Mercurial > repos > bgruening > infernal
changeset 8:c9e29ac5d099 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
| author | bgruening |
|---|---|
| date | Thu, 23 Sep 2021 19:38:58 +0000 |
| parents | 477d829d3250 |
| children | |
| files | cmalign.xml cmbuild.xml cmpress.xml cmscan.xml cmsearch.xml cmstat.xml infernal.py infernal.tar.gz macros.xml repository_dependencies.xml test-data/cmsearch_result.tabular test-data/test_cmscan.tabular |
| diffstat | 12 files changed, 205 insertions(+), 130 deletions(-) [+] |
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--- a/cmalign.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/cmalign.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,10 +1,11 @@ -<tool id="infernal_cmalign" name="cmalign" version="@VERSION@.0"> +<tool id="infernal_cmalign" name="cmalign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Align sequences to a covariance model against a sequence database</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> + <expand macro="xrefs"/> <command> <![CDATA[
--- a/cmbuild.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/cmbuild.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,11 +1,12 @@ -<tool id="infernal_cmbuild" name="cmbuild" version="@VERSION@.0"> +<tool id="infernal_cmbuild" name="cmbuild" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Build covariance models from sequence alignments</description> <macros> <import>macros.xml</import> </macros> - <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism> + <!--parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism--> <expand macro="requirements" /> <expand macro="stdio" /> + <expand macro="xrefs"/> <command> <![CDATA[ cmbuild @@ -38,6 +39,9 @@ #if $effective_opts.eminseq --eminseq $effective_opts.eminseq #end if + #if $effective_opts.emaxseq + --emaxseq $effective_opts.emaxseq + #end if #if $effective_opts.ehmmre --ehmmre $effective_opts.ehmmre #end if @@ -151,6 +155,9 @@ <param name="eminseq" type="integer" value="" label="Define the minimum allowed effective sequence number" help="(--eminseq)" optional="true"/> + <param name="emaxseq" type="integer" value="" + label="Define the maximum allowed effective sequence number" help="(--emaxseq)" optional="true"/> + <param name="ehmmre" type="float" value="" label="Set the target HMM mean match state relative entropy" help="(--ehmmre)" optional="true"/> @@ -253,7 +260,7 @@ </inputs> <outputs> - <data format="text" name="summary_outfile" label="cmbuild summary on ${on_string}"> + <data format="txt" name="summary_outfile" label="cmbuild summary on ${on_string}"> <filter>is_summery_output is True</filter> </data> <!--<data format="stockholm" name="annotated_source_alignment_outfile" label="Annotated alignment from ${on_string}"/>--> @@ -324,12 +331,29 @@ <param name="selector" value="true"/> <param name="L" value="0.1"/> </conditional> - <output name="outfile"> + <output name="cmfile_outfile"> <assert_contents> <has_text text="S 0 -1 0 1 4 0 1 89 109 -7.220 -8.465 -0.063 -4.919"/> </assert_contents> </output> </test> + <!-- Test emax seq parameter --> + <test> + <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/> + <conditional name="Calibrate"> + <param name="selector" value="true"/> + <param name="L" value="0.1"/> + </conditional> + <conditional name="effective_opts"> + <param name="effective_opts_selector" value="--eent"/> + <param name="emaxseq" value="100"/> + </conditional> + <output name="cmfile_outfile"> + <assert_contents> + <has_text text="S 0 -1 0 1 4 0 1 89 109 -7.111 -8.357 -0.068 -4.810"/> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[
--- a/cmpress.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/cmpress.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,10 +1,11 @@ -<tool id="infernal_cmpress" name="cmpress" version="@VERSION@.0"> +<tool id="infernal_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description> Prepare a covariance model database for cmscan</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> + <expand macro="xrefs"/> <command> <![CDATA[ ## CM file from the history or stored as database on disc
