def test_demultiplex(): multiout = os.path.join(os.path.dirname(__file__), 'data', 'tmp-demulti.{name}.fasta') params = ['-a', 'first=AATTTCAGGAATT', '-a', 'second=GTTCTCTAGTTCT', '-o', multiout, datapath('twoadapters.fasta')] assert cutadapt.main(params) is None assert files_equal(cutpath('twoadapters.first.fasta'), multiout.format(name='first')) assert files_equal(cutpath('twoadapters.second.fasta'), multiout.format(name='second')) assert files_equal(cutpath('twoadapters.unknown.fasta'), multiout.format(name='unknown')) os.remove(multiout.format(name='first')) os.remove(multiout.format(name='second')) os.remove(multiout.format(name='unknown'))
def test_info_file(): with temporary_path("infotmp.txt") as infotmp: run([ "--info-file", infotmp, '-a', 'adapt=GCCGAACTTCTTAGACTGCCTTAAGGACGT' ], "illumina.fastq", "illumina.fastq.gz") assert files_equal(cutpath('illumina.info.txt'), infotmp)
def test_paired_end_legacy(): '''--paired-output, no -A/-B/-G''' with temporary_path("paired-tmp.fastq") as pairedtmp: # the -m 14 filters out one read, which should then also be filtered out in the second output file run(['-a', 'TTAGACATAT', '-m', '14', '--paired-output', pairedtmp], 'paired.m14.1.fastq', 'paired.1.fastq', 'paired.2.fastq') assert files_equal(cutpath('paired.m14.2.fastq'), pairedtmp)
def test_too_short_no_primer(): '''--too-short-output and --trim-primer''' run( "-c -m 5 -a 330201030313112312 --trim-primer --too-short-output tooshort.tmp.fa", "minlen.noprimer.fa", "lengths.fa") assert files_equal(datapath('tooshort.noprimer.fa'), "tooshort.tmp.fa") os.remove('tooshort.tmp.fa')
def test_untrimmed_paired_output(): with temporary_path("tmp-paired.1.fastq") as tmp1: with temporary_path("tmp-paired.2.fastq") as tmp2: with temporary_path("tmp-untrimmed.1.fastq") as untrimmed1: with temporary_path("tmp-untrimmed.2.fastq") as untrimmed2: params = [ '-a', 'TTAGACATAT', '-o', tmp1, '-p', tmp2, '--untrimmed-output', untrimmed1, '--untrimmed-paired-output', untrimmed2, datapath('paired.1.fastq'), datapath('paired.2.fastq') ] assert cutadapt.main(params) is None assert files_equal(cutpath('paired-untrimmed.1.fastq'), untrimmed1) assert files_equal(cutpath('paired-untrimmed.2.fastq'), untrimmed2) assert files_equal(cutpath('paired-trimmed.1.fastq'), tmp1) assert files_equal(cutpath('paired-trimmed.2.fastq'), tmp2)
def test_demultiplex(): multiout = os.path.join(os.path.dirname(__file__), 'data', 'tmp-demulti.{name}.fasta') params = [ '-a', 'first=AATTTCAGGAATT', '-a', 'second=GTTCTCTAGTTCT', '-o', multiout, datapath('twoadapters.fasta') ] assert cutadapt.main(params) is None assert files_equal(cutpath('twoadapters.first.fasta'), multiout.format(name='first')) assert files_equal(cutpath('twoadapters.second.fasta'), multiout.format(name='second')) assert files_equal(cutpath('twoadapters.unknown.fasta'), multiout.format(name='unknown')) os.remove(multiout.format(name='first')) os.remove(multiout.format(name='second')) os.remove(multiout.format(name='unknown'))
def test_too_long(): '''--too-long-output''' run("-c -M 5 --too-long-output toolong.tmp.fa -a 330201030313112312", "maxlen.fa", "lengths.fa") assert files_equal(datapath('toolong.fa'), "toolong.tmp.fa") os.remove('toolong.tmp.fa')
def test_explicit_format_with_paired(): with temporary_path("paired-tmp.fastq") as pairedtmp: run([ '--format=fastq', '-a', 'TTAGACATAT', '-m', '14', '-p', pairedtmp ], 'paired.m14.1.fastq', 'paired.1.txt', 'paired.2.txt') assert files_equal(cutpath('paired.m14.2.fastq'), pairedtmp)
def test_restfront(): with temporary_path("rest.txt") as path: run(['-g', 'ADAPTER', '-N', '-r', path], "restfront.fa", "rest.fa") assert files_equal(datapath('restfront.txt'), path)
def test_untrimmed_output(): with temporary_path('untrimmed.tmp.fastq') as tmp: run(['-a', 'TTAGACATATCTCCGTCG', '--untrimmed-output', tmp], 'small.trimmed.fastq', 'small.fastq') assert files_equal(cutpath('small.untrimmed.fastq'), tmp)
def test_rest(): '''-r/--rest-file''' with temporary_path('rest.tmp') as rest_tmp: run(['-b', 'ADAPTER', '-N', '-r', rest_tmp], "rest.fa", "rest.fa") assert files_equal(datapath('rest.txt'), rest_tmp)
def test_too_short(): '''--too-short-output''' run("-c -m 5 -a 330201030313112312 --too-short-output tooshort.tmp.fa", "minlen.fa", "lengths.fa") assert files_equal(datapath('tooshort.fa'), "tooshort.tmp.fa") os.remove('tooshort.tmp.fa')
def test_too_short_no_primer(): '''--too-short-output and --trim-primer''' run("-c -m 5 -a 330201030313112312 --trim-primer --too-short-output tooshort.tmp.fa", "minlen.noprimer.fa", "lengths.fa") assert files_equal(datapath('tooshort.noprimer.fa'), "tooshort.tmp.fa") os.remove('tooshort.tmp.fa')
def test_explicit_format_with_paired(): with temporary_path("paired-tmp.fastq") as pairedtmp: run(['--format=fastq', '-a', 'TTAGACATAT', '-m', '14', '-p', pairedtmp], 'paired.m14.1.fastq', 'paired.1.txt', 'paired.2.txt') assert files_equal(cutpath('paired.m14.2.fastq'), pairedtmp)
def test_info_file(): with temporary_path("infotmp.txt") as infotmp: run(["--info-file", infotmp, '-a', 'adapt=GCCGAACTTCTTAGACTGCCTTAAGGACGT'], "illumina.fastq", "illumina.fastq.gz") assert files_equal(cutpath('illumina.info.txt'), infotmp)