[-? | --help] # Print full usage description.
[-i <files!> | --data_in=<files!>] # Comma separated list of files or glob expression to read.
[-n <uint> | --num=<uint>] # Limit number of records to read.
[-I <file> | --stream_in=<file!>] # Read input stream from file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output stream to file - Default=STDOUT
[-v | --verbose] # Verbose output.
read_fasta is part of the Biopieces framework.
maasha@edna:~$ bp_test
Testing Perl version ... OK
Testing required Perl module - "Inline": OK
Testing required Perl module - "SVG": OK
Testing required Perl module - "Time::HiRes": OK
Testing Ruby version ... OK
Testing required Ruby gem - "gnuplot": OK
Testing required Ruby gem - "narray": OK
Testing required Ruby gem - "RubyInline": OK
Testing required Ruby gem - "terminal-table": OK
Testing auxiliary program - "blastall": OK
Testing auxiliary program - "blat": WARNING
Testing auxiliary program - "bwa": WARNING
Testing auxiliary program - "bowtie": WARNING
Testing auxiliary program - "bowtie2": WARNING
Testing auxiliary program - "formatdb": OK
Testing auxiliary program - "hmmsearch": WARNING
Testing auxiliary program - "gnuplot": OK
Testing auxiliary program - "idba_hybrid": WARNING
Testing auxiliary program - "muscle": OK
Testing auxiliary program - "mummer": OK
Testing auxiliary program - "mysql": WARNING
Testing auxiliary program - "prodigal": OK
Testing auxiliary program - "Ray": OK
Testing auxiliary program - "scan_for_matches": OK
Testing auxiliary program - "usearch": OK
Testing auxiliary program - "velveth": WARNING
Testing auxiliary program - "velvetg": WARNING
Testing auxiliary program - "vmatch": WARNING
Testing add_ident -I $BP_DIR/tests/in/
add_ident.in -O $BP_TMP/maasha.add_ident.out ... OK
Testing add_ident -I $BP_DIR/tests/in/
add_ident.in -k CUSTOM_KEY -O $BP_TMP/maasha.add_ident.out ... OK
Testing add_ident -I $BP_DIR/tests/in/
add_ident.in -p PREFIX -O $BP_TMP/maasha.add_ident.out ... OK
Testing add_ident -I $BP_DIR/tests/in/
add_ident.in -o 5 -O $BP_TMP/maasha.add_ident.out ... OK
Testing align_seq -I $BP_DIR/tests/in/
align_seq.in -O $BP_TMP/maasha.align_seq.out ... OK
Testing analyze_assembly -I $BP_DIR/tests/in/
analyze_assembly.in -O $BP_TMP/maasha.analyze_assembly.out ... OK
Testing analyze_assembly -I $BP_DIR/tests/in/
analyze_assembly.in -o $BP_TMP/maasha.analyze_assembly.out -x ... OK
Testing analyze_gc -I $BP_DIR/tests/in/
analyze_gc.in -O $BP_TMP/maasha.analyze_gc.out ... OK
Testing analyze_scores -I $BP_DIR/tests/in/
analyze_scores.in -O $BP_TMP/maasha.analyze_scores.out ... OK
Testing analyze_seq -I $BP_DIR/tests/in/
analyze_seq.in -O $BP_TMP/maasha.analyze_seq.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/
analyze_vals.in -O $BP_TMP/maasha.analyze_vals.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/
analyze_vals.in -O $BP_TMP/maasha.analyze_vals.out -x ... OK
Testing analyze_vals -I $BP_DIR/tests/in/
analyze_vals.in -k V0 -O $BP_TMP/maasha.analyze_vals.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/
analyze_vals.in -K V0 -O $BP_TMP/maasha.analyze_vals.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/
analyze_vals.in -o $BP_TMP/maasha.analyze_vals.out -x ... OK
Testing assemble_pairs -I $BP_DIR/tests/in/
assemble_pairs.in -O $BP_TMP/maasha.assemble_pairs.out ... OK
Testing assemble_pairs -o 70 -I $BP_DIR/tests/in/
assemble_pairs.in -O $BP_TMP/maasha.assemble_pairs.out ... OK
Testing bin_vals -I $BP_DIR/tests/in/
bin_vals.in -k V0 -O $BP_TMP/maasha.bin_vals.out ... OK
Testing bin_vals -I $BP_DIR/tests/in/
bin_vals.in -k V0 -b 5 -O $BP_TMP/maasha.bin_vals.out ... OK
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.2 -d $BP_TMP/maasha.test_tmp/nucleotide -O $BP_TMP/maasha.blast_seq.out ... OK
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.2 -d $BP_TMP/maasha.test_tmp/protein -O $BP_TMP/maasha.blast_seq.out ... FAIL
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.4 -d $BP_TMP/maasha.test_tmp/nucleotide -O $BP_TMP/maasha.blast_seq.out ... FAIL
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.4 -d $BP_TMP/maasha.test_tmp/protein -O $BP_TMP/maasha.blast_seq.out ... FAIL
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.2 -d $BP_TMP/maasha.test_tmp/nucleotide -p tblastx -O $BP_TMP/maasha.blast_seq.out ... OK
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.1 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.2 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.3 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.4 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.1 -p tblastx -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing calc_N50 -I $BP_DIR/tests/in/calc_N50.in -O $BP_TMP/maasha.calc_N50.out ... OK
Testing calc_N50 -I $BP_DIR/tests/in/calc_N50.in -o $BP_TMP/maasha.calc_N50.out -x ... OK
Testing calc_bit_scores -I $BP_DIR/tests/in/
calc_bit_scores.in -O $BP_TMP/maasha.calc_bit_scores.out ... OK
Testing clip_adaptor -I $BP_DIR/tests/in/
clip_adaptor.in -O $BP_TMP/maasha.clip_adaptor.out ... OK
Testing clip_seq -I $BP_DIR/tests/in/
clip_seq.in -O $BP_TMP/maasha.clip_seq.out ... OK
Testing complement_seq -I $BP_DIR/tests/in/
complement_seq.in -O $BP_TMP/maasha.complement_seq.out ... OK
Testing create_blast_index -I $BP_DIR/tests/in/create_blast_index.in.1 -d $BP_TMP/maasha.test_tmp -i 'index' -x ... OK
Testing create_blast_index -I $BP_DIR/tests/in/create_blast_index.in.2 -d $BP_TMP/maasha.test_tmp -i 'index' -x ... OK
Testing create_seq_index -I $BP_DIR/tests/in/
create_seq_index.in -d $BP_TMP/maasha.test_tmp -i test -x ... OK
Testing digest_seq -p GGATCC -c 1 -I $BP_DIR/tests/in/
digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing digest_seq -p GGACTT -c 1 -I $BP_DIR/tests/in/
digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing digest_seq -p GGATCC -c 1000 -I $BP_DIR/tests/in/
digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing digest_seq -p GGATCC -c -1000 -I $BP_DIR/tests/in/
digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing duplicate_record -I $BP_DIR/tests/in/
duplicate_record.in -k COUNT -O $BP_TMP/maasha.duplicate_record.out ... OK
Testing find_SNPs -I $BP_DIR/tests/in/find_SNPs.in -O $BP_TMP/maasha.find_SNPs.out ... OK
Testing find_SNPs -I $BP_DIR/tests/in/find_SNPs.in -c -O $BP_TMP/maasha.find_SNPs.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -F TCGTATGCCGTCTTCTGCTT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -R TGACTACGACTACGACTACT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -L 1 -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 10 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 10 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 10 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/
find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 1 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 1 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 1 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -Rrg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_gaps -I $BP_DIR/tests/in/
find_gaps.in -O $BP_TMP/maasha.find_gaps.out ... OK
Testing find_gaps -I $BP_DIR/tests/in/
find_gaps.in -m 3 -O $BP_TMP/maasha.find_gaps.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/
find_homopolymers.in -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/
find_homopolymers.in -m 3 -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/
find_homopolymers.in -m 3 -l 1 -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/
find_homopolymers.in -m 3 -L -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/
find_orfs.in -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/
find_orfs.in -s 'GTG' -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/
find_orfs.in -S 'TAA' -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/
find_orfs.in -m 700 -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/
find_orfs.in -M 100 -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/
find_orfs.in -n -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orphans -I $BP_DIR/tests/in/find_orphans.in.1 -O $BP_TMP/maasha.find_orphans.out ... OK
Testing find_orphans -I $BP_DIR/tests/in/find_orphans.in.2 -O $BP_TMP/maasha.find_orphans.out ... OK
Testing find_pairs -I $BP_DIR/tests/in/