--- a/cmscan.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/cmscan.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,10 +1,11 @@ -<tool id="infernal_cmscan" name="cmscan" version="@VERSION@.0"> +<tool id="infernal_cmscan" name="cmscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description> Search sequences against collections of covariance models</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> + <expand macro="xrefs"/> <command> <![CDATA[ ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy @@ -73,8 +74,19 @@ #end if ## sequence file '$seqdb' - && - sed 's/ \+ /\t/g' '\$temp_tabular_output' > '$outfile' + ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984 + ## remove the header + && tail -n +3 '\$temp_tabular_output' > headless_file + ## extract the last column, since the description includes a variable number of spaces (so, is not considered as a column by awk) + && awk '{$1=$2=$3=$4=$5=$6=$7=$8=$9=$10=$11=$12=$13=$14=$15=$16=$17=""; print $0}' headless_file > description_column + ## fix the tabulation the rest content (except the description column) + && awk 'OFS="\t" {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17 > ("tabulated_columns")}' headless_file + ## add the description column to the tabulated data + && paste -d"\t" tabulated_columns description_column > joined_file + ## include a correct header + && echo -e '#target\tname\taccession\tquery name\taccession\tmdl\tmdl from\tmdl to\tseq from\tseq to\tstrand\ttrunc\tpass\tgc\tbias\tscore\tE-value\tinc\tdescription of target' > header + ## export the result + && cat header joined_file > '$outfile' ]]> </command> @@ -226,12 +238,10 @@ label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/> </section> - - - </inputs> <outputs> <data format="tabular" name="outfile" label="cmscan on ${on_string}"/> + </outputs> <tests> <test> @@ -241,8 +251,9 @@ </conditional> <param name="aux_files" value="minifam.tar" ftype="tar"/> <param name="seqdb" value="metag-example.fa"/> - <output name="outfile"> + <output name="outfile" file="test_cmscan.tabular" ftype="tabular" lines_diff="8"> <assert_contents> + <has_n_lines n="15"/> <has_text text="AAGA01015927.1"/> </assert_contents> </output>
--- a/cmsearch.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/cmsearch.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,11 +1,12 @@ -<tool id="infernal_cmsearch" name="cmsearch" version="@VERSION@.0"> +<tool id="infernal_cmsearch" name="cmsearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Search covariance model(s) against a sequence database </description> <macros> <import>macros.xml</import> </macros> - <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism> + <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism--> <expand macro="requirements"/> <expand macro="stdio" /> + <expand macro="xrefs"/> <command> <![CDATA[ ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy @@ -24,10 +25,10 @@ $notrunc $anytrunc $nonull3 - #if $smxsize <> 128.0 + #if str($smxsize) != "128.0" --smxsize $smxsize #end if - #if $mxsize <> 128.0 + #if str($mxsize) != "128.0" --mxsize $mxsize #end if --tblout \$temp_tabular_output @@ -247,7 +248,6 @@ </conditional> <param name="seqdb" value="cmsearch_input2.fa"/> <output name="outfile" file="cmsearch_result.tabular"/> - </test> </tests>
--- a/cmstat.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/cmstat.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,10 +1,11 @@ -<tool id="infernal_cmstat" name="cmstat" version="@VERSION@.0"> +<tool id="infernal_cmstat" name="cmstat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Summary statistics for covariance model </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio" /> + <expand macro="xrefs"/> <command> <![CDATA[ ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
--- a/infernal.py Sat Nov 11 16:01:09 2017 -0500 +++ b/infernal.py Thu Sep 23 19:38:58 2021 +0000 @@ -1,76 +1,88 @@ # -*- coding: utf-8 -*- -from galaxy.datatypes.data import Text -from galaxy.datatypes.sniff import get_headers, get_test_fname -from galaxy.datatypes.data import get_file_peek +import logging +import os import subprocess -import os +from galaxy.datatypes.data import get_file_peek, Text from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes import metadata + -def count_special_lines( word, filename, invert = False ): +def count_special_lines(word, filename, invert=False): """ - searching for special 'words' using the grep tool - grep is used to speed up the searching and counting - The number of hits is returned. + searching for special 'words' using the grep tool + grep is used to speed up the searching and counting + The number of hits is returned. """ try: cmd = ["grep", "-c"] if invert: - cmd.append('-v') + cmd.append("-v") cmd.extend([word, filename]) out = subprocess.Popen(cmd, stdout=subprocess.PIPE) return int(out.communicate()[0].split()[0]) - except: + except Exception: pass return 0 -def count_lines( filename, non_empty = False): + +def count_lines(filename, non_empty=False): """ - counting the number of lines from the 'filename' file + counting the number of lines from the 'filename' file """ try: if non_empty: - out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE) + out = subprocess.Popen( + ["grep", "-cve", "^\s*$", filename], stdout=subprocess.PIPE # noqa W605 + ) else: - out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE) + out = subprocess.Popen(["wc", "-l", filename], stdout=subprocess.PIPE) return int(out.communicate()[0].split()[0]) - except: + except Exception: pass return 0 -class Infernal_CM_1_1( Text ): +class Infernal_CM_1_1(Text): file_ext = "cm" - MetadataElement( name="number_of_models", default=0, desc="Number of covariance models", readonly=True, visible=True, optional=True, no_value=0 ) + MetadataElement( + name="number_of_models", + default=0, + desc="Number of covariance models", + readonly=True, + visible=True, + optional=True, + no_value=0, + ) - def set_peek( self, dataset, is_multi_byte=False ): + def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: - dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - if (dataset.metadata.number_of_models == 1): + dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte) + if dataset.metadata.number_of_models == 1: dataset.blurb = "1 model" else: dataset.blurb = "%s models" % dataset.metadata.number_of_models - dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte) else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disc' + dataset.peek = "file does not exist" + dataset.blurb = "file purged from disc" - def sniff( self, filename ): + def sniff(self, filename): if count_special_lines("^INFERNAL1/a", filename) > 0: return True else: return False - def set_meta( self, dataset, **kwd ): + def set_meta(self, dataset, **kwd): """ Set the number of models in dataset. """ - dataset.metadata.number_of_models = count_special_lines("^INFERNAL1/a", dataset.file_name) + dataset.metadata.number_of_models = count_special_lines( + "^INFERNAL1/a", dataset.file_name + ) - def split( cls, input_datasets, subdir_generator_function, split_params): + def split(cls, input_datasets, subdir_generator_function, split_params): """ Split the input files by model records. """ @@ -82,14 +94,17 @@ input_files = [ds.file_name for ds in input_datasets] chunk_size = None - if split_params['split_mode'] == 'number_of_parts': - raise Exception('Split mode "%s" is currently not implemented for CM-files.' % split_params['split_mode']) - elif split_params['split_mode'] == 'to_size': - chunk_size = int(split_params['split_size']) + if split_params["split_mode"] == "number_of_parts": + raise Exception( + 'Split mode "%s" is currently not implemented for CM-files.' + % split_params["split_mode"] + ) + elif split_params["split_mode"] == "to_size": + chunk_size = int(split_params["split_size"]) else: - raise Exception('Unsupported split mode %s' % split_params['split_mode']) + raise Exception("Unsupported split mode %s" % split_params["split_mode"]) - def _read_cm_records( filename ): + def _read_cm_records(filename): lines = [] with open(filename) as handle: for line in handle: @@ -97,32 +112,33 @@ yield lines lines = [line] else: - lines.append( line ) + lines.append(line) yield lines - def _write_part_cm_file( accumulated_lines ): + def _write_part_cm_file(accumulated_lines): part_dir = subdir_generator_function() - part_path = os.path.join( part_dir, os.path.basename( input_files[0] ) ) - part_file = open( part_path, 'w' ) - part_file.writelines( accumulated_lines ) + part_path = os.path.join(part_dir, os.path.basename(input_files[0])) + part_file = open(part_path, "w") + part_file.writelines(accumulated_lines) part_file.close() try: - cm_records = _read_cm_records( input_files[0] ) + cm_records = _read_cm_records(input_files[0]) cm_lines_accumulated = [] - for counter, cm_record in enumerate( cm_records, start = 1): - cm_lines_accumulated.extend( cm_record ) + for counter, cm_record in enumerate(cm_records, start=1): + cm_lines_accumulated.extend(cm_record) if counter % chunk_size == 0: - _write_part_cm_file( cm_lines_accumulated ) + _write_part_cm_file(cm_lines_accumulated) cm_lines_accumulated = [] if cm_lines_accumulated: - _write_part_cm_file( cm_lines_accumulated ) - except Exception, e: - log.error('Unable to split files: %s' % str(e)) + _write_part_cm_file(cm_lines_accumulated) + except Exception as e: + logging.error("Unable to split files: %s" % str(e)) raise + split = classmethod(split) -if __name__ == '__main__': + +if __name__ == "__main__": Infernal_CM_1_1() - Stockholm_1_0() - + # Stockholm_1_0() # ???
--- a/macros.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/macros.xml Thu Sep 23 19:38:58 2021 +0000 @@ -2,11 +2,17 @@ <xml name="requirements"> <requirements> <requirement type="package">infernal</requirement> - <requirement type="package" version="1.1.2">infernal</requirement> - <requirement type="package" version="8.25">coreutils</requirement> + <requirement type="package" version="1.1.4">infernal</requirement> + <requirement type="package" version="8.32">coreutils</requirement> </requirements> </xml> - <token name="@VERSION@">1.1.2</token> + <token name="@TOOL_VERSION@">1.1.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">infernal</xref> + </xrefs> + </xml> <xml name="stdio"> <stdio> <exit_code range="1:" />
--- a/repository_dependencies.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/repository_dependencies.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories description="This requires the datatype definitions for Multiple Sequence Alignment (MSA) formats (e.g. STOCKHOLM, SELEX, ClustalW)."> - <repository changeset_revision="70227007b991" name="msa_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository name="msa_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="70227007b991"/> +</repositories> \ No newline at end of file
--- a/test-data/cmsearch_result.tabular Sat Nov 11 16:01:09 2017 -0500 +++ b/test-data/cmsearch_result.tabular Thu Sep 23 19:38:58 2021 +0000 @@ -1,56 +1,56 @@ -NC_013790.1 - tRNA5 - cm 1 72 362026 361955 - no 1 0.50 0.0 71.5 1.3e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2585265 2585193 - no 1 0.60 0.0 70.2 3.3e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 762490 762562 + no 1 0.67 0.0 68.8 9e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2041704 2041632 - no 1 0.67 0.0 68.8 9e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2351254 2351181 - no 1 0.62 0.0 67.4 2.5e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 735136 735208 + no 1 0.59 0.0 67.2 3e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2186013 2185941 - no 1 0.53 0.0 66.4 5.2e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2350593 2350520 - no 1 0.66 0.0 64.8 1.6e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2585187 2585114 - no 1 0.59 0.0 64.1 2.8e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 662185 662259 + no 1 0.61 0.0 62.5 9.1e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 360887 360815 - no 1 0.55 0.0 62.1 1.2e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2350984 2350911 - no 1 0.53 0.0 61.7 1.6e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2186090 2186019 - no 1 0.54 0.0 60.7 3.3e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2680159 2680233 + no 1 0.67 0.0 60.4 4.1e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2749945 2749874 - no 1 0.53 0.0 59.5 7.9e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2749839 2749768 - no 1 0.53 0.0 59.5 7.9e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361676 361604 - no 1 0.51 0.0 59.2 9.8e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2585073 2584999 - no 1 0.60 0.0 59.2 1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2130422 2130349 - no 1 0.59 0.0 59.1 1.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 546056 545947 - no 1 0.61 0.0 58.9 1.2e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361915 361844 - no 1 0.42 0.0 57.3 3.9e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 97724 97795 + no 1 0.49 0.0 57.0 5.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2350717 2350646 - no 1 0.68 0.0 56.7 6.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 1873887 1873815 - no 1 0.64 0.0 56.3 8e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 360730 360659 - no 1 0.40 0.0 55.6 1.4e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2680310 2680384 + no 1 0.52 0.0 54.3 3.5e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2664806 2664732 - no 1 0.60 0.0 54.3 3.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361061 360989 - no 1 0.41 0.0 54.3 3.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2130335 2130262 - no 1 0.55 0.0 53.3 7.5e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2151672 2151745 + no 1 0.65 0.0 53.3 7.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 319297 319370 + no 1 0.62 0.0 51.4 2.9e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361753 361679 - no 1 0.55 0.0 51.1 3.7e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 360983 360912 - no 1 0.50 0.0 51.1 3.8e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361456 361383 - no 1 0.50 0.0 50.5 5.9e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 362798 362727 - no 1 0.51 0.0 50.1 7.4e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 917722 917793 + no 1 0.61 0.0 49.9 8.7e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2583869 2583798 - no 1 0.51 0.0 49.7 1.1e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 362324 362252 - no 1 0.51 0.0 49.4 1.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 360811 360740 - no 1 0.42 0.0 49.3 1.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 1160526 1160609 + no 1 0.60 0.0 47.7 4.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 362403 362331 - no 1 0.49 0.0 46.6 9.8e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2327124 2327042 - no 1 0.63 0.0 46.5 1.1e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 995344 995263 - no 1 0.49 0.0 46.4 1.2e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 256772 256696 - no 1 0.57 0.0 45.5 2.3e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2584830 2584758 - no 1 0.64 0.0 45.3 2.5e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2351071 2350997 - no 1 0.59 0.0 44.1 6.1e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 362552 362482 - no 1 0.55 0.0 44.0 6.5e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 1064775 1064858 + no 1 0.63 0.0 41.2 5.2e-09 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361222 361150 - no 1 0.45 0.0 40.0 1.2e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361369 361297 - no 1 0.60 0.0 40.0 1.2e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 361596 361513 - no 1 0.61 0.0 38.1 4.8e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 1913310 1913227 - no 1 0.64 0.0 35.5 3.2e-07 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 363464 363381 - no 1 0.51 0.0 32.7 2.6e-06 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 2584954 2584872 - no 1 0.58 0.0 32.5 3e-06 ! Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 363803 363716 - no 1 0.50 0.0 20.0 0.027 ? Methanobrevibacter ruminantium M1 chromosome, complete genome -NC_013790.1 - tRNA5 - cm 1 72 984373 984304 - no 1 0.53 0.0 13.4 3.4 ? Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 362026 361955 - no 1 0.50 0.0 71.5 1.3e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2585265 2585193 - no 1 0.60 0.0 70.2 3.3e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 762490 762562 + no 1 0.67 0.0 68.8 9e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2041704 2041632 - no 1 0.67 0.0 68.8 9e-18 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2351254 2351181 - no 1 0.62 0.0 67.4 2.5e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 735136 735208 + no 1 0.59 0.0 67.2 3e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2186013 2185941 - no 1 0.53 0.0 66.4 5.2e-17 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2350593 2350520 - no 1 0.66 0.0 64.8 1.6e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2585187 2585114 - no 1 0.59 0.0 64.1 2.8e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 662185 662259 + no 1 0.61 0.0 62.5 9.1e-16 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 360887 360815 - no 1 0.55 0.0 62.1 1.2e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2350984 2350911 - no 1 0.53 0.0 61.7 1.6e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2186090 2186019 - no 1 0.54 0.0 60.7 3.3e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2680159 2680233 + no 1 0.67 0.0 60.4 4.1e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2749945 2749874 - no 1 0.53 0.0 59.5 7.9e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2749839 2749768 - no 1 0.53 0.0 59.5 7.9e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361676 361604 - no 1 0.51 0.0 59.2 9.8e-15 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2585073 2584999 - no 1 0.60 0.0 59.2 1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2130422 2130349 - no 1 0.59 0.0 59.1 1.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 546056 545947 - no 1 0.61 0.0 58.9 1.2e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361915 361844 - no 1 0.42 0.0 57.3 3.9e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 97724 97795 + no 1 0.49 0.0 57.0 5.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2350717 2350646 - no 1 0.68 0.0 56.7 6.1e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 1873887 1873815 - no 1 0.64 0.0 56.3 8e-14 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 360730 360659 - no 1 0.40 0.0 55.6 1.4e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2680310 2680384 + no 1 0.52 0.0 54.3 3.5e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2664806 2664732 - no 1 0.60 0.0 54.3 3.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361061 360989 - no 1 0.41 0.0 54.3 3.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2130335 2130262 - no 1 0.55 0.0 53.3 7.5e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2151672 2151745 + no 1 0.65 0.0 53.3 7.6e-13 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 319297 319370 + no 1 0.62 0.0 51.4 2.9e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361753 361679 - no 1 0.55 0.0 51.1 3.7e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 360983 360912 - no 1 0.50 0.0 51.1 3.8e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361456 361383 - no 1 0.50 0.0 50.5 5.9e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 362798 362727 - no 1 0.51 0.0 50.1 7.4e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 917722 917793 + no 1 0.61 0.0 49.9 8.7e-12 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2583869 2583798 - no 1 0.51 0.0 49.7 1.1e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 362324 362252 - no 1 0.51 0.0 49.4 1.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 360811 360740 - no 1 0.42 0.0 49.3 1.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 1160526 1160609 + no 1 0.60 0.0 47.7 4.3e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 362403 362331 - no 1 0.49 0.0 46.6 9.8e-11 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2327124 2327042 - no 1 0.63 0.0 46.5 1.1e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 995344 995263 - no 1 0.49 0.0 46.4 1.2e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 256772 256696 - no 1 0.57 0.0 45.5 2.3e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2584830 2584758 - no 1 0.64 0.0 45.3 2.5e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2351071 2350997 - no 1 0.59 0.0 44.1 6.1e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 362552 362482 - no 1 0.55 0.0 44.0 6.5e-10 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 1064775 1064858 + no 1 0.63 0.0 41.2 5.2e-09 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361222 361150 - no 1 0.45 0.0 40.0 1.2e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361369 361297 - no 1 0.60 0.0 40.0 1.2e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 361596 361513 - no 1 0.61 0.0 38.1 4.8e-08 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 1913310 1913227 - no 1 0.64 0.0 35.5 3.2e-07 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 363464 363381 - no 1 0.51 0.0 32.7 2.6e-06 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 2584954 2584872 - no 1 0.58 0.0 32.5 3e-06 ! Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 363803 363716 - no 1 0.50 0.0 20.0 0.027 ? Methanobrevibacter ruminantium M1 chromosome, complete genome +NC_013790.1 - tRNA5 - cm 1 72 984373 984304 - no 1 0.53 0.0 13.4 3.4 ? Methanobrevibacter ruminantium M1 chromosome, complete genome
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_cmscan.tabular Thu Sep 23 19:38:58 2021 +0000 @@ -0,0 +1,15 @@ +#target name accession query name accession mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc description of target +5S_rRNA RF00001 AAGA01015927.1 - cm 1 119 59 174 + no 1 0.66 0.0 77.3 3.3e-19 ! 5S ribosomal RNA +tRNA5 - AAGA01015927.1 - cm 1 72 229 302 + no 1 0.62 0.0 62.4 9.3e-19 ! - +tRNA5 - AAGA01015927.1 - cm 1 72 314 386 + no 1 0.59 0.0 53.5 6e-16 ! - +Cobalamin RF00174 AAFY01022046.1 - cm 32 191 934 832 - 5' 2 0.48 0.0 30.0 6.1e-09 ! Cobalamin riboswitch +# +# Program: cmscan +# Version: 1.1.4 (Dec 2020) +# Pipeline mode: SCAN +# Query file: /tmp/tmp6jwp47cs/files/a/6/f/dataset_a6fe922b-72aa-4753-b4dd-cd3c716a4ae5.dat +# Target file: cmdb.cm +# Option settings: cmscan -o /dev/null --tblout $temp_tabular_output --default --cpu 1 cmdb.cm /tmp/tmp6jwp47cs/files/a/6/f/dataset_a6fe922b-72aa-4753-b4dd-cd3c716a4ae5.dat +# Current dir: /tmp/tmp6jwp47cs/job_working_directory/000/13/working +# Date: Thu Sep 23 15:21:39 2021 +# [ok]