FAST

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Changes  view on Meta::CPAN

1.00    First post to CPAN
1.01    Disabled much testing for the unfortunate reason of portability issues with Test::Script::Run
1.02    Removed some libraries that were causing permission problems: one involving Nexml from BioPerl 
        and the other Pod::Usage -- Pod::Usage listed as a dep for download from CPAN now
1.03    Added use v5.10.1 in lib/FAST.pm and Makefile.pm because of "use parent" in FAST::Bio::SeqIO 

1.05    Docfixes and edge-cases treated with new options in fasuniq, fascodon, and alnpi
        fasuniq --no-starts suppresses separate tally of start codons
	added fasuniq --count 
1.06    DocFixes to alnpi 
        Fix in name of symbolic link to the popset data-file in t/data. 
	Release corresponding to acceptance in Frontiers in Genetics

MANIFEST  view on Meta::CPAN

lib/FAST/List/Gen/Perl6.pm
lib/FAST/List/Generator.pm
Makefile.PL
MANIFEST			This list of files
README
INSTALL
README.md
t/00-load.t
t/boilerplate.t
t/data/AF194338.1.gb
t/data/ArdellEtAl03_ncbi_popset_32329588.aln
t/data/ArdellEtAl03_ncbi_popset_32329588.fas
t/data/ArdellEtAl03_ncbi_popset_32329588.nexus
t/data/ArdellEtAl03_ncbi_popset_32329588.phylip
t/data/chr01.fsa
t/data/Dros.fas
t/data/fascodon_test.fas
t/data/fascodon_test.output.txt
t/data/fasfilter_test.fas
t/data/fashead_tail_test1.fas
t/data/faslen_test1.fas
t/data/faspaste_test.fas
t/data/faspaste_test2.fas
t/data/fasrc_test.fas

MANIFEST  view on Meta::CPAN

t/data/fasxl_test5.fas
t/data/flybase_fasta_100_cds.fas
t/data/gbfcut_test.fas
t/data/P450.clustalw2.aln
t/data/P450.clustalw2.fas
t/data/P450.fas
t/data/test.fq
t/data/tRNAdb-CE.sample2000.fas
t/data/flybase_fasta_100_cds.fas
t/data/mito-ascaris.gb
t/data/popset_32329588.fas
t/lib/Test/Cmd.pm
t/lib/Test/Cmd/Common.pm
t/pod.t
META.yml                                 Module YAML meta-data (added by MakeMaker)
META.json                                Module JSON meta-data (added by MakeMaker)

bin/alnpi  view on Meta::CPAN

cases, but sometimes Bioperl cannot guess and complains when
processing data).

=back

=head1 EXAMPLES

Generate sliding window of Tajima's D, the data plotted in Fig. 4A of
Ardell et al. (2003) Genetics 165:1761. The data files ship with FAST:

B<fasgrep> -v "(AF194|349[06])" t/data/ArdellEtAl03_ncbi_popset_32329588.fas | B<fastr> --strict -N - | B<alncut> -g | B<alnpi> --window 100:25:d

Statistics for 5'UTRs, the last line in Table 1 of Ardell et al. (2003) Genetics 165:1761:

B<gbfalncut> -k t/data/AF194338.1.gb 5.UTR t/data/ArdellEtAl03_ncbi_popset_32329588.fas | fasgrep -v "(AF194|349[06])" | B<fastr> --strict -N "-"  | B<alncut> -g | B<alnpi>


=head1 SEE ALSO

=over 8

=item C<man perlre>

=item C<perldoc perlre>

bin/fastr  view on Meta::CPAN

=over 8

B<fastr> -nscD 'ACGT' t/data/P450.fas

=back

Control and check the function of B<--strict>: 

=over 8

C<fastr --strict t/data/ArdellEtAl03_ncbi_popset_32329588.fas | fascomp -t>
C<cat t/data/ArdellEtAl03_ncbi_popset_32329588.fas | fascomp -t>

=back

=head1 SEE ALSO

=over 8

=item C<man perlre>

=item C<perldoc perlre>

bin/gbfalncut  view on Meta::CPAN

processing data).

=back

=head1 EXAMPLES

Print alignment of 5'UTRs

=over 8

B<gbfalncut> -k --verbose t/data/AF194338.1.gb 5.UTR t/data/ArdellEtAl03_ncbi_popset_32329588.fas

=back

Print alignment of coding regions (CDS), remove sequences, degap and translate them

=over 8

B<gbfalncut> -k  t/data/AF194338.1.gb CDS t/data/ArdellEtAl03_ncbi_popset_32329588.fas | fasgrep -v "(AF194|3496)" | fastr -snD "-" | fasxl -t 6

=back

=head1 SEE ALSO

=over 8

=item C<man perlre>

=item C<perldoc perlre>