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Shell Programming and Scripting
Retrieving sequences corresponding to start and end position
Post 303023764 by Ibk on Saturday 22nd of September 2018 04:21:33 AM
09-22-2018
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Have to check in a file that the lines starting with 620 and 705
are ending at same posiotin.
82012345
62023232323
70523949558
62023255454
9999
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I Have to check in a file that all the lines are ending at same posiotin.
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Hi,
I am a newbie in unix programming so maybe this is a simple question.
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Example
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2 30
40 80
82 100
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Hi,
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AJJ|KKDD||KKDK||||||||||||
KKD||KD|||LLLD||||LLD|||||
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Need to replace pipes from 8th occurrence of pipe till end.
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-------
-------
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LEARN ABOUT DEBIAN
bio::alignio::fasta
Bio::AlignIO::fasta(3pm) User Contributed Perl Documentation Bio::AlignIO::fasta(3pm) NAME
Bio::AlignIO::fasta - fasta MSA Sequence input/output stream SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class. DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from fasta flat file databases. This is for the fasta alignment format, not for the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module. FEEDBACK
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: https://redmine.open-bio.org/projects/bioperl/ AUTHORS
Peter Schattner APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_aln Title : next_aln Usage : $aln = $stream->next_aln Function: returns the next alignment in the stream. Returns : Bio::Align::AlignI object - returns 0 on end of file or on error Args : -width => optional argument to specify the width sequence will be written (60 chars by default) See Bio::Align::AlignI write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in fasta format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object See Bio::Align::AlignI _get_len Title : _get_len Usage : Function: determine number of alphabetic chars Returns : integer Args : sequence string width Title : width Usage : $obj->width($newwidth) $width = $obj->width; Function: Get/set width of alignment Returns : integer value of width Args : on set, new value (a scalar or undef, optional) perl v5.14.2 2012-03-02 Bio::AlignIO::fasta(3pm)