find_pairs.in -O $BP_TMP/maasha.find_pairs.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -b 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -e 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -l 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -b 10 -l 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -I $BP_DIR/tests/in/get_seq.in.2 -i $BP_TMP/maasha.test_tmp/test -O $BP_TMP/maasha.get_seq.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -p SEQ -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -p SEQ,COUNT -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -P $BP_DIR/tests/in/grab.in.pat -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -p SEQ -i -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -p SEQ -K -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -p SEQ -V -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -p SEQ -k PAT -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -r a -k SEQ -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -r a -k SEQ -c -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/
grab.in -e 'SEQ_LEN<10' -O $BP_TMP/maasha.grab.out ... OK
Testing index_vals -I $BP_DIR/tests/in/
index_vals.in -k MID -O $BP_TMP/maasha.index_vals.out ... OK
Testing join_seq -I $BP_DIR/tests/in/
join_seq.in -O $BP_TMP/maasha.join_seq.out ... OK
Testing join_seq -I $BP_DIR/tests/in/
join_seq.in -d 'X' -O $BP_TMP/maasha.join_seq.out ... OK
Testing kmer_freq -I $BP_DIR/tests/in/
kmer_freq.in -O $BP_TMP/maasha.kmer_freq.out ... OK
Testing length_seq -I $BP_DIR/tests/in/
length_seq.in -O $BP_TMP/maasha.length_seq.out ... OK
Testing length_vals -I $BP_DIR/tests/in/
length_vals.in -k V0,V1 -O $BP_TMP/maasha.length_vals.out ... OK
Testing lowercase_seq -I $BP_DIR/tests/in/
lowercase_seq.in -O $BP_TMP/maasha.lowercase_seq.out ... FAIL
Testing mask_seq -I $BP_DIR/tests/in/
mask_seq.in -O $BP_TMP/maasha.mask_seq.out ... OK
Testing mask_seq -I $BP_DIR/tests/in/
mask_seq.in -c 0 -O $BP_TMP/maasha.mask_seq.out ... OK
Testing mask_seq -I $BP_DIR/tests/in/
mask_seq.in -h -O $BP_TMP/maasha.mask_seq.out ... OK
Testing max_vals -I $BP_DIR/tests/in/
max_vals.in -k V1,V2 -o $BP_TMP/maasha.max_vals.out -x ... OK
Testing max_vals -I $BP_DIR/tests/in/
max_vals.in -l V3 -O $BP_TMP/maasha.max_vals.out ... OK
Testing mean_scores -I $BP_DIR/tests/in/
mean_scores.in -O $BP_TMP/maasha.mean_scores.out ... OK
Testing mean_scores -I $BP_DIR/tests/in/
mean_scores.in -l -O $BP_TMP/maasha.mean_scores.out ... OK
Testing mean_scores -I $BP_DIR/tests/in/
mean_scores.in -l -w 10 -O $BP_TMP/maasha.mean_scores.out ... OK
Testing mean_vals -I $BP_DIR/tests/in/
mean_vals.in -k V1,V2 -o $BP_TMP/maasha.mean_vals.out -x ... OK
Testing mean_vals -I $BP_DIR/tests/in/
mean_vals.in -l V3 -O $BP_TMP/maasha.mean_vals.out ... OK
Testing median_vals -I $BP_DIR/tests/in/
median_vals.in -k V1,V2 -o $BP_TMP/maasha.median_vals.out -x ... OK
Testing median_vals -I $BP_DIR/tests/in/
median_vals.in -l V3 -O $BP_TMP/maasha.median_vals.out ... OK
Testing merge_pair_seq -I $BP_DIR/tests/in/
merge_pair_seq.in -O $BP_TMP/maasha.merge_pair_seq.out ... OK
Testing min_vals -I $BP_DIR/tests/in/
min_vals.in -k V1,V2 -o $BP_TMP/maasha.min_vals.out -x ... OK
Testing min_vals -I $BP_DIR/tests/in/
min_vals.in -l V3 -O $BP_TMP/maasha.min_vals.out ... OK
Testing order_pairs -I $BP_DIR/tests/in/
order_pairs.in -O $BP_TMP/maasha.order_pairs.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -p GACT -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -p GACT -c -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -p GACT -i -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -o -p GG -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.2 -p RARP -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.2 -p RARP -i -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing pcr_seq -f CGATCGAGCT -r AGTCAGTCAT -I $BP_DIR/tests/in/
pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -f CGATCGAGCT -r AGTCAGTCAT -m 1 -I $BP_DIR/tests/in/
pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -F CGATCGAGCT -r AGTCAGTCAT -I $BP_DIR/tests/in/
pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -f CGATCGAGCT -R AGTCAGTCAT -I $BP_DIR/tests/in/
pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -F CGATCGAGCT -R AGTCAGTCAT -I $BP_DIR/tests/in/
pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing plot_distribution -k SEQ_LEN -I $BP_DIR/tests/in/
plot_distribution.in -o $BP_TMP/maasha.plot_distribution.out -x ... FAIL
Testing read_454 -i $BP_DIR/tests/in/
read_454.in -q $BP_DIR/tests/in/read_454.in.qual -O $BP_TMP/maasha.read_454.out ... OK
