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