├── .dockerignore ├── .gitignore ├── .travis.yml ├── AUTHORS ├── CHANGELOG.md ├── Dockerfile ├── LICENSE ├── README.md ├── environment.yml ├── pyproject.toml ├── src └── pyfastaq │ ├── __init__.py │ ├── app_fastaq.py │ ├── caf.py │ ├── genetic_codes.py │ ├── intervals.py │ ├── runners │ ├── __init__.py │ ├── acgtn_only.py │ ├── add_indels.py │ ├── caf_to_fastq.py │ ├── capillary_to_pairs.py │ ├── chunker.py │ ├── count_sequences.py │ ├── deinterleave.py │ ├── enumerate_names.py │ ├── expand_nucleotides.py │ ├── fasta_to_fastq.py │ ├── filter.py │ ├── get_ids.py │ ├── get_seq_flanking_gaps.py │ ├── interleave.py │ ├── make_random_contigs.py │ ├── merge.py │ ├── replace_bases.py │ ├── reverse_complement.py │ ├── scaffolds_to_contigs.py │ ├── search_for_seq.py │ ├── sequence_trim.py │ ├── sort_by_name.py │ ├── sort_by_size.py │ ├── split_by_base_count.py │ ├── strip_illumina_suffix.py │ ├── to_boulderio.py │ ├── to_fake_qual.py │ ├── to_fasta.py │ ├── to_mira_xml.py │ ├── to_orfs_gff.py │ ├── to_perfect_reads.py │ ├── to_random_subset.py │ ├── to_tiling_bam.py │ ├── to_unique_by_id.py │ ├── translate.py │ ├── trim_Ns_at_end.py │ ├── trim_contigs.py │ ├── trim_ends.py │ └── version.py │ ├── sequences.py │ ├── tasks.py │ └── utils.py └── tests ├── caf_test.py ├── data ├── caf_test.caf ├── caf_test.to_fastq.no_trim.min_length_0.fq ├── caf_test.to_fastq.trim.min_length_6.fq ├── readnames_with_comments.fastq ├── readnames_with_comments.fastq.filtered ├── readnames_with_comments.fastq.ids ├── sequences_test.embl ├── sequences_test.embl.bad ├── sequences_test.embl.bad2 ├── sequences_test.embl.to_fasta ├── sequences_test.fa ├── sequences_test.fa.ids ├── sequences_test.fa.qual ├── sequences_test.fa.qual.bad ├── sequences_test.fasta_to_fastq.fq ├── sequences_test.gbk ├── sequences_test.gbk.to_fasta ├── sequences_test.line_length3.fa ├── sequences_test.to_fasta.strip_after_whitespace_non_unique.in.fa ├── sequences_test.to_fasta.strip_after_whitespace_non_unique.out.fa ├── sequences_test.to_fasta.strip_after_whitespace_unique.in.fa ├── sequences_test.to_fasta.strip_after_whitespace_unique.out.fa ├── sequences_test_3-per-line.fa ├── sequences_test_cap_to_read_pairs.fa ├── sequences_test_cap_to_read_pairs.fa.paired.gz ├── sequences_test_cap_to_read_pairs.fa.unpaired.gz ├── sequences_test_deinterleaved_1.fa ├── sequences_test_deinterleaved_2.fa ├── sequences_test_deinterleaved_bad2_1.fa ├── sequences_test_deinterleaved_bad2_2.fa ├── sequences_test_deinterleaved_bad_1.fa ├── sequences_test_deinterleaved_bad_2.fa ├── sequences_test_deinterleaved_no_suffixes_1.fa ├── sequences_test_deinterleaved_no_suffixes_2.fa ├── sequences_test_empty_file ├── sequences_test_enumerate_names.fa ├── sequences_test_enumerate_names.fa.out.add_suffix ├── sequences_test_enumerate_names.fa.out.keep_suffix ├── sequences_test_enumerate_names.fa.out.start.1 ├── sequences_test_enumerate_names.fa.out.start.1.rename_file ├── sequences_test_enumerate_names.fa.out.start.2 ├── sequences_test_fai_test.fa ├── sequences_test_fai_test.fa.fai ├── sequences_test_fail_no_AT.fq ├── sequences_test_fail_no_plus.fq ├── sequences_test_fail_no_qual.fq ├── sequences_test_fail_no_seq.fq ├── sequences_test_fastaq_replace_bases.expected.fa ├── sequences_test_fastaq_replace_bases.fa ├── sequences_test_filter_by_ids_file.fa ├── sequences_test_filter_by_ids_file.fa.filtered ├── sequences_test_filter_by_ids_file.fa.filtered.invert ├── sequences_test_filter_by_ids_file.fa.ids ├── sequences_test_filter_by_regex.fa ├── sequences_test_filter_by_regex.first-char-a.fa ├── sequences_test_filter_by_regex.first-of-pair.fa ├── sequences_test_filter_by_regex.numeric.fa ├── sequences_test_get_seqs_flanking_gaps.fa ├── sequences_test_get_seqs_flanking_gaps.fa.out ├── sequences_test_gffv3.gff ├── sequences_test_gffv3.gff.fasta ├── sequences_test_gffv3.gff.to_fasta ├── sequences_test_gffv3.no_FASTA_line.gff ├── sequences_test_gffv3.no_FASTA_line.gff.to_fasta ├── sequences_test_gffv3.no_seq.2.gff ├── sequences_test_gffv3.no_seq.gff ├── sequences_test_good_file.fq ├── sequences_test_good_file.fq.to_fasta ├── sequences_test_good_file_mira.xml ├── sequences_test_interleaved.fa ├── sequences_test_interleaved.fq ├── sequences_test_interleaved_bad.fa ├── sequences_test_interleaved_with_suffixes.fa ├── sequences_test_length_filter.fa ├── sequences_test_length_filter.min-0.max-1.fa ├── sequences_test_length_filter.min-0.max-inf.fa ├── sequences_test_length_filter.min-4.max-4.fa ├── sequences_test_make_random_contigs.default.fa ├── sequences_test_make_random_contigs.first-42.fa ├── sequences_test_make_random_contigs.name-by-letters.fa ├── sequences_test_make_random_contigs.prefix-p.fa ├── sequences_test_merge_to_one_seq.fa ├── sequences_test_merge_to_one_seq.fq ├── sequences_test_merge_to_one_seq.merged.fa ├── sequences_test_merge_to_one_seq.merged.fq ├── sequences_test_not_a_fastaq_file ├── sequences_test_one-per-line.fa ├── sequences_test_orfs.fa ├── sequences_test_orfs.gff ├── sequences_test_phylip.interleaved ├── sequences_test_phylip.interleaved.to_fasta ├── sequences_test_phylip.interleaved2 ├── sequences_test_phylip.interleaved2.to_fasta ├── sequences_test_phylip.made_by_seaview ├── sequences_test_phylip.made_by_seaview.to_fasta ├── sequences_test_phylip.sequential ├── sequences_test_phylip.sequential.to_fasta ├── sequences_test_revcomp.fa ├── sequences_test_search_string.fa ├── sequences_test_search_string.fa.hits ├── sequences_test_split_fixed_size.fa ├── sequences_test_split_fixed_size.fa.split.1 ├── sequences_test_split_fixed_size.fa.split.2 ├── sequences_test_split_fixed_size.fa.split.3 ├── sequences_test_split_fixed_size.fa.split.4 ├── sequences_test_split_fixed_size.fa.split.5 ├── sequences_test_split_fixed_size.fa.split.6 ├── sequences_test_split_fixed_size.fa.split.coords ├── sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.1 ├── sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.2 ├── sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.3 ├── sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.4 ├── sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords ├── sequences_test_split_fixed_size_onefile.fa ├── sequences_test_split_fixed_size_onefile.out.fa ├── sequences_test_split_fixed_size_onefile.skip_Ns.out.fa ├── sequences_test_split_test.fa ├── sequences_test_split_test.fa.2.1 ├── sequences_test_split_test.fa.2.2 ├── sequences_test_split_test.fa.2.3 ├── sequences_test_split_test.fa.2.4 ├── sequences_test_split_test.fa.3.1 ├── sequences_test_split_test.fa.3.2 ├── sequences_test_split_test.fa.3.3 ├── sequences_test_split_test.fa.4.1 ├── sequences_test_split_test.fa.4.2 ├── sequences_test_split_test.fa.4.3 ├── sequences_test_split_test.fa.6.1 ├── sequences_test_split_test.fa.6.2 ├── sequences_test_split_test.fa.6.limit2.1 ├── sequences_test_split_test.fa.6.limit2.2 ├── sequences_test_split_test.fa.6.limit2.3 ├── sequences_test_split_test.long.fa ├── sequences_test_split_test.long.fa.2.1 ├── sequences_test_split_test.long.fa.2.2 ├── sequences_test_strip_after_whitespace.fa ├── sequences_test_strip_after_whitespace.fa.to_fasta ├── sequences_test_strip_illumina_suffix.fq ├── sequences_test_strip_illumina_suffix.fq.stripped ├── sequences_test_to_fasta_union.in.fa ├── sequences_test_to_fasta_union.out.fa ├── sequences_test_to_unique_by_id.fa ├── sequences_test_to_unique_by_id.fa.out ├── sequences_test_translate.fa ├── sequences_test_translate.fa.frame0 ├── sequences_test_translate.fa.frame1 ├── sequences_test_translate.fa.frame2 ├── sequences_test_trim_Ns_at_end.fa ├── sequences_test_trim_Ns_at_end.fa.trimmed ├── sequences_test_trim_contigs.fa ├── sequences_test_trim_contigs.fa.out ├── sequences_test_trimmed.fq ├── sequences_test_untrimmed.fq ├── tasks_test_expend_nucleotides.in.fa ├── tasks_test_expend_nucleotides.in.fq ├── tasks_test_expend_nucleotides.out.fa ├── tasks_test_expend_nucleotides.out.fq ├── tasks_test_fasta_to_fake_qual.in.fa ├── tasks_test_fasta_to_fake_qual.out.default.qual ├── tasks_test_fasta_to_fake_qual.out.q42.qual ├── tasks_test_filter_paired_both_pass.in_1.fa ├── tasks_test_filter_paired_both_pass.in_2.fa ├── tasks_test_filter_paired_both_pass.out_1.fa ├── tasks_test_filter_paired_both_pass.out_2.fa ├── tasks_test_filter_paired_one_pass.in_1.fa ├── tasks_test_filter_paired_one_pass.in_2.fa ├── tasks_test_filter_paired_one_pass.out_1.fa ├── tasks_test_filter_paired_one_pass.out_2.fa ├── tasks_test_length_offsets_from_fai.fa ├── tasks_test_length_offsets_from_fai.fa.fai ├── tasks_test_make_long_reads.input.fa ├── tasks_test_make_long_reads.output.fa ├── tasks_test_mean_length.fa ├── tasks_test_sequence_trim_1.fa ├── tasks_test_sequence_trim_1.trimmed.fa ├── tasks_test_sequence_trim_2.fa ├── tasks_test_sequence_trim_2.trimmed.fa ├── tasks_test_sequences_to_trim.fa ├── tasks_test_sort_by_name.in.fa ├── tasks_test_sort_by_name.out.fa ├── tasks_test_sort_by_size.in.fa ├── tasks_test_sort_by_size.out.fa ├── tasks_test_sort_by_size.out.rev.fa ├── tasks_test_stats_from_fai.in.empty.fai ├── tasks_test_stats_from_fai.in.fai ├── tasks_test_to_boulderio.in.fa ├── tasks_test_to_boulderio.out.boulder ├── tasks_test_to_fastg.fasta ├── tasks_test_to_fastg.fastg ├── tasks_test_to_fastg.ids_to_circularise ├── test_acgtn_only.expected.fa ├── test_acgtn_only.in.fa ├── utils_test_file_transpose.txt ├── utils_test_file_transposed.txt ├── utils_test_not_really_zipped.gz ├── utils_test_scaffolds.fa ├── utils_test_scaffolds.fa.to_contigs.fa ├── utils_test_scaffolds.fa.to_contigs.number_contigs.fa └── utils_test_system_call.txt ├── intervals_test.py ├── sequences_test.py ├── tasks_test.py └── utils_test.py /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/Fastaq/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitignore: 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