Testing read_454 -i $BP_DIR/tests/in/read_454.in.gz -q $BP_DIR/tests/in/read_454.in.qual.gz -O $BP_TMP/maasha.read_454.out ... OK
Testing read_454 -i $BP_DIR/tests/in/
read_454.in -q $BP_DIR/tests/in/read_454.in.qual -n 1 -O $BP_TMP/maasha.read_454.out ... OK
Testing read_blast_tab -i $BP_DIR/tests/in/
read_blast_tab.in -O $BP_TMP/maasha.read_blast_tab.out ... OK
Testing read_blast_tab -i $BP_DIR/tests/in/
read_blast_tab.in -n 1 -O $BP_TMP/maasha.read_blast_tab.out ... OK
Testing read_embl -i $BP_DIR/tests/in/
read_embl.in -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/read_embl.in.gz -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/
read_embl.in -k AC -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/
read_embl.in -k AC -f CDS -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/
read_embl.in -k AC -f CDS -q translation -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_fasta -i $BP_DIR/tests/in/
read_fasta.in -O $BP_TMP/maasha.read_fasta.out ... OK
Testing read_fasta -i $BP_DIR/tests/in/read_fasta.in.gz -O $BP_TMP/maasha.read_fasta.out ... OK
Testing read_fasta -i $BP_DIR/tests/in/
read_fasta.in -n 1 -O $BP_TMP/maasha.read_fasta.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1 -e base_33 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.2 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.2 -e base_64 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1.gz -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1 -n 1 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.3 -j $BP_DIR/tests/in/read_fastq.in.4 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/
read_genbank.in -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/read_genbank.in.gz -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/
read_genbank.in -k AC -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/
read_genbank.in -k AC -f CDS -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/
read_genbank.in -k AC -f CDS -q translation -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_pdb -i $BP_DIR/tests/in/
read_pdb.in -o $BP_TMP/maasha.read_pdb.out ... OK
Testing read_pdb -i $BP_DIR/tests/in/
read_pdb.in -O $BP_TMP/maasha.read_pdb.out --method=atom -M ... OK
Testing read_pdb -i $BP_DIR/tests/in/
read_pdb.in -o $BP_TMP/maasha.read_pdb.out -m seqres -c atom -a CA -r ILE,SER ... OK
Testing read_sff -i $BP_DIR/tests/in/
read_sff.in -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_sff -i $BP_DIR/tests/in/
read_sff.in -n 1 -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_sff -i $BP_DIR/tests/in/
read_sff.in -n 1 -m -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_sff -i $BP_DIR/tests/in/
read_sff.in -n 1 -c -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -k ORGANISM,SEQ,COUNT -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -c 2,1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -c 2,1 -k COUNT,SEQ -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.2 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.2 -n 1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.3 -d ';' -O $BP_TMP/maasha.read_tab.out ... OK
Testing remove_indel_columns -I $BP_DIR/tests/in/
remove_indel_columns.in -O $BP_TMP/maasha.remove_indel_columns.out ... OK
Testing remove_indels -I $BP_DIR/tests/in/
remove_indels.in -O $BP_TMP/maasha.remove_indels.out ... OK
Testing remove_keys -I $BP_DIR/tests/in/
remove_keys.in -k SEQ_NAME,SEQ -O $BP_TMP/maasha.remove_keys.out ... OK
Testing remove_primers -f ACTGAGCTAGCAGCGGTGCG -r TGCTGGACTGGGTGGAGCAC -m 0 -i 0 -d 0 -I $BP_DIR/tests/in/
remove_primers.in -O $BP_TMP/maasha.remove_primers.out ... OK
Testing rename_keys -I $BP_DIR/tests/in/
rename_keys.in -k SEQ,FOO -O $BP_TMP/maasha.rename_keys.out ... OK
Testing replace_vals -I $BP_DIR/tests/in/replace_vals.in.1 -k SEQ_NAME -s test1 -r foo -O $BP_TMP/maasha.replace_vals.out ... OK
Testing replace_vals -I $BP_DIR/tests/in/replace_vals.in.1 -k SEQ_NAME -f $BP_DIR/tests/in/replace_vals.in.2 -O $BP_TMP/maasha.replace_vals.out ... OK
Testing replace_vals -I $BP_DIR/tests/in/replace_vals.in.1 -k SEQ_NAME -f $BP_DIR/tests/in/replace_vals.in.2 -S 2 -R 1 -O $BP_TMP/maasha.replace_vals.out ... OK
Testing reverse_seq -I $BP_DIR/tests/in/
reverse_seq.in -O $BP_TMP/maasha.reverse_seq.out ... OK
Testing scores_to_dec -I $BP_DIR/tests/in/
scores_to_dec.in -O $BP_TMP/maasha.scores_to_dec.out ... OK
