diff --git a/core/pymod/pm3argparse.py b/core/pymod/pm3argparse.py
index b8b6a640bf92ae736bfdfe6a3bddb827919f68ea..33aa1fac81338e5bc137701951cbd1bdef9ec64c 100644
--- a/core/pymod/pm3argparse.py
+++ b/core/pymod/pm3argparse.py
@@ -232,6 +232,17 @@ def _LoadEntity(filename):
str(exc), 33)
return ent
+def _FetchProfileFromFile(filename):
+ """Load generic profile file from filename and return it."""
+ argstr = "'--seqprof " + filename + "'"
+ helper.FileExists("Profile", 51, filename)
+ try:
+ prof = io.LoadSequenceProfile(filename)
+ except Exception, exc:
+ helper.MsgErrorAndExit(argstr + ": failure to parse profile file: " +
+ str(exc), 52)
+ return prof
+
def _GetChains(structures, structure_sources):
"""Get chain id to entity view (single chain) mapping (dict)."""
# IDs: (file_base = base file name with no extensions)
@@ -398,6 +409,8 @@ class PM3ArgumentParser(argparse.ArgumentParser):
self._AssembleAlignment()
if 'STRUCTURE' in self.activate:
self._AssembleStructure()
+ if 'PROFILE' in self.activate:
+ self._AssembleProfile()
def AddAlignment(self, allow_multitemplate=False):
"""Commandline options for alignments.
@@ -474,7 +487,7 @@ class PM3ArgumentParser(argparse.ArgumentParser):
def AddStructure(self, attach_views=False):
"""Commandline options for structures.
- Activate everything needed to load alignments to the argument parser.
+ Activate everything needed to load structures to the argument parser.
Command line arguments are then added in :meth:`AssembleParser` and the
input is post processed and checked in :meth:`Parse`.
@@ -532,6 +545,46 @@ class PM3ArgumentParser(argparse.ArgumentParser):
if attach_views:
self.activate.add('ATTACH_VIEWS')
+ def AddProfile(self):
+ """Commandline options for profiles
+
+ Activate everything needed to load profiles to the argument parser.
+ Command line arguments are then added in :meth:`AssembleParser` and the
+ input is post processed and checked in :meth:`Parse`.
+
+ Options/arguments added:
+
+ * ``-s/--seqprof <FILE>`` - Sequence profile in any format readable
+ by the :meth:`ost.io.LoadSequenceProfile` method. Format is chosen by
+ file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
+ .pssm.gz.
+
+ Notes:
+
+ * the profiles are mapped based on exact matches towards the gapless
+ target sequences, i.e. one profile is mapped to several chains in
+ case of homo-oligomers
+
+ * every profile must have a unique sequence to avoid ambiguities
+
+ * all or nothing - you cannot provide profiles for only a subset of
+ target sequences
+
+ Attributes added to the namespace returned by :meth:`Parse`:
+
+ * :attr:`profiles` - :class:`list` of :class:`ost.seq.ProfileHandle`,
+ ordered to match the target sequences.
+
+ Exit codes related to profile input:
+
+ * 51 - a given profile file does not exist
+ * 52 - failure to read a given profile file
+ * 53 - a profile cannot be mapped to any target sequence
+ * 54 - profile sequences are not unique
+ * 55 - only subset of target sequences is covered by profile
+ """
+ self.activate.add('PROFILE')
+
def _AssembleAlignment(self):
"""Actually add alignment arguments/options."""
aln_grp = self.add_mutually_exclusive_group(required=True)
@@ -571,6 +624,14 @@ class PM3ArgumentParser(argparse.ArgumentParser):
".ent.gz, .pdb.gz, .cif, .cif.gz.",
action='append', default=list())
+ def _AssembleProfile(self):
+ self.add_argument('-s', '--seqprof', metavar=('<FILE>'),
+ help="Sequence profile in any format readable by "+
+ "OST's io.LoadSequenceProfile method. Format is "+
+ "chosen by file ending. Recognized File Extensions: "+
+ ".hhm, .hhm.gz, .pssm, .pssm.gz", action='append',
+ default=list())
+
class PM3OptionsNamespace(object):
# class will grow, so for the moment pylint is ignored
#pylint: disable=too-few-public-methods
@@ -591,6 +652,8 @@ class PM3OptionsNamespace(object):
self._PostProcessStructure()
if 'ATTACH_VIEWS' in activated:
self._AttachViews()
+ if 'PROFILE' in activated:
+ self._PostProcessProfile()
def _PostProcessAlignment(self):
#pylint: disable=no-member
@@ -640,6 +703,42 @@ class PM3OptionsNamespace(object):
for aln in self.alignments:
_AttachViewsToAln(aln, chain_entities)
+ def _PostProcessProfile(self):
+ """Get Profiles from command line input."""
