[med-svn] [fastaq] branch master updated (7b74436 -> deeba8e)
Jorge Soares
jssoares-guest at moszumanska.debian.org
Wed Oct 8 13:05:07 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a change to branch master
in repository fastaq.
from 7b74436 Removed all the source code
new e8b8a82 initial upstream branch
new 7210af1 Merge branch 'upstream'
new ba05c94 Imported Upstream version 1.5.0
new deeba8e Adding new source
The 4 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:
AUTHORS | 1 +
fastaq/__init__.py | 2 +
fastaq/intervals.py | 117 ++++
fastaq/sequences.py | 638 ++++++++++++++++++
fastaq/tasks.py | 727 +++++++++++++++++++++
fastaq/tests/data/sequences_test.embl | 203 ++++++
fastaq/tests/data/sequences_test.embl.bad | 202 ++++++
fastaq/tests/data/sequences_test.embl.bad2 | 202 ++++++
fastaq/tests/data/sequences_test.embl.to_fasta | 64 ++
fastaq/tests/data/sequences_test.fa | 19 +
fastaq/tests/data/sequences_test.fa.ids | 4 +
fastaq/tests/data/sequences_test.fa.qual | 17 +
fastaq/tests/data/sequences_test.fa.qual.bad | 17 +
fastaq/tests/data/sequences_test.fasta_to_fastq.fq | 16 +
fastaq/tests/data/sequences_test.gbk | 170 +++++
fastaq/tests/data/sequences_test.gbk.to_fasta | 10 +
fastaq/tests/data/sequences_test.line_length3.fa | 12 +
fastaq/tests/data/sequences_test_3-per-line.fa | 19 +
.../tests/data/sequences_test_cap_to_read_pairs.fa | 16 +
.../sequences_test_cap_to_read_pairs.fa.paired.gz | Bin 0 -> 92 bytes
...sequences_test_cap_to_read_pairs.fa.unpaired.gz | Bin 0 -> 92 bytes
.../tests/data/sequences_test_deinterleaved_1.fa | 4 +
.../tests/data/sequences_test_deinterleaved_2.fa | 4 +
.../data/sequences_test_deinterleaved_bad2_1.fa | 2 +
.../data/sequences_test_deinterleaved_bad2_2.fa | 4 +
.../data/sequences_test_deinterleaved_bad_1.fa | 4 +
.../data/sequences_test_deinterleaved_bad_2.fa | 2 +
fastaq/tests/data/sequences_test_empty_file | 0
.../tests/data/sequences_test_enumerate_names.fa | 8 +
...quences_test_enumerate_names.fa.out.keep_suffix | 8 +
.../sequences_test_enumerate_names.fa.out.start.1 | 8 +
...test_enumerate_names.fa.out.start.1.rename_file | 5 +
.../sequences_test_enumerate_names.fa.out.start.2 | 8 +
fastaq/tests/data/sequences_test_extend_gaps.fa | 8 +
.../tests/data/sequences_test_extend_gaps.fa.out | 4 +
fastaq/tests/data/sequences_test_fai_test.fa | 8 +
fastaq/tests/data/sequences_test_fai_test.fa.fai | 4 +
fastaq/tests/data/sequences_test_fail_no_AT.fq | 5 +
fastaq/tests/data/sequences_test_fail_no_plus.fq | 4 +
fastaq/tests/data/sequences_test_fail_no_qual.fq | 3 +
fastaq/tests/data/sequences_test_fail_no_seq.fq | 5 +
...sequences_test_fastaq_replace_bases.expected.fa | 2 +
.../data/sequences_test_fastaq_replace_bases.fa | 2 +
...sequences_test_fastaq_to_quasr_primers.expected | 2 +
.../data/sequences_test_fastaq_to_quasr_primers.fa | 4 +
.../data/sequences_test_filter_by_ids_file.fa | 8 +
.../sequences_test_filter_by_ids_file.fa.filtered | 4 +
...nces_test_filter_by_ids_file.fa.filtered.invert | 4 +
.../data/sequences_test_filter_by_ids_file.fa.ids | 2 +
.../tests/data/sequences_test_filter_by_regex.fa | 10 +
.../sequences_test_filter_by_regex.first-char-a.fa | 6 +
...sequences_test_filter_by_regex.first-of-pair.fa | 4 +
.../data/sequences_test_filter_by_regex.numeric.fa | 2 +
.../data/sequences_test_get_seqs_flanking_gaps.fa | 4 +
.../sequences_test_get_seqs_flanking_gaps.fa.out | 3 +
fastaq/tests/data/sequences_test_gffv3.gff | 9 +
