Sponsored Content
Full Discussion: Help with tail command
Top Forums Shell Programming and Scripting Help with tail command Post 302392597 by trey85stang on Friday 5th of February 2010 12:59:05 AM
Old 02-05-2010
hmm.. whats in Tempfile?
 

10 More Discussions You Might Find Interesting

1. UNIX for Advanced & Expert Users

help with !(tail -2) command.. using pipes

I am trying to using pipe (|) with ! (not) operator to list all the other files except the latest two and I am using the following command. $ ls -ltr *.lst|!(tail -2) ksh: 20050211180252.lst: cannot execute but it is trying to execute the file returned by tail -2. I am able to do that in 4... (8 Replies)
Discussion started by: sdlayeeq
8 Replies

2. Shell Programming and Scripting

tail command

Hi , I have found a interesting thing about tail command: when I tried to use 'tail -1 *' to look at every file with the current derectory, I only got one line of result of one file. But if I use 'head -1 *', I would get multiple lines. Is there a way to do get multiple lines with 'tail -1 *'... (3 Replies)
Discussion started by: whatisthis
3 Replies

3. Shell Programming and Scripting

tail command..

I was wondering how can I do this I have file myfile.txt wc -l is: 5 000 000 I have to remove first 1 000 000 lines from header.. I tryed with tail -4000000 myfile.txt>newfile.txt but it does not work... any help?? (2 Replies)
Discussion started by: amon
2 Replies

4. Solaris

Tail command in one line

HI i have to copy the last 5000 lines form a log file and copy the same in the same file .overwriting the same log file. ex: tail -5000 testfile1 > testfile2 cat testfile2 mv tesftfile2 testfile1 will produce the correct result.but i want to have this done in one line???? (4 Replies)
Discussion started by: saurabh84g
4 Replies

5. UNIX for Dummies Questions & Answers

Tail command with wildcard file name

Please help with the following command tail -f /appdata/logs/alert_audit517.txt | grep "Sep 02" The problem I have is with the file name "alert_audit517.txt". The 3 digit number at the end of the file name changes, so I need the file name to use a wildcard. Ive tried alert_audit***.txt, but... (5 Replies)
Discussion started by: robertson1995
5 Replies

6. Shell Programming and Scripting

tail command problems

Hi, In my home directory, there are so many files. i tried to get the lastly created file by following command. file=`ls -lrt MXOfiles* | tail -1` As there are so many files, it displays "$ : 0403-027 The parameter list is too long." Can someone tell me how can i get the recent file... (1 Reply)
Discussion started by: JSKOBS
1 Replies

7. Shell Programming and Scripting

tail command help

Hi does anyone know how to create a file using the tail command? My book has this file I need to create and it says to use the tail command and that it is possible but I have no idea. Thanks. (4 Replies)
Discussion started by: drew211
4 Replies

8. Homework & Coursework Questions

Using tail with the filter command

Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted! 1. The problem statement, all variables and given/known data: Devise a chain of filters using some or all of the following programs pr, cut, cat, tail to display a numbered... (8 Replies)
Discussion started by: hbell221
8 Replies

9. How to Post in the The UNIX and Linux Forums

Usage of tail command in .awk

Hi, I want to do file format using awk script, for that i wan to use 'tail'. Here is the scenario. I will be having set of files in a directory. Those files i need to write to another directory with same file name, but while writing the file to out directory, i need to write the last line as... (3 Replies)
Discussion started by: Venkata Madhu
3 Replies

10. UNIX for Beginners Questions & Answers

Tail -f Command help

Hi Team, Can anyone help me here: I have to access server logs via putty and these logs file is a trailing file (continously updating) with ERROR and WARNINGS... I need to know if I can pull this trailing file to a local drive so that I can do some higlighting on some keywords through Notepad... (13 Replies)
Discussion started by: jitensetia
13 Replies
Bio::Tools::Run::Hmmer(3pm)				User Contributed Perl Documentation			       Bio::Tools::Run::Hmmer(3pm)

