[med-svn] [fastaq] 04/04: Adding new source
Jorge Soares
jssoares-guest at moszumanska.debian.org
Wed Oct 8 13:05:08 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a commit to branch master
in repository fastaq.
commit deeba8edb3c19f942736c0a50662365c8bdb2f4c
Merge: 7210af1 ba05c94
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Wed Oct 8 14:12:16 2014 +0100
Adding new source
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 +++
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 | 23 +
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_quasr_primers_file | 12 +
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 | 21 -
205 files changed, 5647 insertions(+), 21 deletions(-)
diff --cc setup.py
index 2fe7a90,1a4976d..0000000
deleted file mode 100644,100644
--- a/setup.py
+++ /dev/null
@@@ -1,21 -1,21 +1,0 @@@
--import os
--import glob
--from setuptools import setup, find_packages
--
--def read(fname):
-- return open(os.path.join(os.path.dirname(__file__), fname)).read()
--
--setup(
-- name='Fastaq',
- version='0.1',
- version='1.5.0',
-- description='Scripts to manipulate FASTA and FASTQ files, plus API for developers',
-- long_description=read('README.md'),
-- packages = find_packages(),
-- author='Martin Hunt',
-- author_email='mh12 at sanger.ac.uk',
-- url='https://github.com/martinghunt/Fastaq',
-- scripts=glob.glob('scripts/*'),
-- test_suite='nose.collector',
-- install_requires=['nose >= 1.3'],
-- license='GPLv3',
--)
--
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