fastaq/tests/data/sequences_test_gffv3.gff.fasta | 4 +
.../tests/data/sequences_test_gffv3.gff.to_fasta | 4 +
.../data/sequences_test_gffv3.no_FASTA_line.gff | 8 +
...sequences_test_gffv3.no_FASTA_line.gff.to_fasta | 4 +
.../tests/data/sequences_test_gffv3.no_seq.2.gff | 6 +
fastaq/tests/data/sequences_test_gffv3.no_seq.gff | 4 +
fastaq/tests/data/sequences_test_good_file.fq | 11 +
.../data/sequences_test_good_file.fq.to_fasta | 4 +
.../tests/data/sequences_test_good_file_mira.xml | 13 +
fastaq/tests/data/sequences_test_interleaved.fa | 8 +
fastaq/tests/data/sequences_test_interleaved.fq | 16 +
.../tests/data/sequences_test_interleaved_bad.fa | 6 +
fastaq/tests/data/sequences_test_length_filter.fa | 6 +
.../sequences_test_length_filter.min-0.max-1.fa | 0
.../sequences_test_length_filter.min-0.max-inf.fa | 6 +
.../sequences_test_length_filter.min-4.max-4.fa | 2 +
.../sequences_test_make_random_contigs.default.fa | 4 +
.../sequences_test_make_random_contigs.first-42.fa | 4 +
...ces_test_make_random_contigs.name-by-letters.fa | 56 ++
.../sequences_test_make_random_contigs.prefix-p.fa | 4 +
.../tests/data/sequences_test_merge_to_one_seq.fa | 8 +
.../tests/data/sequences_test_merge_to_one_seq.fq | 8 +
.../data/sequences_test_merge_to_one_seq.merged.fa | 2 +
.../data/sequences_test_merge_to_one_seq.merged.fq | 4 +
fastaq/tests/data/sequences_test_not_a_fastaq_file | 1 +
fastaq/tests/data/sequences_test_one-per-line.fa | 14 +
fastaq/tests/data/sequences_test_orfs.fa | 18 +
fastaq/tests/data/sequences_test_orfs.gff | 15 +
.../tests/data/sequences_test_phylip.interleaved | 8 +
.../sequences_test_phylip.interleaved.to_fasta | 6 +
.../tests/data/sequences_test_phylip.interleaved2 | 7 +
.../sequences_test_phylip.interleaved2.to_fasta | 6 +
.../data/sequences_test_phylip.made_by_seaview | 6 +
.../sequences_test_phylip.made_by_seaview.to_fasta | 6 +
fastaq/tests/data/sequences_test_phylip.sequential | 7 +
.../data/sequences_test_phylip.sequential.to_fasta | 6 +
fastaq/tests/data/sequences_test_revcomp.fa | 8 +
fastaq/tests/data/sequences_test_search_string.fa | 2 +
.../data/sequences_test_search_string.fa.hits | 4 +
.../tests/data/sequences_test_split_fixed_size.fa | 12 +
.../sequences_test_split_fixed_size.fa.split.1 | 2 +
.../sequences_test_split_fixed_size.fa.split.2 | 2 +
.../sequences_test_split_fixed_size.fa.split.3 | 2 +
.../sequences_test_split_fixed_size.fa.split.4 | 2 +
.../sequences_test_split_fixed_size.fa.split.5 | 4 +
.../sequences_test_split_fixed_size.fa.split.6 | 2 +
...sequences_test_split_fixed_size.fa.split.coords | 2 +
...test_split_fixed_size.fa.split.skip_if_all_Ns.1 | 2 +
...test_split_fixed_size.fa.split.skip_if_all_Ns.2 | 2 +
...test_split_fixed_size.fa.split.skip_if_all_Ns.3 | 4 +
...test_split_fixed_size.fa.split.skip_if_all_Ns.4 | 2 +
...split_fixed_size.fa.split.skip_if_all_Ns.coords | 1 +
fastaq/tests/data/sequences_test_split_test.fa | 8 +
fastaq/tests/data/sequences_test_split_test.fa.2.1 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.2.2 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.2.3 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.2.4 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.3.1 | 4 +
fastaq/tests/data/sequences_test_split_test.fa.3.2 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.3.3 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.4.1 | 4 +
fastaq/tests/data/sequences_test_split_test.fa.4.2 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.4.3 | 2 +
