Thank you singh,
Your command prints all the sequences. However, I need to print only few sequences length as listed in id.txt file. If I did not understand your commands properly, please let me know, where to include id.txt file in your command?
Oh ok, I was in impression that you want to print all seq strings length in a single Input_file, could you please try following now.
Output will be as follows.
Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
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)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 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)
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT DEBIAN
gappletviewer
GAPPLETVIEWER(1) GNU GAPPLETVIEWER(1)NAME
gappletviewer - Load and runs an applet
SYNOPSIS
appletviewer [OPTION]... URL...
appletviewer [OPTION]... -code CODE
appletviewer [OPTION]... -plugin INPUT,OUTPUT
DESCRIPTION
The appletviewer tool loads and runs an applet.
Use the first form to test applets specified by tag. The URL should resolve to an HTML document from which the appletviewer will extract
applet tags. The APPLET, EMBED and OBJECT tags are supported. If a given document contains multiple applet tags, all the applets will be
loaded, with each applet appearing in its own window. Likewise, when multiple URLs are specified, each applet tag instance is given its
own window. If a given document contains no recognized tags the appletviewer does nothing.
appletviewer http://www.gnu.org/software/classpath/
Use the second form to test an applet in development. This form allows applet tag attributes to be supplied on the command line. Only one
applet may be specified using the -code option. The -code option overrides the URL form -- any URLs specified will be ignored.
appletviewer -code Test.class -param datafile,data.txt
gcjwebplugin uses the third form to communicate with the appletviewer through named pipes.
OPTIONS
URL OPTIONS
-debug
This option is not yet implemented but is provided for compatibility.
-encoding CHARSET
Use this option to specify an alternate character encoding for the specified HTML page.
APPLET TAG OPTIONS
-code CODE
Use the -code option to specify the value of the applet tag CODE attribute.
-codebase CODEBASE
Use the -codebase option to specify the value of the applet tag CODEBASE attribute.
-archive ARCHIVE
Use the -archive option to specify the value of the applet tag ARCHIVE attribute.
-width WIDTH
Use the -width option to specify the value of the applet tag WIDTH attribute.
-height HEIGHT
Use the -height option to specify the value of the applet tag HEIGHT attribute.
-param NAME,VALUE
Use the -param option to specify values for the NAME and VALUE attributes of an applet PARAM tag.
PLUGIN OPTION
-plugin INPUT,OUTPUT
gcjwebplugin uses the -plugin option to specify the named pipe the appletviewer should use for receiving commands (INPUT) and the one
it should use for sending commands to gcjwebplugin (OUTPUT).
DEBUGGING OPTION
-verbose
Use the -verbose option to have the appletviewer print debugging messages.
STANDARD OPTIONS
-help
Use the -help option to have the appletviewer print a usage message, then exit.
-version
Use the -version option to have the appletviewer print its version, then exit.
-JOPTION
Use the -J option to pass OPTION to the virtual machine that will run the appletviewer. Unlike other options, there must not be a
space between the -J and OPTION.
BUGS SEE ALSO AUTHOR 0.98 2010-07-05 GAPPLETVIEWER(1)