAGGGTTTCCC >EMPTY-SEQUENCE >REGULAR-SEQUENCE-2 AAGTAGTAGTAGTAGT GTATTTTATAT
SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
to get a better layout as well as an overview about connected FASTX tools.
fasta_formatter 0.0.13.2 May 2012 FASTA_FORMATTER(1)
Hello all,
I'm having trouble trying to get the output of a variable passed from an INFILE. Here is what i have so far.
/tmp/INFILE --- inside INFILE will be 2 or more filenames like so
/apps/opt/FTTP_`date '+%m%d%y'`.txt
/apps/opt/DSLFeed.`date '+%m%d%y'`.txt
--Here is just a... (2 Replies)
Hi All,
I got an output after executing oracle query in unix mechine. While executing the query the output it should automatically store in a table
Query:-
1. i am expected an report for the output.
2. How the output it will automatically store in an table.
Is there script available... (1 Reply)
Hi,
Please help me.
This script is responsible of storing all the report in a line.
penfilename=`echo ${OUTFILE}*"(${daterange})".csv`
OUTFILE=${OUT_DIR}"/PenetrationReport" and the OUT_DIR is this -
OUT_DIR=${MMHOME}/data/preticketing/penrpt.
The example of the generated report... (1 Reply)
Hi,
Currently my STDOUT is configured as tty0,
Is there a way to change it during runtime?
I need to use this serial for other external device
Thanks,
Alex (2 Replies)
My file looks like this:
But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ)
Would it be possible to use awk to perform this task? (2 Replies)
Hi,
I would like to avoid re-directing line by line to a file.
What is the best way to re-direct STDOUT to a file in a subshell?
Thanks in advance.
Cheers
Vj (1 Reply)
Hello all,
I have a for loop executing in a script that I want to redirect STDOUT to screen and to file, while directing STDERR to the bit bucket. Here is the general sentax of what I'm doing:
for i in thingy
do
some_command ${i}
done 1>&1 | tee ${LOGFILE} 2> /dev/null
What I am... (2 Replies)
File name is
INFILE="ABC_BMWPPI_20120909_00073.DAT.ASDFGHJK" -> 44 character long
mv INFILE GEPB_${INFILE:${#INFILE}-27:15}dat
result is GEPB_20120909_00073.DAT.
I am confused in how we get it.
If I evaluate
1- GEPB_${INFILE:${#INFILE}-27:15}dat
2- GEPB_${INFILE:${44}-27:15}dat
3-... (2 Replies)
Dear all,
redirecting STDOUT & STDERR to file is quite simple, I'm currently using:
exec 1>>/tmp/tmp.log; exec 2>>/tmp/tmp.logBut during script execution I would like the output come back again to screen, how to do that?
Thanks
Lucas (4 Replies)
I have to redirect STDERR messages both to screen and also capture the same in a file but STDOUT only to the same file.
I have searched in this formum for a solution, but something like
srcipt 3>&1 >&2 2>&3 3>&- | tee errs
doesn't work for me...
Has anyone an idea??? (18 Replies)
I'm using a script that does some modifications to data on disc and updates the database. The script (perl) uses STDOUT so the results are printed to the screen. I don't have permissions to modify the script. I want to capture the results in a file so I can see if errors occurred and also keep... (3 Replies)
I have posted this before but did not get much feedback. So I will try again. I need to remove sequences from a file based on values listed on a second file.
The sequences file looks like this:
Sequences.txt
>Sample1 Freq 59
ggatatgatgatgaactggt
>Sample1 Freq 54
ggatatgatgttgaactggt... (4 Replies)
I have this file:
>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC
Add I am trying to use this script to output sequences longer than 15 characters:
sed -r '/^>/N;{/^.{,15}$/d}'
The desire output would be this:
>ID4... (8 Replies)