+ self.profiles = list()
+
+ if len(self.seqprof) == 0:
+ # no profiles provided, remember the all or nothing principle
+ # so not having any profile is fine
+ return
+
+ loaded_profiles = list()
+ for src in self.seqprof:
+ loaded_profiles.append(_FetchProfileFromFile(src))
+
+ prof_sequences = [p.sequence for p in loaded_profiles]
+
+ # check uniqueness of loaded profiles
+ if len(set(prof_sequences)) != len(prof_sequences):
+ helper.MsgErrorAndExit("All sequence profiles must have unique " +
+ "sequence.", 54)
+
+ # map onto alignment target sequences
+ trg_sequences = [aln.GetSequence(0).GetGaplessString() \
+ for aln in self.alignments]
+ for s in trg_sequences:
+ try:
+ self.profiles.append(loaded_profiles[prof_sequences.index(s)])
+ except Exception, exc:
+ helper.MsgErrorAndExit("Could not find profile with sequence " +
+ "that exactly matches trg seq: " + s, 55)
+
+ # We found a profile for every target sequence. So if the size of unique
+ # target sequences is not the same as for unique profile sequences,
+ # we know that we have additional profiles that never got mapped
+ if len(set(trg_sequences)) != len(set(prof_sequences)):
+ helper.MsgErrorAndExit("Could not map every profile to a target " +
+ "sequence", 53)
# LocalWords: param attr prog argparse ArgumentParser bool sys os init str
# LocalWords: progattr descattr argpinit argv formatter meth args namespace
diff --git a/core/tests/CMakeLists.txt b/core/tests/CMakeLists.txt
index b7eebec0e86b04939ab02ac83281e74ac17ab1ef..829a9961c6ff7488d0b5ea3761f75bbe7b40987a 100644
--- a/core/tests/CMakeLists.txt
+++ b/core/tests/CMakeLists.txt
@@ -23,6 +23,10 @@ set(CORE_TEST_DATA
data/aln_tpl/5d52-1_cut.pdb
data/aln_tpl/5d52-1_cut_A.fasta
data/aln_tpl/5d52-1_cut_B.fasta
+ data/aln_tpl/1crn.hhm
+ data/aln_tpl/1crn_corrupted.hhm
+ data/aln_tpl/5ua4_B.fasta
+ data/aln_tpl/5ua4_B.hhm
data/fasta/alignment.fas
data/fasta/1ake.fas
data/fasta/1ake_1.fas
@@ -31,6 +35,7 @@ set(CORE_TEST_DATA
data/fasta/1ake.fas.gz
data/fasta/1ake_nel.fas
data/fasta/1ake_sw.fas
+
)
promod3_unittest(MODULE core
diff --git a/core/tests/data/aln_tpl/1crn.hhm b/core/tests/data/aln_tpl/1crn.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..eb35d07151bbc66ea6f979f155f3f1fef9cf2d40
--- /dev/null
+++ b/core/tests/data/aln_tpl/1crn.hhm
@@ -0,0 +1,180 @@
+HHsearch 1.5
+NAME c6a0deb50c4f69619d193f0fde0517c2
+FAM
+FILE seq01
+COM /scicore/soft/apps/HH-suite/2.0.16-goolf-1.4.10/bin/hhmake -i /scratch/14369431.1.short.q/tmpqOaEJI/seq01.a3m -o /scratch/14369431.1.short.q/tmpqOaEJI/seq01.hhm
+DATE Mon Mar 7 14:19:45 2016
+LENG 46 match states, 46 columns in multiple alignment
+FILT 55 out of 57 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCHHHHHHHHHCCCCCCCHHHHHHHCCCEEECCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9877783554421111168998455542048366208989999999
+>Consensus
+xsCCpstxaRnxYnxCrxxgxsxxxCaxxsgCkixsgxxCPxxyxx
+>c6a0deb50c4f69619d193f0fde0517c2
+TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
+>gi|115605364|gb|ABJ15789.1| putative thionin precursor [Polygonum sibiricum]
+-SCCQTTTARNIYNSCRLAGGSRERCASLSGCKHVTGNTCSPGWEK
+>gi|4007745|emb|CAA65316.1| purothionin [Secale cereale]
+-SCCKSTLGRNCYNLCRTRGAQK-LCANFCRCKLISSTSCPKEFPK
+>gi|17381172|gb|AAL36398.1| putative thionin protein [Arabidopsis thaliana]gi|62320644|dbj|BAD95310.1| putative thionin [Arabidopsis thaliana]
+-TCCPSQSTRKGFEDCISEGNLQILCSAESGCRDTYVGYCPSGFPY
+>gi|802170|gb|AAB33011.1| crambin precursor=thionin variant Thi2Ca12 [Crambe abyssinica, seeds, Peptide Partial, 135 aa]
+-SCCPTKSARNTFDVCRLTGTSMGLCAAISECKILSVTKCPSNLPY
+>gi|21553588|gb|AAM62681.1| thionin Thi2.2 [Arabidopsis thaliana]
+-ICCPTKDDRSVYFVCMLSVSSQFYCLLKSKCKNTSQTICPPGYTN
+>gi|15218931|ref|NP_176784.1| thionin [Arabidopsis thaliana]gi|44888531|sp|Q9C8D6.1|THN24_ARATH RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|12322605|gb|AAG51299.1|AC026480_6 thionin, putative [Arabidopsis thaliana]gi|14190505|gb|AAK55733.1|AF380652_1 At1g66100/F15E12_20 [Arabidopsis thaliana]gi|15809774|gb|AAL06815.1| At1g66100/F15E12_20 [Arabidopsis thaliana]gi|332196341|gb|AEE34462.1| thionin [Arabidopsis thaliana]
+-ICCPSIQARTFYNACLFAVGSPSSCIRNSSCLDISESTCPRGYTN
+>gi|1729954|sp|Q05806.1|THN5_WHEAT RecName: Full=Type-5 thionin; Contains: RecName: Full=Type-5 thionin; AltName: Full=Type V thionin; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|21885|emb|CAA43844.1| wheat type V thionin [Triticum aestivum]gi|21887|emb|CAA43845.1| wheat type V thionin [Triticum aestivum]
+-DCGANPFKVACFNSCLLGPSTVFQCADFCACRLPAG---------
+>gi|120564556|gb|ABM30200.1| thionin [Brassica juncea]
+-SCCPSTAARWAYYLCTNSWPLTPLCISHTGC-IESETTCPPGYPY
+>gi|545031|gb|AAB29760.1| thionin precursor {clone Thi1Va1} [Viscum album=mistletoe, Peptide, 115 aa]
+-ICCRAPAGKKCYNLCTA-lLSSE-TCANTCYCKDVSGETCPAD---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * * * * * 0 * * * 1
+ 0 * * * * * * 1000 0 0
+
+T 2 * * 4186 * * 5283 * 2677 * 5264 * * * * * 833 3153 3986 * * 2
+ 0 * * * * * * 3941 0 0
+
+C 3 * 0 * * * * * * * * * * * * * * * * * * 3
+ 0 * * * * * * 3941 0 0
+
+C 4 * 122 * * 5259 4186 * * * * * * * * * * * * * * 4
+ 0 * * * * * * 3941 0 0
+
+P 5 4186 * * * * * * * 3250 * * * 549 5753 2856 * * * * * 5
+ 0 * * * * * * 3941 0 0
+
+S 6 5271 * 4429 * * * * * * * * 2329 * * 5941 866 2612 * * * 6
+ 0 * * * * * * 3941 0 0
+
+I 7 * * 5440 4820 * * * 3810 4212 * 5935 4983 3272 3386 4684 5283 1068 5174 * * 7
+ 0 * * * * * * 3941 0 0
+
+V 8 2614 * 4805 * 4186 * * 3036 * 3320 * * * 4094 * 2750 1838 5660 5873 * 8
+ 0 * * * * * * 3941 0 0
+
+A 9 646 * 4264 * * 2749 * * 4186 * * * * * * 3803 4903 * * * 9
+ 0 * * * * * * 3941 0 0
+
+R 10 * * * * * * * 5975 4265 * * * * * 189 * * 4186 * * 10
+ 0 * * * * * * 3941 0 0
+
+S 11 4186 * * 3803 * * * 5935 3608 * * 836 * * * 2953 5214 * 4935 5259 11
+ 0 * * * * * * 3941 0 0
+
+N 12 4935 1544 * 4787 5214 3942 * 2698 5264 * 4684 3736 * 5164 5174 * 3934 3625 * * 12
+ 0 * * * * * * 3941 0 0
+
+F 13 * * * * 2199 * * * * * * * * * * * * * * 354 13
+ 0 * * * * * * 3941 0 0
+
+N 14 * * 4222 3844 4805 * * * * 5264 * 510 * * * 4983 5283 5464 * 4935 14
+ 0 * * * * * * 3941 0 0
+
+V 15 2800 * 3844 * * * * 5271 * 2403 5174 * * * * 2663 3074 1902 * * 15
+ 0 * * * * * * 3941 0 0
+
+C 16 * 0 * * * * * * * * * * * * * * * * * * 16
+ 0 * * * * * * 3941 0 0
+
+R 17 * * * * * * 6200 2932 * 3611 4805 * * * 558 * 4093 * * * 17
+ 0 * * * * * * 3941 0 0
+
+L 18 3969 * * * 2171 * * 3956 * 1318 5174 4935 * * 5264 3115 6073 4979 * * 18
+ 38 * 5271 * * * * 3941 0 0
+
+P 19 3003 * * 4863 * 3441 * * * 5901 * * 2369 4784 2418 3812 2907 3735 * 4814 19
+ 41 * 5155 0 * 0 * 3898 1025 1025
+
+G 20 * * * * 4949 454 6123 * * 4542 * * 3604 * * * * 3948 4909 * 20
+ 72 * 4354 * * * 0 3901 0 1033
+
+T 21 2209 5224 * * * 2278 * * * * * 3752 4867 * * 2344 2028 * * * 21
+ 39 5224 * 0 * 669 1430 3845 1023 1191
+
+P 22 5624 * * * * * * 5870 * 3138 * * 1935 4054 * 1200 3439 * * * 22
+ 0 * * * * 0 * 3903 0 1033
+
+E 23 5952 6850 * 3099 * * 4802 5475 3316 * 4903 * 4232 2872 1627 5880 4176 4193 * 5287 23
+ 184 * 3059 * * * * 3943 0 0
+
+A 24 4442 * 3710 2779 2989 4157 * 4702 * * * * 1565 * 5707 4382 3234 * * * 24
+ 28 5707 * 0 * 0 * 3843 1000 1329
+
+I 25 4358 * * * 6658 * 5279 3244 4611 2579 * 5958 * 4193 3566 3476 2812 2484 * 4816 25
+ 0 * * * * * * 3943 0 0
+
+C 26 * 31 * * * * * * * * * * * * * 5573 * * * * 26
+ 0 * * * * * * 3943 0 0
+