fastaq/tests/data/sequences_test_split_test.fa.6.1 | 6 +
fastaq/tests/data/sequences_test_split_test.fa.6.2 | 2 +
.../data/sequences_test_split_test.fa.6.limit2.1 | 4 +
.../data/sequences_test_split_test.fa.6.limit2.2 | 2 +
.../data/sequences_test_split_test.fa.6.limit2.3 | 2 +
.../tests/data/sequences_test_split_test.long.fa | 4 +
.../data/sequences_test_split_test.long.fa.2.1 | 2 +
.../data/sequences_test_split_test.long.fa.2.2 | 2 +
.../data/sequences_test_strip_after_whitespace.fa | 6 +
...quences_test_strip_after_whitespace.fa.to_fasta | 6 +
.../data/sequences_test_strip_illumina_suffix.fq | 12 +
...equences_test_strip_illumina_suffix.fq.stripped | 12 +
.../tests/data/sequences_test_to_fasta_union.in.fa | 7 +
.../data/sequences_test_to_fasta_union.out.fa | 2 +
.../tests/data/sequences_test_to_unique_by_id.fa | 11 +
.../data/sequences_test_to_unique_by_id.fa.out | 6 +
fastaq/tests/data/sequences_test_translate.fa | 2 +
.../tests/data/sequences_test_translate.fa.frame0 | 3 +
.../tests/data/sequences_test_translate.fa.frame1 | 3 +
.../tests/data/sequences_test_translate.fa.frame2 | 3 +
fastaq/tests/data/sequences_test_trim_Ns_at_end.fa | 10 +
.../data/sequences_test_trim_Ns_at_end.fa.trimmed | 8 +
fastaq/tests/data/sequences_test_trimmed.fq | 8 +
fastaq/tests/data/sequences_test_untrimmed.fq | 16 +
.../tests/data/tasks_test_expend_nucleotides.in.fa | 4 +
.../tests/data/tasks_test_expend_nucleotides.in.fq | 8 +
.../data/tasks_test_expend_nucleotides.out.fa | 6 +
.../data/tasks_test_expend_nucleotides.out.fq | 12 +
.../tests/data/tasks_test_fasta_to_fake_qual.in.fa | 5 +
.../tasks_test_fasta_to_fake_qual.out.default.qual | 5 +
.../tasks_test_fasta_to_fake_qual.out.q42.qual | 5 +
.../tests/data/tasks_test_make_long_reads.input.fa | 2 +
.../data/tasks_test_make_long_reads.output.fa | 10 +
fastaq/tests/data/tasks_test_sequence_trim_1.fa | 12 +
.../data/tasks_test_sequence_trim_1.trimmed.fa | 8 +
fastaq/tests/data/tasks_test_sequence_trim_2.fa | 12 +
.../data/tasks_test_sequence_trim_2.trimmed.fa | 8 +
fastaq/tests/data/tasks_test_sequences_to_trim.fa | 8 +
fastaq/tests/data/utils_test_file_transpose.txt | 5 +
fastaq/tests/data/utils_test_file_transposed.txt | 3 +
fastaq/tests/data/utils_test_not_really_zipped.gz | 1 +
fastaq/tests/data/utils_test_scaffolds.fa | 8 +
.../data/utils_test_scaffolds.fa.to_contigs.fa | 10 +
..._test_scaffolds.fa.to_contigs.number_contigs.fa | 10 +
fastaq/tests/data/utils_test_system_call.txt | 1 +
fastaq/tests/intervals_test.py | 212 ++++++
fastaq/tests/sequences_test.py | 656 +++++++++++++++++++
fastaq/tests/tasks_test.py | 538 +++++++++++++++
fastaq/tests/utils_test.py | 80 +++
fastaq/utils.py | 86 +++
{src => scripts}/fastaq_capillary_to_pairs | 0
{src => scripts}/fastaq_chunker | 0
{src => scripts}/fastaq_count_sequences | 0
{src => scripts}/fastaq_deinterleave | 0
{src => scripts}/fastaq_enumerate_names | 0
scripts/fastaq_expand_nucleotides | 15 +
{src => scripts}/fastaq_extend_gaps | 0
{src => scripts}/fastaq_fasta_to_fastq | 0
{src => scripts}/fastaq_filter | 0
{src => scripts}/fastaq_get_ids | 0
{src => scripts}/fastaq_get_seq_flanking_gaps | 0
{src => scripts}/fastaq_insert_or_delete_bases | 0
{src => scripts}/fastaq_interleave | 0
scripts/fastaq_long_read_simulate | 50 ++
{src => scripts}/fastaq_make_random_contigs | 0
scripts/fastaq_merge | 18 +
{src => scripts}/fastaq_replace_bases | 0
{src => scripts}/fastaq_reverse_complement | 0
