fastaq 1.5.0-1 (amd64 binary) in ubuntu vivid

 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.
 .
 fastaq_capillary_to_pairs -
 Given a fasta/q file of capillary reads,
 makes an interleaved file of read pairs
 .
 fastaq_chunker -
 Splits a multi fasta/q file into separate files.
 Splits sequences into chunks of a fixed size.
 .
 fastaq_count_sequences -
 Counts the number of sequences in a fasta/q file
 .
 fastaq_deinterleave -
 Deinterleaves fasta/q file, so that reads are written
 alternately between two output files
 .
 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