+A 27 560 6231 * * * 4233 * 3636 * 4029 4985 * * * * 3609 * * * * 27
+ 0 * * * * * * 3943 0 0
+
+T 28 2460 * 3819 * * 4273 * 5850 2738 4816 * 3203 * 4985 3239 2607 3596 * * * 28
+ 0 * * * * * * 3943 0 0
+
+Y 29 4929 * 5658 4919 2879 4802 4950 3737 4252 1699 5444 5287 5995 * 5262 * 3899 3734 * 4566 29
+ 0 * * * * * * 3943 0 0
+
+T 30 3911 1554 * * * * * * * * * * * * * 1040 3227 * * * 30
+ 0 * * * * * * 3943 0 0
+
+G 31 4193 * 3877 5850 * 811 * * 4816 * * * * * 2699 4815 4659 * * 5301 31
+ 0 * * * * * * 3943 0 0
+
+C 32 * 0 * * * * * * * * * * * * * * * * * * 32
+ 47 * 4950 * * * * 3943 0 0
+
+I 33 * * * 4672 * * * 2865 809 3414 * * * 4933 3475 * * 4789 * * 33
+ 0 * * * * 0 * 3904 0 1044
+
+I 34 * * 3573 4802 * * 3933 921 * 2779 * 3898 * * 4839 * 5475 5952 * * 34
+ 0 * * * * * * 3943 0 0
+
+I 35 * * 5287 4950 4358 * * 1603 * 3869 * * 4193 6130 * 3498 3006 2227 * * 35
+ 46 * 4985 * * * * 3943 0 0
+
+P 36 4173 * 2874 * 5250 * * 5139 * 4792 * * 4633 4645 5394 1055 4050 * * 3805 36
+ 201 * 2941 * * * 0 3881 0 1045
+
+G 37 5480 * 5485 3849 * 869 * * * * * * * 4548 5245 3819 4686 2648 * * 37
+ 22 * 6064 * * 0 * 3796 0 1453
+
+A 38 4564 * 4944 5167 * 1910 * * 4653 4470 * 3572 4946 * 5111 2927 1892 * * * 38
+ 0 * * * * 0 * 3775 0 1000
+
+T 39 * 4660 * 5366 4744 6406 * 3919 2193 * * 4099 * 5382 5207 3976 1348 * * 4782 39
+ 0 * * * * * * 3764 0 0
+
+C 40 * 58 * * * * * * 4660 * * * * * * * * * * * 40
+ 0 * * * * * * 3764 0 0
+
+P 41 * * 4306 * * * * * 3731 * * 6351 322 4587 * 5643 * * * * 41
+ 0 * * * * * * 3764 0 0
+
+G 42 4398 * 6402 * * 4592 * * 4079 * * 4374 1200 * 3395 2109 5063 * * * 42
+ 0 * * * * * * 3764 0 0
+
+D 43 * * 2024 6014 4769 1231 4660 * * * * 4386 3096 4744 * 4862 * * * * 43
+ 0 * * * * * * 3764 0 0
+
+Y 44 * * * * 2991 * 4830 * * 3705 * * * * * * * * 2806 691 44
+ 0 * * * * * * 3718 0 0
+
+A 45 4566 * 3231 5056 * * * 3467 * * * 5405 1034 * 5100 6384 2896 4532 * * 45
+ 35 5366 * 4087 87 * * 3718 1002 0
+
+N 46 * * 4370 * * * 2588 * 1723 * * 2200 * * 5953 * * * * 2008 46
+ 0 * * 0 * * * 3699 0 0
+
+//
diff --git a/core/tests/data/aln_tpl/1crn_corrupted.hhm b/core/tests/data/aln_tpl/1crn_corrupted.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..01765421ff452e8094d103970ff78277a80e1a5e
--- /dev/null
+++ b/core/tests/data/aln_tpl/1crn_corrupted.hhm
@@ -0,0 +1,185 @@
+#######################################################################
+# THIS FILE IS CORRUPTED!!!!!!!!! #
+# First three amino acids do not have the right number of frequencies #
+#######################################################################
+
+HHsearch 1.5
+NAME c6a0deb50c4f69619d193f0fde0517c2
+FAM
+FILE seq01
+COM /scicore/soft/apps/HH-suite/2.0.16-goolf-1.4.10/bin/hhmake -i /scratch/14369431.1.short.q/tmpqOaEJI/seq01.a3m -o /scratch/14369431.1.short.q/tmpqOaEJI/seq01.hhm
+DATE Mon Mar 7 14:19:45 2016
+LENG 46 match states, 46 columns in multiple alignment
+FILT 55 out of 57 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCHHHHHHHHHCCCCCCCHHHHHHHCCCEEECCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9877783554421111168998455542048366208989999999
+>Consensus
+xsCCpstxaRnxYnxCrxxgxsxxxCaxxsgCkixsgxxCPxxyxx
+>c6a0deb50c4f69619d193f0fde0517c2
+TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
+>gi|115605364|gb|ABJ15789.1| putative thionin precursor [Polygonum sibiricum]
+-SCCQTTTARNIYNSCRLAGGSRERCASLSGCKHVTGNTCSPGWEK
+>gi|4007745|emb|CAA65316.1| purothionin [Secale cereale]
+-SCCKSTLGRNCYNLCRTRGAQK-LCANFCRCKLISSTSCPKEFPK
+>gi|17381172|gb|AAL36398.1| putative thionin protein [Arabidopsis thaliana]gi|62320644|dbj|BAD95310.1| putative thionin [Arabidopsis thaliana]
+-TCCPSQSTRKGFEDCISEGNLQILCSAESGCRDTYVGYCPSGFPY
+>gi|802170|gb|AAB33011.1| crambin precursor=thionin variant Thi2Ca12 [Crambe abyssinica, seeds, Peptide Partial, 135 aa]
+-SCCPTKSARNTFDVCRLTGTSMGLCAAISECKILSVTKCPSNLPY
+>gi|21553588|gb|AAM62681.1| thionin Thi2.2 [Arabidopsis thaliana]
+-ICCPTKDDRSVYFVCMLSVSSQFYCLLKSKCKNTSQTICPPGYTN
+>gi|15218931|ref|NP_176784.1| thionin [Arabidopsis thaliana]gi|44888531|sp|Q9C8D6.1|THN24_ARATH RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|12322605|gb|AAG51299.1|AC026480_6 thionin, putative [Arabidopsis thaliana]gi|14190505|gb|AAK55733.1|AF380652_1 At1g66100/F15E12_20 [Arabidopsis thaliana]gi|15809774|gb|AAL06815.1| At1g66100/F15E12_20 [Arabidopsis thaliana]gi|332196341|gb|AEE34462.1| thionin [Arabidopsis thaliana]
+-ICCPSIQARTFYNACLFAVGSPSSCIRNSSCLDISESTCPRGYTN
+>gi|1729954|sp|Q05806.1|THN5_WHEAT RecName: Full=Type-5 thionin; Contains: RecName: Full=Type-5 thionin; AltName: Full=Type V thionin; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|21885|emb|CAA43844.1| wheat type V thionin [Triticum aestivum]gi|21887|emb|CAA43845.1| wheat type V thionin [Triticum aestivum]
+-DCGANPFKVACFNSCLLGPSTVFQCADFCACRLPAG---------
+>gi|120564556|gb|ABM30200.1| thionin [Brassica juncea]
+-SCCPSTAARWAYYLCTNSWPLTPLCISHTGC-IESETTCPPGYPY
+>gi|545031|gb|AAB29760.1| thionin precursor {clone Thi1Va1} [Viscum album=mistletoe, Peptide, 115 aa]
+-ICCRAPAGKKCYNLCTA-lLSSE-TCANTCYCKDVSGETCPAD---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * * * * * 0 * *
+ 0 * * * * * * 1000 0 0
+
+T 2 * * 4186 * * 5283 * 2677 * 5264 * * * * * 833 3153 3986 *
+ 0 * * * * * * 3941 0 0
+
+C 3 * 0 * * * * * * * * * * * * * * * * *
+ 0 * * * * * * 3941 0 0
+
+C 4 * 122 * * 5259 4186 * * * * * * * * * * * * * * 4
+ 0 * * * * * * 3941 0 0
+
+P 5 4186 * * * * * * * 3250 * * * 549 5753 2856 * * * * * 5
+ 0 * * * * * * 3941 0 0
+
+S 6 5271 * 4429 * * * * * * * * 2329 * * 5941 866 2612 * * * 6
+ 0 * * * * * * 3941 0 0
+
+I 7 * * 5440 4820 * * * 3810 4212 * 5935 4983 3272 3386 4684 5283 1068 5174 * * 7
+ 0 * * * * * * 3941 0 0
+
+V 8 2614 * 4805 * 4186 * * 3036 * 3320 * * * 4094 * 2750 1838 5660 5873 * 8
+ 0 * * * * * * 3941 0 0
+
+A 9 646 * 4264 * * 2749 * * 4186 * * * * * * 3803 4903 * * * 9
+ 0 * * * * * * 3941 0 0
+
+R 10 * * * * * * * 5975 4265 * * * * * 189 * * 4186 * * 10
+ 0 * * * * * * 3941 0 0
+
+S 11 4186 * * 3803 * * * 5935 3608 * * 836 * * * 2953 5214 * 4935 5259 11
+ 0 * * * * * * 3941 0 0
+
+N 12 4935 1544 * 4787 5214 3942 * 2698 5264 * 4684 3736 * 5164 5174 * 3934 3625 * * 12
+ 0 * * * * * * 3941 0 0
+
+F 13 * * * * 2199 * * * * * * * * * * * * * * 354 13
+ 0 * * * * * * 3941 0 0
+
+N 14 * * 4222 3844 4805 * * * * 5264 * 510 * * * 4983 5283 5464 * 4935 14
+ 0 * * * * * * 3941 0 0
+
+V 15 2800 * 3844 * * * * 5271 * 2403 5174 * * * * 2663 3074 1902 * * 15
+ 0 * * * * * * 3941 0 0
+
+C 16 * 0 * * * * * * * * * * * * * * * * * * 16
+ 0 * * * * * * 3941 0 0
+
+R 17 * * * * * * 6200 2932 * 3611 4805 * * * 558 * 4093 * * * 17
+ 0 * * * * * * 3941 0 0
+
+L 18 3969 * * * 2171 * * 3956 * 1318 5174 4935 * * 5264 3115 6073 4979 * * 18
+ 38 * 5271 * * * * 3941 0 0
+
+P 19 3003 * * 4863 * 3441 * * * 5901 * * 2369 4784 2418 3812 2907 3735 * 4814 19
+ 41 * 5155 0 * 0 * 3898 1025 1025
+
+G 20 * * * * 4949 454 6123 * * 4542 * * 3604 * * * * 3948 4909 * 20
+ 72 * 4354 * * * 0 3901 0 1033
+
+T 21 2209 5224 * * * 2278 * * * * * 3752 4867 * * 2344 2028 * * * 21
+ 39 5224 * 0 * 669 1430 3845 1023 1191
+
+P 22 5624 * * * * * * 5870 * 3138 * * 1935 4054 * 1200 3439 * * * 22
+ 0 * * * * 0 * 3903 0 1033
+
+E 23 5952 6850 * 3099 * * 4802 5475 3316 * 4903 * 4232 2872 1627 5880 4176 4193 * 5287 23
+ 184 * 3059 * * * * 3943 0 0
+
+A 24 4442 * 3710 2779 2989 4157 * 4702 * * * * 1565 * 5707 4382 3234 * * * 24
+ 28 5707 * 0 * 0 * 3843 1000 1329
+
+I 25 4358 * * * 6658 * 5279 3244 4611 2579 * 5958 * 4193 3566 3476 2812 2484 * 4816 25
+ 0 * * * * * * 3943 0 0
+
+C 26 * 31 * * * * * * * * * * * * * 5573 * * * * 26
+ 0 * * * * * * 3943 0 0
+
+A 27 560 6231 * * * 4233 * 3636 * 4029 4985 * * * * 3609 * * * * 27
+ 0 * * * * * * 3943 0 0
+
+T 28 2460 * 3819 * * 4273 * 5850 2738 4816 * 3203 * 4985 3239 2607 3596 * * * 28
+ 0 * * * * * * 3943 0 0
+
+Y 29 4929 * 5658 4919 2879 4802 4950 3737 4252 1699 5444 5287 5995 * 5262 * 3899 3734 * 4566 29
+ 0 * * * * * * 3943 0 0
+
+T 30 3911 1554 * * * * * * * * * * * * * 1040 3227 * * * 30
+ 0 * * * * * * 3943 0 0
+
+G 31 4193 * 3877 5850 * 811 * * 4816 * * * * * 2699 4815 4659 * * 5301 31
+ 0 * * * * * * 3943 0 0
+
+C 32 * 0 * * * * * * * * * * * * * * * * * * 32
+ 47 * 4950 * * * * 3943 0 0
+
+I 33 * * * 4672 * * * 2865 809 3414 * * * 4933 3475 * * 4789 * * 33
+ 0 * * * * 0 * 3904 0 1044
+
+I 34 * * 3573 4802 * * 3933 921 * 2779 * 3898 * * 4839 * 5475 5952 * * 34
+ 0 * * * * * * 3943 0 0
+
+I 35 * * 5287 4950 4358 * * 1603 * 3869 * * 4193 6130 * 3498 3006 2227 * * 35
+ 46 * 4985 * * * * 3943 0 0
+
+P 36 4173 * 2874 * 5250 * * 5139 * 4792 * * 4633 4645 5394 1055 4050 * * 3805 36
+ 201 * 2941 * * * 0 3881 0 1045
+
+G 37 5480 * 5485 3849 * 869 * * * * * * * 4548 5245 3819 4686 2648 * * 37
+ 22 * 6064 * * 0 * 3796 0 1453
+
+A 38 4564 * 4944 5167 * 1910 * * 4653 4470 * 3572 4946 * 5111 2927 1892 * * * 38
+ 0 * * * * 0 * 3775 0 1000
+
+T 39 * 4660 * 5366 4744 6406 * 3919 2193 * * 4099 * 5382 5207 3976 1348 * * 4782 39
+ 0 * * * * * * 3764 0 0
+
+C 40 * 58 * * * * * * 4660 * * * * * * * * * * * 40
+ 0 * * * * * * 3764 0 0
+
+P 41 * * 4306 * * * * * 3731 * * 6351 322 4587 * 5643 * * * * 41
+ 0 * * * * * * 3764 0 0
+
+G 42 4398 * 6402 * * 4592 * * 4079 * * 4374 1200 * 3395 2109 5063 * * * 42
+ 0 * * * * * * 3764 0 0
+
+D 43 * * 2024 6014 4769 1231 4660 * * * * 4386 3096 4744 * 4862 * * * * 43
+ 0 * * * * * * 3764 0 0
+
+Y 44 * * * * 2991 * 4830 * * 3705 * * * * * * * * 2806 691 44
+ 0 * * * * * * 3718 0 0
+
+A 45 4566 * 3231 5056 * * * 3467 * * * 5405 1034 * 5100 6384 2896 4532 * * 45
+ 35 5366 * 4087 87 * * 3718 1002 0
+
+N 46 * * 4370 * * * 2588 * 1723 * * 2200 * * 5953 * * * * 2008 46
+ 0 * * 0 * * * 3699 0 0
+
+//
diff --git a/core/tests/data/aln_tpl/5ua4_B.fasta b/core/tests/data/aln_tpl/5ua4_B.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..92c2692ce0377b23b6f6fc861ee165c3e39eb344
--- /dev/null
+++ b/core/tests/data/aln_tpl/5ua4_B.fasta
@@ -0,0 +1,4 @@
+>target
+SESQEAVIRDIARHLARIGDRMEYGIRPGLVDSL
+>pdb_id=4bd2, chain=B, assembly_id=1, offset=0 atoms
+SESQEDIIRNIARHLAQVGDSMDRSIPPGL----
diff --git a/core/tests/data/aln_tpl/5ua4_B.hhm b/core/tests/data/aln_tpl/5ua4_B.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..a038b72184271d8c02f22a4f5f40cb28efa2fbe9
--- /dev/null
+++ b/core/tests/data/aln_tpl/5ua4_B.hhm
@@ -0,0 +1,144 @@
+HHsearch 1.5
+NAME target
+FAM
+FILE query_hhblits
+COM /scicore/soft/apps/HH-suite/2.0.16-goolf-1.4.10-Boost-1.53.0/bin/hhmake -i <101 characters> -o <101 characters>
+DATE Sat Dec 31 05:49:23 2016
+LENG 34 match states, 34 columns in multiple alignment
+FILT 11 out of 13 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
+>ss_conf PSIPRED confidence values
+9159999999999999975443036780111159
+>Consensus
+SEsQEeiIxxiArxLAqiGDxmdxsIxPxlvxxL
+>target
+SESQEAVIRDIARHLARIGDRMEYGIRPGLVDSL
+>gi|12083631|ref|NP_073175.1| BH3-interacting domain death agonist [Rattus norvegicus]gi|88909592|sp|Q9JLT6.2|BID_RAT RecName: Full=BH3-interacting domain death agonist; AltName: Full=p22 BID; Short=BID; Contains: RecName: Full=BH3-interacting domain death agonist p15; AltName: Full=p15 BID; Contains: RecName: Full=BH3-interacting domain death agonist p13; AltName: Full=p13 BID; Contains: RecName: Full=BH3-interacting domain death agonist p11; AltName: Full=p11 BIDgi|8050830|gb|AAF71759.1|AF259503_1 BID protein [Rattus norvegicus]gi|149049571|gb|EDM02025.1| BH3 interacting domain death agonist [Rattus norvegicus]gi|157041211|dbj|BAF79674.1| desmocollin type 4 [Rattus norvegicus]
+SESQDEVIHNIARHLAQAGDELDHSIQPTLVRQL
+>gi|115495761|ref|NP_001068914.1| BH3 interacting domain death agonist [Bos taurus]gi|109658413|gb|AAI18360.1| BH3 interacting domain death agonist [Bos taurus]gi|296486995|gb|DAA29108.1| BH3 interacting domain death agonist [Bos taurus]
+SERQEEAVREVARQLAQIGDRLEGSIHPGMVAGL
+>gi|281341033|gb|EFB16617.1| hypothetical protein PANDA_016465 [Ailuropoda melanoleuca]
+SQGQEEIIQDIARQLAQIGDDMDHSIHPGLMNNL
+>gi|307335680|gb|ADN43410.1| BH3 interacting domain death agonist [Lemur catta]
+SESEEDLIQTLARQLAQIGDSMERSIPPRLVDHL
+>gi|307335678|gb|ADN43409.1| BH3 interacting domain death agonist [Felis catus]
+SESQEEIIQDIARQLAQIGDRMDHSIHPRVVNNL
+>gi|307335682|gb|ADN43411.1| BH3 interacting domain death agonist [Saimiri boliviensis]
+SESQEDIIRNIARQLAQVGDSMDRSIPPGLVNRL
+>gi|291412643|ref|XP_002722593.1| PREDICTED: BH3 interacting domain death agonist-like [Oryctolagus cuniculus]
+SESQEEVIRNIARRLAQIGDRMDHHIQPELLNNL
+>gi|296191314|ref|XP_002743575.1| PREDICTED: hypothetical protein LOC100403496 [Callithrix jacchus]
+SESQEDVIRSIARHLAHIGDSMDRSIPLDLVDRL
+>gi|334348150|ref|XP_001373913.2| PREDICTED: envelope glycoprotein-like [Monodelphis domestica]
+SESQEEIIQRIAMQLAKIGDNIENSIQPRVVDEL
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * * * * * * * * * * * 0 * * * * 1
+ 0 * * * * * * 1973 0 0
+
+E 2 * * * 143 * * * * * * * * * 3405 * * * * * * 2
+ 0 * * * * * * 1973 0 0
+
+S 3 * * * * * 3405 * * * * * * * * 2994 358 * * * * 3
+ 0 * * * * * * 1973 0 0
+
+Q 4 * * * 3344 * * * * * * * * * 150 * * * * * * 4
+ 0 * * * * * * 1973 0 0
+
+E 5 * * 3425 141 * * * * * * * * * * * * * * * * 5
+ 0 * * * * * * 1973 0 0
+
+A 6 3391 * 1939 635 * * * * * * * * * * * * * * * * 6
+ 0 * * * * * * 1973 0 0
+
+V 7 2994 * * * * * * 1285 * 3344 * * * * * * * 1452 * * 7
+ 0 * * * * * * 1973 0 0
+
+I 8 * * * * * * * 194 * * * * * * * * * 2994 * * 8
+ 0 * * * * * * 1973 0 0
+
+R 9 * * * * * * 2586 * * * * * * 1457 1092 * * * * * 9
+ 0 * * * * * * 1973 0 0
+
+D 10 * * 1981 2994 * * * * * * * 1628 * * 3212 3454 3344 * * * 10
+ 0 * * * * * * 1973 0 0
+
+I 11 * * * * * * * 366 * 3344 * * * * * * * 2994 * * 11
+ 0 * * * * * * 1973 0 0
+
+A 12 0 * * * * * * * * * * * * * * * * * * * 12
+ 0 * * * * * * 1973 0 0
+
+R 13 * * * * * * * * * * 3212 * * * 165 * * * * * 13
+ 0 * * * * * * 1973 0 0
+
+H 14 * * * * * * 1502 * * * * * * 834 3540 * * * * * 14
+ 0 * * * * * * 1973 0 0
+
+L 15 * * * * * * * * * 0 * * * * * * * * * * 15
+ 0 * * * * * * 1973 0 0
+
+A 16 0 * * * * * * * * * * * * * * * * * * * 16
+ 0 * * * * * * 1973 0 0
+
+R 17 * * * * * * 3454 * 3212 * * * * 503 3391 * * * * * 17
+ 0 * * * * * * 1973 0 0
+
+I 18 3425 * * * * * * 259 * * * * * * * * * 3816 * * 18
+ 0 * * * * * * 1973 0 0
+
+G 19 * * * * * 0 * * * * * * * * * * * * * * 19
+ 0 * * * * * * 1973 0 0
+
+D 20 * * 0 * * * * * * * * * * * * * * * * * 20
+ 0 * * * * * * 1973 0 0
+
+R 21 * * 3405 2586 * * * * * * * 3212 * * 1433 1939 * * * * 21
+ 0 * * * * * * 1973 0 0
+
+M 22 * * * * * * * 3212 * 2194 570 * * * * * * * * * 22
+ 0 * * * * * * 1973 0 0
+
+E 23 * * 804 1227 * * * * * * * * * * * * * * * * 23
+ 0 * * * * * * 1973 0 0
+
+Y 24 * * * * * 2994 1285 * * * * 3212 * * 1939 * * * * 3391 24
+ 0 * * * * * * 1973 0 0
+
+G 25 * * * * * 3391 3540 * * * * 3766 * * * 424 * * * * 25
