[med-svn] [fastaq_tmp] branch upstream updated (9134772 -> e255484)
Andreas Tille
tille at debian.org
Tue Mar 3 07:46:50 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository fastaq_tmp.
from 9134772 Imported Upstream version 1.6.0
new e255484 Imported Upstream version 3.2.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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(-)
delete mode 100644 fastaq/__init__.py
create mode 100644 pyfastaq/__init__.py
create mode 100644 pyfastaq/caf.py
create mode 100644 pyfastaq/common.py
create mode 100644 pyfastaq/genetic_codes.py
rename {fastaq => pyfastaq}/intervals.py (100%)
copy fastaq/tests/data/sequences_test_empty_file => pyfastaq/runners/__init__.py (100%)
create mode 100644 pyfastaq/runners/add_indels.py
create mode 100644 pyfastaq/runners/caf_to_fastq.py
create mode 100644 pyfastaq/runners/capillary_to_pairs.py
create mode 100644 pyfastaq/runners/chunker.py
create mode 100644 pyfastaq/runners/count_sequences.py
create mode 100644 pyfastaq/runners/deinterleave.py
create mode 100644 pyfastaq/runners/enumerate_names.py
create mode 100644 pyfastaq/runners/expand_nucleotides.py
create mode 100644 pyfastaq/runners/fasta_to_fastq.py
create mode 100644 pyfastaq/runners/filter.py
create mode 100644 pyfastaq/runners/get_ids.py
create mode 100644 pyfastaq/runners/get_seq_flanking_gaps.py
create mode 100644 pyfastaq/runners/interleave.py
create mode 100644 pyfastaq/runners/long_read_simulate.py
create mode 100644 pyfastaq/runners/make_random_contigs.py
create mode 100644 pyfastaq/runners/merge.py
create mode 100644 pyfastaq/runners/replace_bases.py
create mode 100644 pyfastaq/runners/reverse_complement.py
create mode 100644 pyfastaq/runners/scaffolds_to_contigs.py
create mode 100644 pyfastaq/runners/search_for_seq.py
create mode 100644 pyfastaq/runners/sequence_trim.py
create mode 100644 pyfastaq/runners/sort_by_size.py
create mode 100644 pyfastaq/runners/split_by_base_count.py
create mode 100644 pyfastaq/runners/strip_illumina_suffix.py
create mode 100644 pyfastaq/runners/to_fake_qual.py
create mode 100644 pyfastaq/runners/to_fasta.py
create mode 100644 pyfastaq/runners/to_mira_xml.py
create mode 100644 pyfastaq/runners/to_orfs_gff.py
create mode 100644 pyfastaq/runners/to_perfect_reads.py
create mode 100644 pyfastaq/runners/to_random_subset.py
create mode 100644 pyfastaq/runners/to_tiling_bam.py
create mode 100644 pyfastaq/runners/to_unique_by_id.py
create mode 100644 pyfastaq/runners/translate.py
create mode 100644 pyfastaq/runners/trim_Ns_at_end.py
create mode 100644 pyfastaq/runners/trim_contigs.py
create mode 100644 pyfastaq/runners/trim_ends.py
create mode 100644 pyfastaq/runners/version.py
rename {fastaq => pyfastaq}/sequences.py (96%)
rename {fastaq => pyfastaq}/tasks.py (85%)
create mode 100644 pyfastaq/tests/caf_test.py
create mode 100644 pyfastaq/tests/data/caf_test.caf
create mode 100644 pyfastaq/tests/data/caf_test.to_fastq.no_trim.min_length_0.fq
create mode 100644 pyfastaq/tests/data/caf_test.to_fastq.trim.min_length_6.fq
rename {fastaq => pyfastaq}/tests/data/sequences_test.embl (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.embl.bad (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.embl.bad2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.embl.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.fa.ids (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.fa.qual (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.fa.qual.bad (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.fasta_to_fastq.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.gbk (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.gbk.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test.line_length3.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_3-per-line.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_cap_to_read_pairs.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_cap_to_read_pairs.fa.paired.gz (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_cap_to_read_pairs.fa.unpaired.gz (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_deinterleaved_1.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_deinterleaved_2.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_deinterleaved_bad2_1.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_deinterleaved_bad2_2.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_deinterleaved_bad_1.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_deinterleaved_bad_2.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_empty_file (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_enumerate_names.fa (100%)
create mode 100644 pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.add_suffix
rename {fastaq => pyfastaq}/tests/data/sequences_test_enumerate_names.fa.out.keep_suffix (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_enumerate_names.fa.out.start.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_enumerate_names.fa.out.start.1.rename_file (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_enumerate_names.fa.out.start.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fai_test.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fai_test.fa.fai (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fail_no_AT.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fail_no_plus.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fail_no_qual.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fail_no_seq.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fastaq_replace_bases.expected.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_fastaq_replace_bases.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_ids_file.