[med-svn] [fastaq_tmp] 02/02: Merge tag 'upstream/3.2.0'
Andreas Tille
tille at debian.org
Tue Mar 3 07:46:49 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fastaq_tmp.
commit 5fc692306ea092f782fa2e1caf519a1730bd280d
Merge: a87529d e255484
Author: Andreas Tille <tille at debian.org>
Date: Tue Mar 3 08:45:33 2015 +0100
Merge tag 'upstream/3.2.0'
Upstream version 3.2.0
MANIFEST.in | 2 +-
README.md | 99 ++++++++++++---
fastaq/__init__.py | 2 -
pyfastaq/__init__.py | 11 ++
pyfastaq/caf.py | 79 ++++++++++++
pyfastaq/common.py | 1 +
pyfastaq/genetic_codes.py | 139 +++++++++++++++++++++
{fastaq => pyfastaq}/intervals.py | 0
.../runners/__init__.py | 0
pyfastaq/runners/add_indels.py | 93 ++++++++++++++
pyfastaq/runners/caf_to_fastq.py | 19 +++
pyfastaq/runners/capillary_to_pairs.py | 12 ++
pyfastaq/runners/chunker.py | 30 +++++
pyfastaq/runners/count_sequences.py | 10 ++
pyfastaq/runners/deinterleave.py | 13 ++
pyfastaq/runners/enumerate_names.py | 20 +++
pyfastaq/runners/expand_nucleotides.py | 14 +++
pyfastaq/runners/fasta_to_fastq.py | 12 ++
pyfastaq/runners/filter.py | 32 +++++
pyfastaq/runners/get_ids.py | 11 ++
pyfastaq/runners/get_seq_flanking_gaps.py | 13 ++
pyfastaq/runners/interleave.py | 12 ++
pyfastaq/runners/long_read_simulate.py | 49 ++++++++
pyfastaq/runners/make_random_contigs.py | 24 ++++
pyfastaq/runners/merge.py | 16 +++
pyfastaq/runners/replace_bases.py | 13 ++
pyfastaq/runners/reverse_complement.py | 11 ++
pyfastaq/runners/scaffolds_to_contigs.py | 12 ++
pyfastaq/runners/search_for_seq.py | 12 ++
pyfastaq/runners/sequence_trim.py | 24 ++++
pyfastaq/runners/sort_by_size.py | 16 +++
pyfastaq/runners/split_by_base_count.py | 14 +++
pyfastaq/runners/strip_illumina_suffix.py | 11 ++
pyfastaq/runners/to_fake_qual.py | 17 +++
pyfastaq/runners/to_fasta.py | 20 +++
pyfastaq/runners/to_mira_xml.py | 11 ++
pyfastaq/runners/to_orfs_gff.py | 12 ++
pyfastaq/runners/to_perfect_reads.py | 85 +++++++++++++
pyfastaq/runners/to_random_subset.py | 35 ++++++
pyfastaq/runners/to_tiling_bam.py | 77 ++++++++++++
pyfastaq/runners/to_unique_by_id.py | 11 ++
pyfastaq/runners/translate.py | 12 ++
pyfastaq/runners/trim_Ns_at_end.py | 11 ++
pyfastaq/runners/trim_contigs.py | 12 ++
pyfastaq/runners/trim_ends.py | 13 ++
pyfastaq/runners/version.py | 4 +
{fastaq => pyfastaq}/sequences.py | 77 ++----------
{fastaq => pyfastaq}/tasks.py | 123 ++++++++++++++++--
pyfastaq/tests/caf_test.py | 47 +++++++
pyfastaq/tests/data/caf_test.caf | 48 +++++++
.../data/caf_test.to_fastq.no_trim.min_length_0.fq | 8 ++
.../data/caf_test.to_fastq.trim.min_length_6.fq | 4 +
.../tests/data/sequences_test.embl | 0
.../tests/data/sequences_test.embl.bad | 0
.../tests/data/sequences_test.embl.bad2 | 0
.../tests/data/sequences_test.embl.to_fasta | 0
{fastaq => pyfastaq}/tests/data/sequences_test.fa | 0
.../tests/data/sequences_test.fa.ids | 0
.../tests/data/sequences_test.fa.qual | 0
.../tests/data/sequences_test.fa.qual.bad | 0
.../tests/data/sequences_test.fasta_to_fastq.fq | 0
{fastaq => pyfastaq}/tests/data/sequences_test.gbk | 0
.../tests/data/sequences_test.gbk.to_fasta | 0
.../tests/data/sequences_test.line_length3.fa | 0
.../tests/data/sequences_test_3-per-line.fa | 0
.../tests/data/sequences_test_cap_to_read_pairs.fa | 0
.../sequences_test_cap_to_read_pairs.fa.paired.gz | Bin
...sequences_test_cap_to_read_pairs.fa.unpaired.gz | Bin
.../tests/data/sequences_test_deinterleaved_1.fa | 0
.../tests/data/sequences_test_deinterleaved_2.fa | 0
.../data/sequences_test_deinterleaved_bad2_1.fa | 0
.../data/sequences_test_deinterleaved_bad2_2.fa | 0
.../data/sequences_test_deinterleaved_bad_1.fa | 0
.../data/sequences_test_deinterleaved_bad_2.fa | 0
.../tests/data/sequences_test_empty_file | 0
.../tests/data/sequences_test_enumerate_names.fa | 0
...equences_test_enumerate_names.fa.out.add_suffix | 8 ++
...quences_test_enumerate_names.fa.out.keep_suffix | 0
.../sequences_test_enumerate_names.fa.out.start.1 | 0
...test_enumerate_names.fa.out.start.1.rename_file | 0
.../sequences_test_enumerate_names.fa.out.start.2 | 0
.../tests/data/sequences_test_fai_test.fa | 0
.../tests/data/sequences_test_fai_test.fa.fai | 0
.../tests/data/sequences_test_fail_no_AT.fq | 0
.../tests/data/sequences_test_fail_no_plus.fq | 0
.../tests/data/sequences_test_fail_no_qual.fq | 0
.../tests/data/sequences_test_fail_no_seq.fq | 0
...sequences_test_fastaq_replace_bases.expected.fa | 0
.../data/sequences_test_fastaq_replace_bases.fa | 0
.../data/sequences_test_filter_by_ids_file.fa | 0
.../sequences_test_filter_by_ids_file.fa.filtered | 0
...nces_test_filter_by_ids_file.fa.filtered.invert | 0
.../data/sequences_test_filter_by_ids_file.fa.ids | 0
.../tests/data/sequences_test_filter_by_regex.fa | 0
.../sequences_test_filter_by_regex.first-char-a.fa | 0
...sequences_test_filter_by_regex.first-of-pair.fa | 0
.../data/sequences_test_filter_by_regex.numeric.fa | 0
.../data/sequences_test_get_seqs_flanking_gaps.fa | 0
.../sequences_test_get_seqs_flanking_gaps.fa.out | 0
.../tests/data/sequences_test_gffv3.gff | 0
.../tests/data/sequences_test_gffv3.gff.fasta | 0
.../tests/data/sequences_test_gffv3.gff.to_fasta | 0
.../data/sequences_test_gffv3.no_FASTA_line.gff | 0
...sequences_test_gffv3.no_FASTA_line.gff.to_fasta | 0
.../tests/data/sequences_test_gffv3.no_seq.2.gff | 0
.../tests/data/sequences_test_gffv3.no_seq.gff | 0
.../tests/data/sequences_test_good_file.fq | 0
.../data/sequences_test_good_file.fq.to_fasta | 0
.../tests/data/sequences_test_good_file_mira.xml | 0
.../tests/data/sequences_test_interleaved.fa | 0
.../tests/data/sequences_test_interleaved.fq | 0
.../tests/data/sequences_test_interleaved_bad.fa | 0
.../tests/data/sequences_test_length_filter.fa | 0
.../sequences_test_length_filter.min-0.max-1.fa | 0
.../sequences_test_length_filter.min-0.max-inf.fa | 0
.../sequences_test_length_filter.min-4.max-4.fa | 0
.../sequences_test_make_random_contigs.default.fa | 0
.../sequences_test_make_random_contigs.first-42.fa | 0
...ces_test_make_random_contigs.name-by-letters.fa | 0
.../sequences_test_make_random_contigs.prefix-p.fa | 0
.../tests/data/sequences_test_merge_to_one_seq.fa | 0
.../tests/data/sequences_test_merge_to_one_seq.fq | 0
.../data/sequences_test_merge_to_one_seq.merged.fa | 0
.../data/sequences_test_merge_to_one_seq.merged.fq | 0
.../tests/data/sequences_test_not_a_fastaq_file | 0
.../tests/data/sequences_test_one-per-line.fa | 0
.../tests/data/sequences_test_orfs.fa | 0
.../tests/data/sequences_test_orfs.gff | 0
.../tests/data/sequences_test_phylip.interleaved | 0
.../sequences_test_phylip.interleaved.to_fasta | 0
.../tests/data/sequences_test_phylip.interleaved2 | 0
.../sequences_test_phylip.interleaved2.to_fasta | 0
