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# -----------------------------------------------------------------------------
# Copyright (c) 2011-2017, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
# no hits or library seeds
uc_empty = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
"""
# label not in qiime post-split-libraries format
uc_invalid_id = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S 0 133 * * * * * 1539 *
"""
# contains single new (de novo) seed hit
uc_minimal = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S 0 133 * * * * * f2_1539 *
"""
# contains single library (reference) seed hit
uc_lib_minimal = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
L 3 1389 * * * * * 295053 *
H 3 133 100.0 + 0 0 519I133M737I f2_1539 295053
"""
# contains new seed (de novo) hits only
uc_seed_hits = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S 0 133 * * * * * f2_1539 *
H 0 141 100.0 + 0 0 133M8D f3_42 f2_1539
H 0 141 100.0 + 0 0 133M8D f2_43 f2_1539
S 0 133 * * * * * f3_44 *
"""
# contains library (reference) and new seed (de novo) hits
uc_mixed_hits = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S 0 133 * * * * * f2_1539 *
H 0 141 100.0 + 0 0 133M8D f3_42 f2_1539
H 0 141 100.0 + 0 0 133M8D f2_43 f2_1539
S 0 133 * * * * * f3_44 *
L 3 1389 * * * * * 295053 *
H 3 133 100.0 + 0 0 519I133M737I f2_1539 295053
"""
# contains library (reference) and new seed (de novo) hits
# and sample ids contain underscores
uc_underscores_in_sample_id = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S 0 133 * * * * * _f_2__1539 *
H 0 141 100.0 + 0 0 133M8D f_3_42 _f_2__1539
H 0 141 100.0 + 0 0 133M8D _f_2__43 _f_2__1539
S 0 133 * * * * * f_3_44 *
L 3 1389 * * * * * 295053 *
H 3 133 100.0 + 0 0 519I133M737I _f_2__1539 295053
"""
uc = """# uclust --input /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/UclustExactMatchFilterrW47Ju.fasta --id 0.97 --tmpdir /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T --w 8 --stepwords 8 --usersort --maxaccepts 1 --stable_sort --maxrejects 8 --uc dn-otus/uclust_picked_otus/seqs_clusters.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S 0 133 * * * * * f2_1539 *
S 0 133 * * * * * f3_1540 *
H 0 141 100.0 + 0 0 133M8D f3_42 f2_1539
"""
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