NAME
Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch SYNOPSIS
# run hmmsearch (similar for hmmpfam) my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm'); # Pass the factory a Bio::Seq object or a file name, returns a Bio::SearchIO my $searchio = $factory->hmmsearch($seq); while (my $result = $searchio->next_result){ while(my $hit = $result->next_hit){ while (my $hsp = $hit->next_hsp){ print join(" ", ( $result->query_name, $hsp->query->start, $hsp->query->end, $hit->name, $hsp->hit->start, $hsp->hit->end, $hsp->score, $hsp->evalue, $hsp->seq_str, )), " "; } } } # build a hmm using hmmbuild my $aio = Bio::AlignIO->new(-file => "protein.msf", -format => 'msf'); my $aln = $aio->next_aln; my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm'); $factory->hmmbuild($aln); # calibrate the hmm $factory->calibrate(); # emit a sequence stream from the hmm my $seqio = $factory->hmmemit(); # align sequences to the hmm my $alnio = $factory->hmmalign(@seqs); DESCRIPTION
Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam and hmmsearch. Binaries are available at http://hmmer.janelia.org/ You can pass most options understood by the command-line programs to new(), or set the options by calling methods with the same name as the argument. In both instances, case sensitivity matters. Additional methods are hmm() to specifiy the hmm file (needed for all HMMER programs) which you would normally set in the call to new(). The HMMER programs must either be in your path, or you must set the environment variable HMMERDIR to point to their location. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://redmine.open-bio.org/projects/bioperl/ AUTHOR - Shawn Hoon Email: shawnh-at-gmx.net CONTRIBUTORS
Shawn Hoon shawnh-at-gmx.net Jason Stajich jason -at- bioperl -dot- org Scott Markel scott -at- scitegic -dot com Sendu Bala bix@sendu.me.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $HMMER->new(@params) Function: Creates a new HMMER factory Returns : Bio::Tools::Run::HMMER Args : -hmm => filename # the hmm, used by all program types; if not set # here, must be set with hmm() method prior to # running anything -_READMETHOD => 'hmmer' (default) || 'hmmer_pull' # the parsing # module to use for # hmmpfam/hmmsearch Any option supported by a Hmmer program, where switches are given a true value, eg. -q => 1, EXCEPT for the following which are handled internally/ incompatible: h verbose a compat pvm WARNING: the default sequence format passed to hmmpfam is msf. If you are using a different format, you need to pass it with informat. e.g. my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm', -informat => 'fasta'); -q is synonymous with -quiet -o is synonymous with -outfile # may be specified here, allowing run() to be used, or # it can be omitted and the corresponding method (eg. # hmmalign()) used later. -program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch run Title : run Usage : $obj->run($seqFile) Function: Runs one of the Hmmer programs, according to the current setting of program() (as typically set during new(-program => 'name')). Returns : A Bio::SearchIO, Bio::AlignIO, Bio::SeqIO or boolean depending on the program being run (see method corresponding to program name for details). Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename hmmalign Title : hmmalign Usage : $obj->hmmalign() Function: Runs hmmalign Returns : A Bio::AlignIO Args : list of Bio::SeqI OR Bio::Align::AlignI OR filename of file with sequences or an alignment hmmbuild Title : hmmbuild Usage : $obj->hmmbuild() Function: Runs hmmbuild, outputting an hmm to the file currently set by method hmm() or db(), or failing that, o() or outfile(), or failing that, to a temp location. Returns : true on success Args : Bio::Align::AlignI OR filename of file with an alignment hmmcalibrate Title : hmmcalibrate Usage : $obj->hmmcalibrate() Function: Runs hmmcalibrate Returns : true on success Args : none (hmm() must be set, most likely by the -hmm option of new()), OR optionally supply an hmm filename to set hmm() and run hmmemit Title : hmmemit Usage : $obj->hmmemit() Function: Runs hmmemit Returns : A Bio::SeqIO Args : none (hmm() must be set, most likely by the -hmm option of new()), OR optionally supply an hmm filename to set hmm() and run hmmpfam Title : hmmpfam Usage : $obj->hmmpfam() Function: Runs hmmpfam Returns : A Bio::SearchIO Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename hmmsearch Title : hmmsearch Usage : $obj->hmmsearch() Function: Runs hmmsearch Returns : A Bio::SearchIO Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename _setinput Title : _setinput Usage : $obj->_setinput() Function: Internal(not to be used directly) Returns : filename Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename _run Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : Bio::SearchIO Args : file name _setparams Title : _setparams Usage : Internal function, not to be called directly Function: creates a string of params to be used in the command string Returns : string of params Args : none program_name Title : program_name Usage : $factory>program_name() Function: holds the program name Returns : string Args : none program_dir Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns : string Args : none _writeSeqFile Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal(not to be used directly) Returns : filename Args : list of Bio::SeqI _writeAlignFile Title : _writeAlignFile Usage : obj->_writeAlignFile($seq) Function: Internal(not to be used directly) Returns : filename Args : list of Bio::Align::AlignI perl v5.12.3 2011-06-18 Bio::Tools::Run::Hmmer(3pm)
All times are GMT -4. The time now is 12:56 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy