Search results for "distribution:FAST cookbook"
FAST::List::Gen::Cookbook - how to get the most out of FAST::List::Gen
DHARD/FAST-1.06
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21 Apr 2015 08:04:25 UTC
FAST::List::Gen - provides functions for generating lists
DHARD/FAST-1.06
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21 Apr 2015 08:04:25 UTC
FAST::List::Generator - provides functions for generating lists
DHARD/FAST-1.06
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21 Apr 2015 08:04:25 UTC
faswc - tally sequences and sequence characters
faswc takes sequence or alignment data on input and outputs tallies of sequences and/or sequence characters directly to STDOUT (in analogy to wc). If a list of files are given as arguments to faswc, tallies are calculated by file as well as in total....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fasrc - reverse complement nucleotide sequences and alignments
fasrc takes multifasta format nucleotide sequences or alignments as input, and generates reverse complements of those sequences as output. Options specific to fasrc: -n, --nobrand don't "brand" sequence ids with "-rc" extension Options general to FAS...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fastr - character-based transformations on sequence records
fastr takes multifasta format sequence or alignment data as input, and faciliates character transliterations on identifiers (by default), sequences or descriptions using the Perl tr/// character transliteration operator. This faciliates character rem...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fasxl - translate sequences by a genetic code.
fasxl takes multifasta format DNA or RNA codon sequences or alignments as input, and generates biological translations of those sequences as output. Gapped sequences on input are allowed with the -g, -k or -o options; the gap character "-" is require...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
faslen - annotate sequence lengths to descriptions
faslen takes sequence or alignment data on input, computes sequence lengths, and annotates sequence record descriptions with their lengths in the format "length:<value>." All sequence characters get counted, including gap characters. Identifiers and ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fassub - regex-based substitutions on sequence records
fassub takes multifasta format sequence or alignment data as input, and faciliates text substitutions on sequence identifiers (by default), sequences or descriptions using the Perl s/// substitution operator. fassub takes two mandatory arguments corr...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
gbfcut - search features from GenBank files and print corresponding sequences
gbfcut takes GenBank-sequence input and outputs subsequences that correspond to features annotated on all input sequences in Multi-Fasta format. Both simple and more complex split features are supported. Optionally, gbfcut may be directed to only out...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
alncut - filter sites in alignments based on variation and gap-content
alncut takes multifasta format alignment data as input and returns that data filtered for sites with various properties. By default, only invariant sites (sites with no variation) are returned. When the -f option is used, sites will be returned that ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fastax - select sequence records by NCBI taxonomic names or IDs
fastax takes NCBI Taxonomy data and sequence or alignment data on input and, if directed to valid NCBI Taxonomic ID labels in the sequence records, outputs sequence records that belong to a taxonomic clade as specified by a query argument. For exampl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fascut - select biosequence record data by character or field ranges
fascut takes biological sequence records on input, and on output, transforms one component (e.g. sequence, description or identifier) of each record as the concatenation of index- and range-based selections of input data. Data is indexed by character...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fastail - print last sequence records on input
fastail takes sequence or alignment data as input, and outputs the last n sequence records of each input file or, if no files are specified, of the standard input. fastail by default prints the last 10 sequence records. Options specific to fastail: -...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fasuniq - Remove duplicate sequence records in a multifasta file or datastream.
fasuniq eliminates redundant sequence records from the input. A redundant record is one in which a specific data field tests equal as a string against the same field in one or more records that immediately follow it in the input multifasta file or da...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fascomp - analysis of monomer frequencies
fascomp takes multifasta format sequence or alignment data as input, and counts the absolute or relative frequencies of monomers in each sequence individually and for all data on input. By default, absolute frequencies are computed and appended to th...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fashead - print first sequence records on input
fashead takes sequence or alignment data as input, and outputs the first n sequence records of each input file or, if no files are specified, of the standard input. fashead by default prints the first 10 sequence records. Options specific to fashead:...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fassort - sort sequences based on identifiers
fassort takes sequence or alignment data as input, and outputs sequence records sorted by some user-defined criteria. By default, sequences are sorted ASCIIbetically by their identifiers. Optionally sequences may be sorted by their sequences, descrip...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fasgrep - print sequence records matching a pattern
fasgrep takes sequence or alignment data as input, and outputs sequence records whose data match a perl regular expression (regex) argument. By default, the regex is tested for matching against sequence identifiers. fasgrep takes one argument, a perl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
fascodon - counts codon usage
fascodon takes multifasta format sequence or alignment data as input, and analyzes codon usage and other coding characteristics of the data. By default, fascodon analyzes each sequence record individually, outputting raw codon frequencies appended to...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC