01-30-2014
Is it also possible to modify this code, for example using a for-loop, to perform this action on all .fasta files in a directory (outputing the modified files to a new directory or similarly)?
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Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
21|22|23|23... (1 Reply)
Discussion started by: marut_ashu
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2. Shell Programming and Scripting
Hello,
A bioperl problem I thought could be done with awk: convert the fasta format (Note: the length of each row is not the same for each entry as they were combined from different files!) to tabular format.
input.fasta:
>YAL069W-1.334 Putative promoter sequence... (6 Replies)
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Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
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Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
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5. Shell Programming and Scripting
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
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I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
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I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
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I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
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I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG
I need to rename the gene1.fasta file based on the sequence position specified in list.txt as follows,
list.txt
position1=org5... (5 Replies)
Discussion started by: dineshkumarsrk
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LEARN ABOUT DEBIAN
cups-genppdupdate
CUPS-GENPPDUPDATE(8) Gutenprint Manual Pages CUPS-GENPPDUPDATE(8)
NAME
cups-genppdupdate - update CUPS+Gutenprint PPD files
SYNOPSIS
cups-genppdupdate [-h] [-n] [-N] [-q | -v] [-s ppd-directory] [-s output-directory] [PPD-FILES or QUEUES...]
DESCRIPTION
cups-genppdupdate regenerates the Gutenprint PPD files in use by CUPS, using the PPD files under /usr/share/cups/model/gutenprint as tem-
plates. The new PPD file replaces the old PPD file under /etc/cups/ppd, but all the options set in the old PPD will be merged into the new
PPD, provided that they are still valid in the new file.
If no files or queue names are specified, cups-genppdupdate updates all Gutenprint PPD files in /etc/cups/ppd. Otherwise, cups-genppdup-
date updates all files or queues listed on the command line.
cups-genppdupdate does not update Foomatic PPD files or PPD files from Gimp-Print 4.2 or earlier.
cups-genppdupdate does not restart cupsd. cupsd will need manually reloading (or send SIGHUP) once cups-genppdupdate has completed.
OPTIONS
-h Show a help message.
-n No action. The program will run, but the old PPD files will not be replaced.
-q Quiet mode. No messages will be issued, apart from errors.
-v Verbose mode. More informative messages will be issued. Note that extremely verbose output may be turned on by setting $debug=1 in
the source, but this output will not be of use to the average user.
-s ppd-directory
Use ppd-directory as the base directory to read PPD files from. By default, the base directory is /usr/share/cups/model/gutenprint.
Under this directory, the PPD files are located in subdirectories according to language code and territory.
-o output-directory
Place updated PPD files in output-directory. By default, this is the same as the input directory.
-N Reset all options to their defaults (do not merge options from the current PPD file)
SEE ALSO
cups-genppd(8), cups-genppdconfig(8), CUPS Software Administrators Manual, http://localhost:631/documentation.html
COPYRIGHT
Copyright (C) 2002-2006 Roger Leigh (rleigh@debian.org) and Robert Krawitz (rlk@alum.mit.edu)
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 2, as
published by the Free Software Foundation.
This manual page was written by Roger Leigh (rleigh@debian.org).
Version 5.2.9 07 Jul 2012 CUPS-GENPPDUPDATE(8)