{src => scripts}/fastaq_scaffolds_to_contigs | 0
{src => scripts}/fastaq_search_for_seq | 0
scripts/fastaq_sequence_trim | 23 +
{src => scripts}/fastaq_split_by_base_count | 0
{src => scripts}/fastaq_strip_illumina_suffix | 0
scripts/fastaq_to_fake_qual | 18 +
{src => scripts}/fastaq_to_fasta | 0
{src => scripts}/fastaq_to_mira_xml | 0
scripts/fastaq_to_orfs_gff | 13 +
{src => scripts}/fastaq_to_perfect_reads | 0
{src => scripts}/fastaq_to_quasr_primers_file | 0
{src => scripts}/fastaq_to_random_subset | 0
{src => scripts}/fastaq_to_tiling_bam | 0
{src => scripts}/fastaq_to_unique_by_id | 0
{src => scripts}/fastaq_translate | 0
{src => scripts}/fastaq_trim_Ns_at_end | 0
{src => scripts}/fastaq_trim_ends | 0
setup.py | 21 -
205 files changed, 4988 insertions(+), 21 deletions(-)
create mode 100644 AUTHORS
create mode 100644 fastaq/__init__.py
create mode 100644 fastaq/intervals.py
create mode 100644 fastaq/sequences.py
create mode 100644 fastaq/tasks.py
create mode 100644 fastaq/tests/data/sequences_test.embl
create mode 100644 fastaq/tests/data/sequences_test.embl.bad
create mode 100644 fastaq/tests/data/sequences_test.embl.bad2
create mode 100644 fastaq/tests/data/sequences_test.embl.to_fasta
create mode 100644 fastaq/tests/data/sequences_test.fa
create mode 100644 fastaq/tests/data/sequences_test.fa.ids
create mode 100644 fastaq/tests/data/sequences_test.fa.qual
create mode 100644 fastaq/tests/data/sequences_test.fa.qual.bad
create mode 100644 fastaq/tests/data/sequences_test.fasta_to_fastq.fq
create mode 100644 fastaq/tests/data/sequences_test.gbk
create mode 100644 fastaq/tests/data/sequences_test.gbk.to_fasta
create mode 100644 fastaq/tests/data/sequences_test.line_length3.fa
create mode 100644 fastaq/tests/data/sequences_test_3-per-line.fa
create mode 100644 fastaq/tests/data/sequences_test_cap_to_read_pairs.fa
create mode 100644 fastaq/tests/data/sequences_test_cap_to_read_pairs.fa.paired.gz
create mode 100644 fastaq/tests/data/sequences_test_cap_to_read_pairs.fa.unpaired.gz
create mode 100644 fastaq/tests/data/sequences_test_deinterleaved_1.fa
create mode 100644 fastaq/tests/data/sequences_test_deinterleaved_2.fa
create mode 100644 fastaq/tests/data/sequences_test_deinterleaved_bad2_1.fa
create mode 100644 fastaq/tests/data/sequences_test_deinterleaved_bad2_2.fa
create mode 100644 fastaq/tests/data/sequences_test_deinterleaved_bad_1.fa
create mode 100644 fastaq/tests/data/sequences_test_deinterleaved_bad_2.fa
create mode 100644 fastaq/tests/data/sequences_test_empty_file
create mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa
create mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa.out.keep_suffix
create mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1
create mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1.rename_file
create mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa.out.start.2
create mode 100644 fastaq/tests/data/sequences_test_extend_gaps.fa
create mode 100644 fastaq/tests/data/sequences_test_extend_gaps.fa.out
create mode 100644 fastaq/tests/data/sequences_test_fai_test.fa
create mode 100644 fastaq/tests/data/sequences_test_fai_test.fa.fai
create mode 100644 fastaq/tests/data/sequences_test_fail_no_AT.fq
create mode 100644 fastaq/tests/data/sequences_test_fail_no_plus.fq
create mode 100644 fastaq/tests/data/sequences_test_fail_no_qual.fq
create mode 100644 fastaq/tests/data/sequences_test_fail_no_seq.fq