+ 0 * * * * * * 1973 0 0
+
+I 26 * * * * * * * 0 * * * * * * * * * * * * 26
+ 0 * * * * * * 1973 0 0
+
+R 27 * * * * * * 1819 * * * * * 1939 1472 3391 * * * * * 27
+ 0 * * * * * * 1973 0 0
+
+P 28 * * * * * * * * * 3454 * * 138 * * * * * * * 28
+ 0 * * * * * * 1973 0 0
+
+G 29 * * 3454 3540 * 1372 * * * * * * * * 1889 * 2586 * * * 29
+ 0 * * * * * * 1973 0 0
+
+L 30 * * * * * * * * * 508 2994 * * * * * * 2544 * * 30
+ 0 * * * * * * 1973 0 0
+
+V 31 * * * * * * * * * 3540 3405 * * * * * * 287 * * 31
+ 0 * * * * * * 1973 0 0
+
+D 32 2994 * 1348 * * * * * * * * 1667 * * 2586 * * * * * 32
+ 0 * * * * * * 1973 0 0
+
+S 33 * * * 3212 * 2994 3344 * * * * 2036 * 2586 2624 3391 * * * * 33
+ 0 * * * * * * 1973 0 0
+
+L 34 * * * * * * * * * 0 * * * * * * * * * * 34
+ 0 * * 0 * * * 1973 0 0
+
+//
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index 0e0d617c98734c9348cae38e24015a779077871e..0b2310e8cf0db4494185ac68bf521e6a7b7fb681 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -1101,7 +1101,113 @@ class PM3ArgParseTests(unittest.TestCase):
self.assertEqual(len(self.log.messages['ERROR']), 1)
self.assertEqual(self.log.messages['ERROR'],
['Could not find chain with ID tpl (should be '+
- '<FILE>.<CHAIN>) to attach to sequence named tpl'])
+ '<FILE>.<CHAIN>) to attach to sequence named tpl'])
+
+ def testProfileDoesNotExist(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/IDoNotExist.hhm'])
+ self.assertEqual(ecd.exception.code, 51)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testProfileIsFuckedUp(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn_corrupted.hhm'])
+ self.assertEqual(ecd.exception.code, 52)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testAdditionalProfile(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm',
+ '-s', 'data/aln_tpl/5ua4_B.hhm'])
+ self.assertEqual(ecd.exception.code, 53)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testUniqueProfiles(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+ self.assertEqual(ecd.exception.code, 54)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testAllCovered(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-f', 'data/aln_tpl/5d52-1_cut_A.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+ self.assertEqual(ecd.exception.code, 55)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testAllGoodOneChain(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+
+ opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+
+ self.assertEqual(len(opts.alignments), 1)
+ self.assertEqual(len(opts.profiles), 1)
+ self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+ opts.profiles[0].sequence)
+
+ def testAllGoodHomoOligo(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+
+ opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+ self.assertEqual(len(opts.alignments), 2)
+ self.assertEqual(len(opts.profiles), 2)
+ self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+ opts.profiles[0].sequence)
+ self.assertEqual(opts.alignments[1].GetSequence(0).GetGaplessString(),
+ opts.profiles[1].sequence)
+
+ def testAllGoodHeteroOligo(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+
+ opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-f', 'data/aln_tpl/5ua4_B.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm',
+ '-s', 'data/aln_tpl/5ua4_B.hhm'])
+ self.assertEqual(len(opts.alignments), 2)
+ self.assertEqual(len(opts.profiles), 2)
+ self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+ opts.profiles[0].sequence)
+ self.assertEqual(opts.alignments[1].GetSequence(0).GetGaplessString(),
+ opts.profiles[1].sequence)
+
# test options: --disable-aln check (for amino acids)
# test options: --disable-input-checks (for all)