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_ids_file.fa.filtered (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_ids_file.fa.filtered.invert (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_ids_file.fa.ids (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_regex.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_regex.first-char-a.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_regex.first-of-pair.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_filter_by_regex.numeric.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_get_seqs_flanking_gaps.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_get_seqs_flanking_gaps.fa.out (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_gffv3.gff (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_gffv3.gff.fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_gffv3.gff.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_gffv3.no_FASTA_line.gff (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_gffv3.no_FASTA_line.gff.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_gffv3.no_seq.2.gff (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_gffv3.no_seq.gff (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_good_file.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_good_file.fq.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_good_file_mira.xml (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_interleaved.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_interleaved.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_interleaved_bad.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_length_filter.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_length_filter.min-0.max-1.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_length_filter.min-0.max-inf.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_length_filter.min-4.max-4.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_make_random_contigs.default.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_make_random_contigs.first-42.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_make_random_contigs.name-by-letters.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_make_random_contigs.prefix-p.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_merge_to_one_seq.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_merge_to_one_seq.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_merge_to_one_seq.merged.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_merge_to_one_seq.merged.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_not_a_fastaq_file (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_one-per-line.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_orfs.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_orfs.gff (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.interleaved (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.interleaved.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.interleaved2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.interleaved2.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.made_by_seaview (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.made_by_seaview.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.sequential (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_phylip.sequential.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_revcomp.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_search_string.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_search_string.fa.hits (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.3 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.4 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.5 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.6 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.coords (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.3 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.4 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords (100%)
create mode 100644 pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.fa
create mode 100644 pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.out.fa
create mode 100644 pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.skip_Ns.out.fa
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.2.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.2.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.2.3 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.2.4 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.3.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.3.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.3.3 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.4.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.4.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.4.3 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.6.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.6.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.6.limit2.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.6.limit2.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.fa.6.limit2.3 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.long.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.long.fa.2.1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_split_test.long.fa.2.2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_strip_after_whitespace.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_strip_after_whitespace.fa.to_fasta (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_strip_illumina_suffix.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_strip_illumina_suffix.fq.stripped (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_to_fasta_union.in.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_to_fasta_union.out.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_to_unique_by_id.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_to_unique_by_id.fa.out (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_translate.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_translate.fa.frame0 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_translate.fa.frame1 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_translate.fa.frame2 (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_trim_Ns_at_end.fa (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_trim_Ns_at_end.fa.trimmed (100%)
rename fastaq/tests/data/sequences_test_extend_gaps.fa => pyfastaq/tests/data/sequences_test_trim_contigs.fa (100%)
rename fastaq/tests/data/sequences_test_extend_gaps.fa.out => pyfastaq/tests/data/sequences_test_trim_contigs.fa.out (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_trimmed.fq (100%)
rename {fastaq => pyfastaq}/tests/data/sequences_test_untrimmed.fq (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_expend_nucleotides.in.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_expend_nucleotides.in.fq (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_expend_nucleotides.out.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_expend_nucleotides.out.fq (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_fasta_to_fake_qual.in.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_fasta_to_fake_qual.out.default.qual (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_fasta_to_fake_qual.out.q42.qual (100%)
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_both_pass.in_1.fa
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_both_pass.in_2.fa
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_both_pass.out_1.fa
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_both_pass.out_2.fa
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_one_pass.in_1.fa
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_one_pass.in_2.fa
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_one_pass.out_1.fa
create mode 100644 pyfastaq/tests/data/tasks_test_filter_paired_one_pass.out_2.fa
rename {fastaq => pyfastaq}/tests/data/tasks_test_make_long_reads.input.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_make_long_reads.output.fa (100%)
create mode 100644 pyfastaq/tests/data/tasks_test_mean_length.fa
rename {fastaq => pyfastaq}/tests/data/tasks_test_sequence_trim_1.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_sequence_trim_1.trimmed.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_sequence_trim_2.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_sequence_trim_2.trimmed.fa (100%)
rename {fastaq => pyfastaq}/tests/data/tasks_test_sequences_to_trim.fa (100%)
create mode 100644 pyfastaq/tests/data/tasks_test_sort_by_size.in.fa
create mode 100644 pyfastaq/tests/data/tasks_test_sort_by_size.out.fa
create mode 100644 pyfastaq/tests/data/tasks_test_sort_by_size.out.rev.fa
rename {fastaq => pyfastaq}/tests/data/utils_test_file_transpose.txt (100%)
rename {fastaq => pyfastaq}/tests/data/utils_test_file_transposed.txt (100%)
rename {fastaq => pyfastaq}/tests/data/utils_test_not_really_zipped.gz (100%)
rename {fastaq => pyfastaq}/tests/data/utils_test_scaffolds.fa (100%)
rename {fastaq => pyfastaq}/tests/data/utils_test_scaffolds.fa.to_contigs.fa (100%)
rename {fastaq => pyfastaq}/tests/data/utils_test_scaffolds.fa.to_contigs.number_contigs.fa (100%)
rename {fastaq => pyfastaq}/tests/data/utils_test_system_call.txt (100%)
rename {fastaq => pyfastaq}/tests/intervals_test.py (99%)
rename {fastaq => pyfastaq}/tests/sequences_test.py (97%)
rename {fastaq => pyfastaq}/tests/tasks_test.py (83%)
rename {fastaq => pyfastaq}/tests/utils_test.py (99%)
rename {fastaq => pyfastaq}/utils.py (100%)
create mode 100755 scripts/fastaq
delete mode 100755 scripts/fastaq_capillary_to_pairs
delete mode 100755 scripts/fastaq_chunker
delete mode 100755 scripts/fastaq_count_sequences
delete mode 100755 scripts/fastaq_deinterleave
delete mode 100755 scripts/fastaq_enumerate_names
delete mode 100755 scripts/fastaq_expand_nucleotides
delete mode 100755 scripts/fastaq_extend_gaps
delete mode 100755 scripts/fastaq_fasta_to_fastq
delete mode 100755 scripts/fastaq_filter
delete mode 100755 scripts/fastaq_get_ids
delete mode 100755 scripts/fastaq_get_seq_flanking_gaps
delete mode 100755 scripts/fastaq_insert_or_delete_bases
delete mode 100755 scripts/fastaq_interleave
delete mode 100755 scripts/fastaq_long_read_simulate
delete mode 100755 scripts/fastaq_make_random_contigs
delete mode 100755 scripts/fastaq_merge
delete mode 100755 scripts/fastaq_replace_bases
delete mode 100755 scripts/fastaq_reverse_complement
delete mode 100755 scripts/fastaq_scaffolds_to_contigs
delete mode 100755 scripts/fastaq_search_for_seq
delete mode 100755 scripts/fastaq_sequence_trim
delete mode 100755 scripts/fastaq_split_by_base_count
delete mode 100755 scripts/fastaq_strip_illumina_suffix
delete mode 100755 scripts/fastaq_to_fake_qual
delete mode 100755 scripts/fastaq_to_fasta
delete mode 100755 scripts/fastaq_to_mira_xml
delete mode 100755 scripts/fastaq_to_orfs_gff
delete mode 100755 scripts/fastaq_to_perfect_reads
delete mode 100755 scripts/fastaq_to_random_subset
delete mode 100755 scripts/fastaq_to_tiling_bam
delete mode 100755 scripts/fastaq_to_unique_by_id
delete mode 100755 scripts/fastaq_translate
delete mode 100755 scripts/fastaq_trim_Ns_at_end
delete mode 100755 scripts/fastaq_trim_ends
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