[med-svn] [fastaq] 01/02: New extended description in control file and correct ITP number in changelog

Thu Oct 23 13:38:23 UTC 2014

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jssoares-guest pushed a commit to branch master
in repository fastaq.

commit 6fdb7f9808fb555833ccc704bdc77c43ccad2ed3
Author: js21 <js21 at localhost.localdomain>
Date:   Thu Oct 23 14:36:05 2014 +0100

    New extended description in control file and correct ITP number in changelog
---
 debian/changelog |   4 +-
 debian/control   | 154 +++++++++++++++++++++++++++++++++++++++++++++++++++----
 2 files changed, 147 insertions(+), 11 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 9dec707..1a5d577 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
 fastaq (1.5.0-1) UNRELEASED; urgency=low
 
-  * Initial release (Closes: #1234)
+  * Initial release (Closes: #766321)
 
- -- DMPT <debian-med-packaging at lists.alioth.debian.org>  Thu, 24 May 2012 14:30:13 +0200
+ -- Jorge Soares <j.s.soares at gmail.com>  Thu, 24 May 2012 14:30:13 +0200
diff --git a/debian/control b/debian/control
index 82c37e6..ab630f3 100644
--- a/debian/control
+++ b/debian/control
@@ -15,22 +15,158 @@ Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/fastaq.git
 Homepage: https://github.com/sanger-pathogens/Fastaq
 
 Package: fastaq
-Architecture: any
-Depends: ${python3:Depends},
-         ${misc:Depends},
+Architecture: all
+Depends: ${python3:Depends}, ${misc:Depends}
 Description:  FASTA and FASTQ file manipulation tools
- All scripts automatically detect whether the input is a FASTA or FASTQ file.
+ A collection of scripts that perform useful and common
+ fasta/q manipulation tasks.
+ .
+ All scripts automatically detect whether the input is
+ a FASTA or FASTQ file.
  .
  Input and output files can be gzipped.
  .
- An input file is assumed to be gzipped if its name ends with .gz.
+ fastaq_capillary_to_pairs -
+ Given a fasta/q file of capillary reads,
+ makes an interleaved file of read pairs
  .
- To gzip an output file, just name it with .gz at the end.
+ fastaq_chunker -
+ Splits a multi fasta/q file into separate files.
+ Splits sequences into chunks of a fixed size.
  .
- You can use a minus sign for a filename to use stdin or stdout,
+ fastaq_count_sequences -
+ Counts the number of sequences in a fasta/q file
  .
- so scripts can be piped together.
+ fastaq_deinterleave -
+ Deinterleaves fasta/q file, so that reads are written
+ alternately between two output files
  .
- A developer API is also provided by this package.
+ fastaq_enumerate_names -
+ Renames sequences in a file, calling them 1,2,3...
+ .
+ fastaq_expand_nucleotides -
+ Makes all combinations of sequences in input file
+ by using all possibilities of redundant bases.
+ e.g. ART could be AAT or AGT.
+ .
+ fastaq_extend_gaps -
+ Extends the length of all gaps (and trims the start/end
+ of sequences) in a fasta/q file.
+ .
+ fastaq_fasta_to_fastq -
+ Given a fasta and qual file, makes a fastq file.
+ .
+ fastaq_filter -
+ Filters a fasta/q file by sequence length and/or
+ by name matching a regular expression.
+ .
+ fastaq_get_ids -
+ Gets IDs from each sequence in a fasta or fastq file.
+ .
+ fastaq_get_seq_flanking_gaps -
+ Gets the sequences either side of gaps in a fasta/q file.
+ .
+ fastaq_insert_or_delete_bases -
+ Deletes or inserts bases at given position(s)
+ from a fasta/q file.
+ .
+ fastaq_interleave -
+ Interleaves two fasta/q files, so that reads are written
+ alternately first/second in output file.
+ .
+ fastaq_long_read_simulate -
+ Simulates long reads from a fasta/q file. Can optionally
+ make insertions into the reads, like pacbio does.
+ .
+ fastaq_make_random_contigs -
+ Makes a multi-fasta file of random sequences,
+ all of the same length. Each base has equal chance of
+ being A,C,G or T
+ .
+ fastaq_merge -
+ Converts multi fasta/q file to single sequence file,
+ preserving original order of sequences.
+ .
+ fastaq_replace_bases -
+ Replaces all occurences of one letter with another in
+ a fasta/q file.
+ .
+ fastaq_reverse_complement -
+ Reverse complements all sequences in a fasta/q file
+ .
+ fastaq_scaffolds_to_contigs -
+ Creates a file of contigs from a file of scaffolds - i.e.
+ breaks at every gap in the input.
+ .
+ fastaq_search_for_seq -
+ Searches for an exact match on a given string and its
+ reverese complement, in every sequences of a fasta/q file.
+ Case insensitive. Guaranteed to find all hits.
  .
+ fastaq_sequence_trim -
+ Trims sequences off the start of all sequences in a pair
+ of fasta/q files, whenever there is a perfect match.
+ Only keeps a read pair if both reads of the pair are at
+ least a minimum length after any trimming.
+ .
+ fastaq_split_by_base_count -
+ Splits a multi fasta/q file into separate files.
+ Does not split sequences. Puts up to max_bases
+ into each split file. The exception is that any
+ sequence longer than max_bases is put into its own file.
+ .
+ fastaq_strip_illumina_suffix -
+ Strips /1 or /2 off the end of every read name
+ in a fasta/q file.
+ .
+ fastaq_to_fake_qual -
+ Makes fake quality scores file from a fasta/q file.
+ .
+ fastaq_to_fasta -
+ Converts sequence file to FASTA format.
+ .
+ fastaq_to_mira_xml -
+ Creates an xml file from a fasta/q file of reads,
+ for use with Mira assembler.
+ .
+ fastaq_to_orfs_gff -
+ Writes a GFF file of open reading frames from a fasta/q file
+ .
+ fastaq_to_perfect_reads -
+ Makes perfect paired end fastq reads from a fasta/q file,
+ with insert sizes sampled from a normal distribution.
+ Read orientation is innies. Output is an interleaved fastq file.
+ .
+ fastaq_to_quasr_primers_file -
+ Converts a fasta/q file to QUASR primers format:
+ just the sequence on each line and its reverse complement,
+ tab separated.
+ .
+ fastaq_to_random_subset -
+ Takes a random subset of reads from a fasta/q file and optionally
+ the corresponding read from a mates file.
+ Ouptut is interleaved if mates file given.
+ .
+ fastaq_to_tiling_bam -
+ Takes a fasta/q file. Makes a BAM file containing perfect
+ (unpaired) reads tiling the whole genome.
+ .
+ fastaq_to_unique_by_id -
+ Removes duplicate sequences from a fasta/q file,
+ based on their names. If the same name is found
+ more than once, then the longest sequence is kept.
+ Order of sequences is preserved in output.
+ .
+ fastaq_translate -
+ Translates all sequences in a fasta or fastq file.
+ Output is always fasta format
+ .
+ fastaq_trim_ends -
+ Trims set number of bases off each sequence in a fasta/q file
+ .
+ fastaq_trim_Ns_at_end -
+ Trims any Ns off each sequence in a fasta/q file.
+ Does nothing to gaps in the middle, just trims the ends
+ .
+ A developer API is also provided by this package.
  There are plenty of examples in tasks.py
\ No newline at end of file

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