create mode 100644 fastaq/tests/data/sequences_test_fastaq_replace_bases.expected.fa
create mode 100644 fastaq/tests/data/sequences_test_fastaq_replace_bases.fa
create mode 100644 fastaq/tests/data/sequences_test_fastaq_to_quasr_primers.expected
create mode 100644 fastaq/tests/data/sequences_test_fastaq_to_quasr_primers.fa
create mode 100644 fastaq/tests/data/sequences_test_filter_by_ids_file.fa
create mode 100644 fastaq/tests/data/sequences_test_filter_by_ids_file.fa.filtered
create mode 100644 fastaq/tests/data/sequences_test_filter_by_ids_file.fa.filtered.invert
create mode 100644 fastaq/tests/data/sequences_test_filter_by_ids_file.fa.ids
create mode 100644 fastaq/tests/data/sequences_test_filter_by_regex.fa
create mode 100644 fastaq/tests/data/sequences_test_filter_by_regex.first-char-a.fa
create mode 100644 fastaq/tests/data/sequences_test_filter_by_regex.first-of-pair.fa
create mode 100644 fastaq/tests/data/sequences_test_filter_by_regex.numeric.fa
create mode 100644 fastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa
create mode 100644 fastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa.out
create mode 100644 fastaq/tests/data/sequences_test_gffv3.gff
create mode 100644 fastaq/tests/data/sequences_test_gffv3.gff.fasta
create mode 100644 fastaq/tests/data/sequences_test_gffv3.gff.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff
create mode 100644 fastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_gffv3.no_seq.2.gff
create mode 100644 fastaq/tests/data/sequences_test_gffv3.no_seq.gff
create mode 100644 fastaq/tests/data/sequences_test_good_file.fq
create mode 100644 fastaq/tests/data/sequences_test_good_file.fq.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_good_file_mira.xml
create mode 100644 fastaq/tests/data/sequences_test_interleaved.fa
create mode 100644 fastaq/tests/data/sequences_test_interleaved.fq
create mode 100644 fastaq/tests/data/sequences_test_interleaved_bad.fa
create mode 100644 fastaq/tests/data/sequences_test_length_filter.fa
create mode 100644 fastaq/tests/data/sequences_test_length_filter.min-0.max-1.fa
create mode 100644 fastaq/tests/data/sequences_test_length_filter.min-0.max-inf.fa
create mode 100644 fastaq/tests/data/sequences_test_length_filter.min-4.max-4.fa
create mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.default.fa
create mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.first-42.fa
create mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.name-by-letters.fa
create mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.prefix-p.fa
create mode 100644 fastaq/tests/data/sequences_test_merge_to_one_seq.fa
create mode 100644 fastaq/tests/data/sequences_test_merge_to_one_seq.fq
create mode 100644 fastaq/tests/data/sequences_test_merge_to_one_seq.merged.fa
create mode 100644 fastaq/tests/data/sequences_test_merge_to_one_seq.merged.fq
create mode 100644 fastaq/tests/data/sequences_test_not_a_fastaq_file
create mode 100644 fastaq/tests/data/sequences_test_one-per-line.fa
create mode 100644 fastaq/tests/data/sequences_test_orfs.fa
create mode 100644 fastaq/tests/data/sequences_test_orfs.gff
create mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved
create mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved2
create mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved2.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_phylip.made_by_seaview