.../data/sequences_test_phylip.made_by_seaview | 0
.../sequences_test_phylip.made_by_seaview.to_fasta | 0
.../tests/data/sequences_test_phylip.sequential | 0
.../data/sequences_test_phylip.sequential.to_fasta | 0
.../tests/data/sequences_test_revcomp.fa | 0
.../tests/data/sequences_test_search_string.fa | 0
.../data/sequences_test_search_string.fa.hits | 0
.../tests/data/sequences_test_split_fixed_size.fa | 0
.../sequences_test_split_fixed_size.fa.split.1 | 0
.../sequences_test_split_fixed_size.fa.split.2 | 0
.../sequences_test_split_fixed_size.fa.split.3 | 0
.../sequences_test_split_fixed_size.fa.split.4 | 0
.../sequences_test_split_fixed_size.fa.split.5 | 0
.../sequences_test_split_fixed_size.fa.split.6 | 0
...sequences_test_split_fixed_size.fa.split.coords | 0
...test_split_fixed_size.fa.split.skip_if_all_Ns.1 | 0
...test_split_fixed_size.fa.split.skip_if_all_Ns.2 | 0
...test_split_fixed_size.fa.split.skip_if_all_Ns.3 | 0
...test_split_fixed_size.fa.split.skip_if_all_Ns.4 | 0
...split_fixed_size.fa.split.skip_if_all_Ns.coords | 0
.../sequences_test_split_fixed_size_onefile.fa | 18 +++
.../sequences_test_split_fixed_size_onefile.out.fa | 32 +++++
...es_test_split_fixed_size_onefile.skip_Ns.out.fa | 30 +++++
.../tests/data/sequences_test_split_test.fa | 0
.../tests/data/sequences_test_split_test.fa.2.1 | 0
.../tests/data/sequences_test_split_test.fa.2.2 | 0
.../tests/data/sequences_test_split_test.fa.2.3 | 0
.../tests/data/sequences_test_split_test.fa.2.4 | 0
.../tests/data/sequences_test_split_test.fa.3.1 | 0
.../tests/data/sequences_test_split_test.fa.3.2 | 0
.../tests/data/sequences_test_split_test.fa.3.3 | 0
.../tests/data/sequences_test_split_test.fa.4.1 | 0
.../tests/data/sequences_test_split_test.fa.4.2 | 0
.../tests/data/sequences_test_split_test.fa.4.3 | 0
.../tests/data/sequences_test_split_test.fa.6.1 | 0
.../tests/data/sequences_test_split_test.fa.6.2 | 0
.../data/sequences_test_split_test.fa.6.limit2.1 | 0
.../data/sequences_test_split_test.fa.6.limit2.2 | 0
.../data/sequences_test_split_test.fa.6.limit2.3 | 0
.../tests/data/sequences_test_split_test.long.fa | 0
.../data/sequences_test_split_test.long.fa.2.1 | 0
.../data/sequences_test_split_test.long.fa.2.2 | 0
.../data/sequences_test_strip_after_whitespace.fa | 0
...quences_test_strip_after_whitespace.fa.to_fasta | 0
.../data/sequences_test_strip_illumina_suffix.fq | 0
...equences_test_strip_illumina_suffix.fq.stripped | 0
.../tests/data/sequences_test_to_fasta_union.in.fa | 0
.../data/sequences_test_to_fasta_union.out.fa | 0
.../tests/data/sequences_test_to_unique_by_id.fa | 0
.../data/sequences_test_to_unique_by_id.fa.out | 0
.../tests/data/sequences_test_translate.fa | 0
.../tests/data/sequences_test_translate.fa.frame0 | 0
.../tests/data/sequences_test_translate.fa.frame1 | 0
.../tests/data/sequences_test_translate.fa.frame2 | 0
.../tests/data/sequences_test_trim_Ns_at_end.fa | 0
.../data/sequences_test_trim_Ns_at_end.fa.trimmed | 0
.../tests/data/sequences_test_trim_contigs.fa | 0
.../tests/data/sequences_test_trim_contigs.fa.out | 0
.../tests/data/sequences_test_trimmed.fq | 0
.../tests/data/sequences_test_untrimmed.fq | 0
.../tests/data/tasks_test_expend_nucleotides.in.fa | 0
.../tests/data/tasks_test_expend_nucleotides.in.fq | 0
.../data/tasks_test_expend_nucleotides.out.fa | 0
