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Description: FASTA and FASTQ file manipulation tools
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
Description: FASTA and FASTQ file manipulation tools
Fastaq represents a diverse collection of scripts that perform useful and
common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting,
sorting, trimming, search/replace, etc. Input and output files can be gzipped
(format is automatically detected) and individual Fastaq commands can be piped
together.
--- 227241 Thu Jan 1 00:00:00 1970
+++ 238858 Thu Jan 1 00:00:00 1970
@@ -1,153 +1,6 @@
FASTA and FASTQ file manipulation tools
- A collection of scripts that perform useful and common
+ Fastaq represents a diverse collection of scripts that perform useful and
- fasta/q manipulation tasks.
+ common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting,
- .
+ sorting, trimming, search/replace, etc. Input and output files can be gzipped
- All scripts automatically detect whether the input is
+ (format is automatically detected) and individual Fastaq commands can be piped
- a FASTA or FASTQ file.
+ together.
- .
- 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