create mode 100644 fastaq/tests/data/sequences_test_phylip.made_by_seaview.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_phylip.sequential
create mode 100644 fastaq/tests/data/sequences_test_phylip.sequential.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_revcomp.fa
create mode 100644 fastaq/tests/data/sequences_test_search_string.fa
create mode 100644 fastaq/tests/data/sequences_test_search_string.fa.hits
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.1
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.2
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.3
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.4
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.5
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.6
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.coords
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.1
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.2
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.3
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.4
create mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.2.1
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.2.2
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.2.3
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.2.4
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.3.1
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.3.2
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.3.3
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.4.1
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.4.2
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.4.3
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.1
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.2
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.limit2.1
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.limit2.2
create mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.limit2.3
create mode 100644 fastaq/tests/data/sequences_test_split_test.long.fa
create mode 100644 fastaq/tests/data/sequences_test_split_test.long.fa.2.1
create mode 100644 fastaq/tests/data/sequences_test_split_test.long.fa.2.2
create mode 100644 fastaq/tests/data/sequences_test_strip_after_whitespace.fa
create mode 100644 fastaq/tests/data/sequences_test_strip_after_whitespace.fa.to_fasta
create mode 100644 fastaq/tests/data/sequences_test_strip_illumina_suffix.fq
create mode 100644 fastaq/tests/data/sequences_test_strip_illumina_suffix.fq.stripped
create mode 100644 fastaq/tests/data/sequences_test_to_fasta_union.in.fa
create mode 100644 fastaq/tests/data/sequences_test_to_fasta_union.out.fa
create mode 100644 fastaq/tests/data/sequences_test_to_unique_by_id.fa
create mode 100644 fastaq/tests/data/sequences_test_to_unique_by_id.fa.out
create mode 100644 fastaq/tests/data/sequences_test_translate.fa
create mode 100644 fastaq/tests/data/sequences_test_translate.fa.frame0
create mode 100644 fastaq/tests/data/sequences_test_translate.fa.frame1
create mode 100644 fastaq/tests/data/sequences_test_translate.fa.frame2
create mode 100644 fastaq/tests/data/sequences_test_trim_Ns_at_end.fa
create mode 100644 fastaq/tests/data/sequences_test_trim_Ns_at_end.fa.trimmed
create mode 100644 fastaq/tests/data/sequences_test_trimmed.fq
create mode 100644 fastaq/tests/data/sequences_test_untrimmed.fq
create mode 100644 fastaq/tests/data/tasks_test_expend_nucleotides.in.fa
create mode 100644 fastaq/tests/data/tasks_test_expend_nucleotides.in.fq