Testing shred_seq -I $BP_DIR/tests/in/
shred_seq.in -s 18 -c 2 -O $BP_TMP/maasha.shred_seq.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -b 5 -e 10 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGGCATG -r GCGAACGGGT -m 0 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -F CATGCCGCCA -r GCGAACGGGT -m 0 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGGCATG -R ACCCGTTCGC -m 0 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGgGGCATG -r GCGAtCGGGT -m 1 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGcGCATG -r GCGAtACGGGT -m 0 -i 1 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGCATG -r GCGAAGGGT -m 0 -i 0 -d 1 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f ATACGCTGCGGAGGCTA -r TTGCTACCAGGCGTCGAGCGGCGGACGGG -t $BP_DIR/tests/in/slice_align.in.2 -m 0 -d 0 -i 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -b 5 -e 10 -t $BP_DIR/tests/in/slice_align.in.2 -O $BP_TMP/maasha.slice_align.out ... OK
Testing sort_records -I $BP_DIR/tests/in/
sort_records.in -k SEQ_LEN -O $BP_TMP/maasha.sort_records.out ... OK
Testing sort_records -I $BP_DIR/tests/in/
sort_records.in -k SEQ_LENn -O $BP_TMP/maasha.sort_records.out ... OK
Testing sort_records -I $BP_DIR/tests/in/
sort_records.in -k SEQ_LEN -r -O $BP_TMP/maasha.sort_records.out ... OK
Testing split_pair_seq -I $BP_DIR/tests/in/
split_pair_seq.in -O $BP_TMP/maasha.split_pair_seq.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/
substitute_vals.in -s '\d' -r '' -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/
substitute_vals.in -k SEQ -s 'n' -r '' -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/
substitute_vals.in -k SEQ -s 'n' -r '' -i -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/
substitute_vals.in -k SEQ -s 'n' -r '' -i -g -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/
substitute_vals.in -k SEQ -s 'n{3,}' -r '' -i -g -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing sum_vals -I $BP_DIR/tests/in/
sum_vals.in -k V1,V2 -o $BP_TMP/maasha.sum_vals.out -x ... OK
Testing sum_vals -I $BP_DIR/tests/in/
sum_vals.in -l V3 -O $BP_TMP/maasha.sum_vals.out ... OK
Testing swapcase_seq -I $BP_DIR/tests/in/
swapcase_seq.in -O $BP_TMP/maasha.swapcase_seq.out ... OK
Testing translate_seq -I $BP_DIR/tests/in/
translate_seq.in -O $BP_TMP/maasha.translate_seq.out ... OK
Testing translate_seq -I $BP_DIR/tests/in/
translate_seq.in -f '1,-1' -O $BP_TMP/maasha.translate_seq.out ... OK
Testing transliterate_seq -I $BP_DIR/tests/in/
transliterate_seq.in -s 'N' -r 'A' -O $BP_TMP/maasha.transliterate_seq.out ... OK
Testing transliterate_seq -I $BP_DIR/tests/in/
transliterate_seq.in -d 'N' -O $BP_TMP/maasha.transliterate_seq.out ... OK
Testing transliterate_vals -I $BP_DIR/tests/in/
transliterate_vals.in -k SEQ -s A -r n -O $BP_TMP/maasha.transliterate_vals.out ... OK
Testing transliterate_vals -I $BP_DIR/tests/in/
transliterate_vals.in -k SEQ_NAME -d Tt -O $BP_TMP/maasha.transliterate_vals.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/
trim_seq.in -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/
trim_seq.in -m 25 -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/
trim_seq.in -t both -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/
trim_seq.in -t left -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/
trim_seq.in -t right -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/
trim_seq.in -l 4 -O $BP_TMP/maasha.trim_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/
uclust_seq.in -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/
uclust_seq.in -C 2 -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/
uclust_seq.in -i 1 -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/
uclust_seq.in -i 1 -c -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uniq_seq -I $BP_DIR/tests/in/
uniq_seq.in | sort_records -k SEQ -O $BP_TMP/maasha.uniq_seq.out ... OK
Testing uniq_seq -I $BP_DIR/tests/in/
uniq_seq.in -c | sort_records -k SEQ -O $BP_TMP/maasha.uniq_seq.out ... OK
Testing uniq_vals -I $BP_DIR/tests/in/
uniq_vals.in -k SEQ -O $BP_TMP/maasha.uniq_vals.out ... OK
Testing uniq_vals -I $BP_DIR/tests/in/
uniq_vals.in -k SEQ -i -O $BP_TMP/maasha.uniq_vals.out ... OK
Testing uppercase_seq -I $BP_DIR/tests/in/
uppercase_seq.in -O $BP_TMP/maasha.uppercase_seq.out ... OK
