Bioinfo::Fasta - get one or more sequences from a FASTA file quickly.

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Currently, there do have some modules that can operate the FASTA file such as Bio::SeqIO, But it only provide some basic operation to obtain the information about sequence. In my daily work, I still have to write some repetitive code. So this module ...

PEKINGSAM/Bioinfo-0.1.15 - 24 Sep 2019 02:44:11 UTC - Search in distribution

• Bioinfo::App::Cmd::Fasta - my perl module and CLIs for Biology
• Bioinfo::App::Cmd::Fasta::Cmd::Split - my perl module and CLIs for Biology
• Bioinfo::App::Cmd::Fasta::Cmd::GetByID - my perl module and CLIs for Biology
• 3 more results from Bioinfo »

Bio::DB::Fasta - Fast indexed access to fasta files

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Bio::DB::Fasta provides indexed access to a single Fasta file, several files, or a directory of files. It provides persistent random access to each sequence entry (either as a Bio::PrimarySeqI-compliant object or a string), and to subsequences within...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution

• Bio::Index::Fasta - Interface for indexing (multiple) fasta files
• Bio::SeqIO::fasta - fasta sequence input/output stream
• Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
• 102 more results from BioPerl »

TIGR::FASTA::Writer - TIGR::FASTA::Writer class for writing TIGR::FASTA::Record objects to a file

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This module provides an object definition for a TIGR::FASTA::Writer. The TIGR::FASTA::Writer object accepts TIGR::FASTA::Record objects for printing to an output file....

JORVIS/TIGR-0.03 - 07 Sep 2017 01:24:38 UTC - Search in distribution

• TIGR::FASTA::Record - TIGR::FASTA::Record class describing FASTA records
• TIGR::FASTA::Reader - TIGR::FASTA::Reader class for parsing and navigating FASTA format files.
• TIGR::FASTA::Grammar - module for validating FASTA format records
• 1 more result from TIGR »

Bio::SeqReader::Fasta - Class providing a reader for files in FASTA format.

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Bio::SeqReader::Fasta provides a method for reading a file or stream in FASTA format....

JAC/Bio-SeqReader-0.1.3 - 25 Sep 2012 04:13:30 UTC - Search in distribution

• Bio::SeqReader::FastaRecord - Class providing methods for representing identifier, description, and sequence information in FASTA records.
• Bio::SeqReader - Classes for reading sequence data.

Bio::ViennaNGS::Fasta - Moose wrapper for Bio::DB::Fasta

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Bio::ViennaNGS::Fasta provides a Moose interface to Bio::DB::Fasta, spiced up with a few convenience methods for easy sequence data retrieval. ATTRIBUTES fasta (required) Upcon object construction, this attribute expects an input fasta file, which is...

MTW/Bio-ViennaNGS-v0.19.2 - 11 Dec 2018 13:25:00 UTC - Search in distribution

• fasta_regex.pl - Find sequence motifs in a (multi) Fasta file
• fasta_subgrep.pl - Extract subsequence from a (multi) Fasta file
• fasta_multigrep.pl - Extract individual sequences from a multi Fasta file
• 7 more results from Bio-ViennaNGS »

FAST::Bio::SeqIO::fasta - fasta sequence input/output stream

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This object can transform FAST::Bio::Seq objects to and from fasta flat file databases....

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution

• FAST::Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
• FAST::Bio::SearchIO::fasta - A SearchIO parser for FASTA results
• fastr - character-based transformations on sequence records
• 60 more results from FAST »

BioX::Seq::Stream::FASTA - the FASTA parser for BioX::Seq:Stream;

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This module performs robust parsing of FASTA sequence streams. It is not intended to be used directly but is called by "BioX::Seq::Stream" after file format autodetection. Please see the documentation for that module for more details....

VOLKENING/BioX-Seq-0.008009 - 08 Jan 2024 17:27:54 UTC - Search in distribution

• BioX::Seq - a (very) basic biological sequence object
• BioX::Seq::Fetch - Fetch records from indexed FASTA non-sequentially

GenOO::Data::File::FASTA - Object implementing methods for accessing fasta formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)

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This object offers methods to read a fasta file line by line....

MNSMAR/GenOO-1.5.2 - 06 May 2020 21:51:14 UTC - Search in distribution

• GenOO::Data::File::FASTA::Record - Object representing a record of a fasta file
• GenOO - A Modern Perl Framework for High Throughput Sequencing analysis

Bio::Chaos::Parser::fasta - fasta sequence input/output stream

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generates events with this schema: (fastaseqset (fastaseq* (header "str") (residues "str") (seqlen "int")))...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC - Search in distribution

Bio::Phylo::Parsers::Fasta - Parser used by Bio::Phylo::IO, no serviceable parts inside

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A very symplistic FASTA file parser. To use it, you need to pass an argument that specifies the data type of the FASTA records into the parse function, i.e. my $project = parse( -type => 'dna', # or rna, protein -format => 'fasta', -file => 'infile.f...

RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC - Search in distribution

• Bio::Phylo::Unparsers::Fasta - Serializer used by Bio::Phylo::IO, no serviceable parts inside
• Bio::Phylo::IO - Front end for parsers and serializers

FASTAParse - A light-weight parsing module for handling FASTA formatted sequence within larger perl applications.

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FASTAParse is pretty simple in that it does one of two things: 1) loads a FASTA object from a chunk of text; 2) formats a FASTA object given explicit user input. See SYNOPSIS for example code for both functions. Once populated, individual sections of...

TWYLIE/FASTAParse-0.0.3 - 05 Apr 2008 03:28:25 UTC - Search in distribution

Tie::File::AnyData::Bio::Fasta - Accessing fasta records in a file via a Perl array.

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"Tie::File::AnyData::Bio::Fasta" allows the management of fasta files via a Perl array through "Tie::File::AnyData", so read the documentation of this module for further details on its internals....

MOTIF/Tie-File-AnyData-Bio-Fasta-0.01 - 22 Mar 2008 17:37:35 UTC - Search in distribution

lib/Bio/Gonzales/Seq/Validate/fasta.pm

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JWB/Bio-Gonzales-0.083 - 02 Jan 2021 23:10:48 UTC - Search in distribution

• lib/Bio/Gonzales/Seq/IO/Fasta.pm
• fasta-grep - grep fasta files
• fadiff - diff fasta files
• 7 more results from Bio-Gonzales »

fasta-decoy.pl - decoy input databanks following several moethods

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Reads input fasta file and produce a decoyed databank with several methods: reverse: simply reverse each sequence shuffle: shuffle AA in each sequence shuffle & avoid known cleaved peptides: shuffle sequence but avoid producing known tryptic peptides...

ALEXMASS/InSilicoSpectro-Databanks-0.0.43 - 26 Aug 2008 07:56:20 UTC - Search in distribution

• fasta-shuffle-notryptic.pl - shuffle each sequence, without any original tryptic peptide
• uniprotdat2fasta.pl - converts uniprot native text format (.dat or .seq) into fasta file, reporting varsplic, signal, peptide, PTM, conflicts....
• InSilicoSpectro::Databanks::DBEntryUniprot - Uniprot formated entry
• 4 more results from InSilicoSpectro-Databanks »

lib/Bio/BioVeL/Service/NeXMLMerger/DataReader/fasta.pm

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RVOSA/Bio-BioVeL-0.1 - 21 Mar 2014 10:32:41 UTC - Search in distribution

Benchmark::Perl::Formance::Plugin::Shootout::fasta - benchmark - Generate and write random DNA sequences

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SCHWIGON/Benchmark-Perl-Formance-0.55 - 17 Sep 2021 12:36:46 UTC - Search in distribution

• benchmark-perlformance - Frontend for Benchmark::Perl::Formance

Benchmark::Perl::Formance::Plugin::PerlStone2015::fasta - benchmark - Generate and write random DNA sequences

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SCHWIGON/Benchmark-Perl-Formance-Plugin-PerlStone2015-0.002 - 23 Apr 2016 06:58:04 UTC - Search in distribution

Bio::Roary::SortFasta - sort a fasta file by name

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AJPAGE/Bio-Roary-3.13.0 - 06 Nov 2019 21:32:21 UTC - Search in distribution

• Bio::Roary::ChunkFastaFile - Take in a FASTA file and chunk it up into smaller pieces.
• Bio::Roary::AccessoryBinaryFasta - Output a FASTA file which represents the binary presence and absence of genes in the accessory genome
• query_pan_genome - Take in a groups file and the protein fasta files and output selected data
• 12 more results from Bio-Roary »

Bio::MLST::OutputFasta - Take in two hashes, both containing sequence names and sequences and output fasta files.

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AJPAGE/Bio-MLST-Check-2.1.1706216 - 03 Mar 2017 16:23:59 UTC - Search in distribution

• Bio::MLST::ProcessFasta - Take in a fasta file, lookup the MLST database and create relevant files.
• Bio::MLST::NormaliseFasta - Take in a Fasta file, check for invalid characters and build a corrected file if needed.
• get_sequence_type - Given an assembly find the MLST sequence type.
• 8 more results from Bio-MLST-Check »

Bio::DB::SeqFeature::Store::berkeleydb - Storage and retrieval of sequence annotation data in Berkeleydb files

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Bio::DB::SeqFeature::Store::berkeleydb is the Berkeleydb adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store->new() to do so. See Bio::DB::SeqFeature::Store for complete usage instructio...

CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution

• Bio::DB::SeqFeature::Store - Storage and retrieval of sequence annotation data
• bp_seqfeature_load.pl - Load GFF into a SeqFeature database
• Bio::DB::SeqFeature::Store::FeatureFileLoader - feature file loader for Bio::DB::SeqFeature::Store
• 2 more results from Bio-DB-SeqFeature »