create mode 100644 fastaq/tests/data/tasks_test_expend_nucleotides.out.fa
create mode 100644 fastaq/tests/data/tasks_test_expend_nucleotides.out.fq
create mode 100644 fastaq/tests/data/tasks_test_fasta_to_fake_qual.in.fa
create mode 100644 fastaq/tests/data/tasks_test_fasta_to_fake_qual.out.default.qual
create mode 100644 fastaq/tests/data/tasks_test_fasta_to_fake_qual.out.q42.qual
create mode 100644 fastaq/tests/data/tasks_test_make_long_reads.input.fa
create mode 100644 fastaq/tests/data/tasks_test_make_long_reads.output.fa
create mode 100644 fastaq/tests/data/tasks_test_sequence_trim_1.fa
create mode 100644 fastaq/tests/data/tasks_test_sequence_trim_1.trimmed.fa
create mode 100644 fastaq/tests/data/tasks_test_sequence_trim_2.fa
create mode 100644 fastaq/tests/data/tasks_test_sequence_trim_2.trimmed.fa
create mode 100644 fastaq/tests/data/tasks_test_sequences_to_trim.fa
create mode 100644 fastaq/tests/data/utils_test_file_transpose.txt
create mode 100644 fastaq/tests/data/utils_test_file_transposed.txt
create mode 100644 fastaq/tests/data/utils_test_not_really_zipped.gz
create mode 100644 fastaq/tests/data/utils_test_scaffolds.fa
create mode 100644 fastaq/tests/data/utils_test_scaffolds.fa.to_contigs.fa
create mode 100644 fastaq/tests/data/utils_test_scaffolds.fa.to_contigs.number_contigs.fa
create mode 100644 fastaq/tests/data/utils_test_system_call.txt
create mode 100644 fastaq/tests/intervals_test.py
create mode 100644 fastaq/tests/sequences_test.py
create mode 100644 fastaq/tests/tasks_test.py
create mode 100644 fastaq/tests/utils_test.py
create mode 100644 fastaq/utils.py
copy {src => scripts}/fastaq_capillary_to_pairs (100%)
copy {src => scripts}/fastaq_chunker (100%)
copy {src => scripts}/fastaq_count_sequences (100%)
copy {src => scripts}/fastaq_deinterleave (100%)
copy {src => scripts}/fastaq_enumerate_names (100%)
create mode 100755 scripts/fastaq_expand_nucleotides
copy {src => scripts}/fastaq_extend_gaps (100%)
copy {src => scripts}/fastaq_fasta_to_fastq (100%)
copy {src => scripts}/fastaq_filter (100%)
copy {src => scripts}/fastaq_get_ids (100%)
copy {src => scripts}/fastaq_get_seq_flanking_gaps (100%)
copy {src => scripts}/fastaq_insert_or_delete_bases (100%)
copy {src => scripts}/fastaq_interleave (100%)
create mode 100755 scripts/fastaq_long_read_simulate
copy {src => scripts}/fastaq_make_random_contigs (100%)
create mode 100755 scripts/fastaq_merge
copy {src => scripts}/fastaq_replace_bases (100%)
copy {src => scripts}/fastaq_reverse_complement (100%)
copy {src => scripts}/fastaq_scaffolds_to_contigs (100%)
copy {src => scripts}/fastaq_search_for_seq (100%)
create mode 100755 scripts/fastaq_sequence_trim
copy {src => scripts}/fastaq_split_by_base_count (100%)
copy {src => scripts}/fastaq_strip_illumina_suffix (100%)
create mode 100755 scripts/fastaq_to_fake_qual
copy {src => scripts}/fastaq_to_fasta (100%)
copy {src => scripts}/fastaq_to_mira_xml (100%)
create mode 100755 scripts/fastaq_to_orfs_gff
copy {src => scripts}/fastaq_to_perfect_reads (100%)
copy {src => scripts}/fastaq_to_quasr_primers_file (100%)
copy {src => scripts}/fastaq_to_random_subset (100%)
copy {src => scripts}/fastaq_to_tiling_bam (100%)
copy {src => scripts}/fastaq_to_unique_by_id (100%)
copy {src => scripts}/fastaq_translate (100%)
copy {src => scripts}/fastaq_trim_Ns_at_end (100%)
copy {src => scripts}/fastaq_trim_ends (100%)
delete mode 100644 setup.py
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