.../data/tasks_test_expend_nucleotides.out.fq | 0
.../tests/data/tasks_test_fasta_to_fake_qual.in.fa | 0
.../tasks_test_fasta_to_fake_qual.out.default.qual | 0
.../tasks_test_fasta_to_fake_qual.out.q42.qual | 0
.../tasks_test_filter_paired_both_pass.in_1.fa | 8 ++
.../tasks_test_filter_paired_both_pass.in_2.fa | 8 ++
.../tasks_test_filter_paired_both_pass.out_1.fa | 2 +
.../tasks_test_filter_paired_both_pass.out_2.fa | 2 +
.../data/tasks_test_filter_paired_one_pass.in_1.fa | 8 ++
.../data/tasks_test_filter_paired_one_pass.in_2.fa | 8 ++
.../tasks_test_filter_paired_one_pass.out_1.fa | 6 +
.../tasks_test_filter_paired_one_pass.out_2.fa | 6 +
.../tests/data/tasks_test_make_long_reads.input.fa | 0
.../data/tasks_test_make_long_reads.output.fa | 0
pyfastaq/tests/data/tasks_test_mean_length.fa | 8 ++
.../tests/data/tasks_test_sequence_trim_1.fa | 0
.../data/tasks_test_sequence_trim_1.trimmed.fa | 0
.../tests/data/tasks_test_sequence_trim_2.fa | 0
.../data/tasks_test_sequence_trim_2.trimmed.fa | 0
.../tests/data/tasks_test_sequences_to_trim.fa | 0
pyfastaq/tests/data/tasks_test_sort_by_size.in.fa | 8 ++
pyfastaq/tests/data/tasks_test_sort_by_size.out.fa | 8 ++
.../tests/data/tasks_test_sort_by_size.out.rev.fa | 8 ++
.../tests/data/utils_test_file_transpose.txt | 0
.../tests/data/utils_test_file_transposed.txt | 0
.../tests/data/utils_test_not_really_zipped.gz | 0
.../tests/data/utils_test_scaffolds.fa | 0
.../data/utils_test_scaffolds.fa.to_contigs.fa | 0
..._test_scaffolds.fa.to_contigs.number_contigs.fa | 0
.../tests/data/utils_test_system_call.txt | 0
{fastaq => pyfastaq}/tests/intervals_test.py | 2 +-
{fastaq => pyfastaq}/tests/sequences_test.py | 16 ++-
{fastaq => pyfastaq}/tests/tasks_test.py | 95 +++++++++++++-
{fastaq => pyfastaq}/tests/utils_test.py | 2 +-
{fastaq => pyfastaq}/utils.py | 0
scripts/fastaq | 70 +++++++++++
scripts/fastaq_capillary_to_pairs | 12 --
scripts/fastaq_chunker | 21 ----
scripts/fastaq_count_sequences | 11 --
scripts/fastaq_deinterleave | 14 ---
scripts/fastaq_enumerate_names | 19 ---
scripts/fastaq_expand_nucleotides | 15 ---
scripts/fastaq_extend_gaps | 13 --
scripts/fastaq_fasta_to_fastq | 13 --
scripts/fastaq_filter | 24 ----
scripts/fastaq_get_ids | 12 --
scripts/fastaq_get_seq_flanking_gaps | 14 ---
scripts/fastaq_insert_or_delete_bases | 94 --------------
scripts/fastaq_interleave | 13 --
scripts/fastaq_long_read_simulate | 50 --------
scripts/fastaq_make_random_contigs | 25 ----
scripts/fastaq_merge | 18 ---
scripts/fastaq_replace_bases | 14 ---
scripts/fastaq_reverse_complement | 12 --
scripts/fastaq_scaffolds_to_contigs | 13 --
scripts/fastaq_search_for_seq | 13 --
scripts/fastaq_sequence_trim | 25 ----
scripts/fastaq_split_by_base_count | 15 ---
scripts/fastaq_strip_illumina_suffix | 12 --
scripts/fastaq_to_fake_qual | 18 ---
scripts/fastaq_to_fasta | 19 ---
scripts/fastaq_to_mira_xml | 12 --
scripts/fastaq_to_orfs_gff | 13 --
scripts/fastaq_to_perfect_reads | 86 -------------
scripts/fastaq_to_random_subset | 36 ------
scripts/fastaq_to_tiling_bam | 79 ------------
scripts/fastaq_to_unique_by_id | 12 --
scripts/fastaq_translate | 13 --
scripts/fastaq_trim_Ns_at_end | 12 --
scripts/fastaq_trim_ends | 14 ---
setup.py | 22 +++-
266 files changed, 1721 insertions(+), 893 deletions(-)
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