Testing usearch_seq -I $BP_DIR/tests/in/
usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 1 -O $BP_TMP/maasha.usearch_seq.out ... OK
Testing usearch_seq -I $BP_DIR/tests/in/
usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 1 -p local -O $BP_TMP/maasha.usearch_seq.out ... FAIL
Testing usearch_seq -I $BP_DIR/tests/in/
usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 0.99 -e 0.1 -p local -O $BP_TMP/maasha.usearch_seq.out ... FAIL
Testing usearch_seq -I $BP_DIR/tests/in/
usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 0.99 -O $BP_TMP/maasha.usearch_seq.out ... OK
Testing usearch_seq -I $BP_DIR/tests/in/
usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 1 -m 1 -O $BP_TMP/maasha.usearch_seq.out ... OK
Testing write_blast -I $BP_DIR/tests/in/
write_blast.in -o $BP_TMP/maasha.write_blast.out -x ... OK
Testing write_blast -I $BP_DIR/tests/in/
write_blast.in -c -o $BP_TMP/maasha.write_blast.out -x ... OK
Testing write_blast -I $BP_DIR/tests/in/
write_blast.in -Z -o $BP_TMP/maasha.write_blast.out.gz -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/
write_fasta.in -o $BP_TMP/maasha.write_fasta.out -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/
write_fasta.in -w 4 -o $BP_TMP/maasha.write_fasta.out -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/
write_fasta.in -w 4 -Z gzip -o $BP_TMP/maasha.write_fasta.out.gz -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/
write_fasta.in -w 4 -Z bzip2 -o $BP_TMP/maasha.write_fasta.out.bz2 -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/
write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/
write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/
write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -Z gzip -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/
write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -Z bzip2 -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/
write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -w 4 -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/
write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -p Length -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/
write_fastq.in -o $BP_TMP/maasha.write_fastq.out -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/
write_fastq.in -e base_33 -o $BP_TMP/maasha.write_fastq.out -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/
write_fastq.in -e base_64 -o $BP_TMP/maasha.write_fastq.out -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/
write_fastq.in -Z gzip -o $BP_TMP/maasha.write_fastq.out.gz -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/
write_fastq.in -Z bzip2 -o $BP_TMP/maasha.write_fastq.out.bz2 -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/
write_fastq_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/
write_fastq_files.in -e base_33 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/
write_fastq_files.in -e base_64 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/
write_fastq_files.in -e base_64 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -Z gzip -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/
write_fastq_files.in -e base_64 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -Z bzip2 -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/
write_fastq_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -p Name -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -c -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -d ',' -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -Z gzip -o $BP_TMP/maasha.write_tab.out.gz -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -Z bzip2 -o $BP_TMP/maasha.write_tab.out.bz2 -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -k 'Count' -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -K 'Count' -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -p -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -p -C -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/
write_tab.in -p -c -C -o $BP_TMP/maasha.write_tab.out -x ... OK
Biopieces tested: 86 Tests run: 293 OK: 271 FAIL: 12 WARNING: 10 Time: 41 secs
I realize, I have some FAILs, but that is me having wrong versions of aux programs - that always change output format for every new release (grrrrrrr). But otherwise everything else is working.