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Updating tools/varvamp from version 1.2.0 to 1.2.1 #6372

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Updating tools/varvamp from version 1.2.0 to 1.2.1 #6372

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b9b410a
Updating tools/varvamp from version 1.2.0 to 1.2.1
Sep 30, 2024
3be7e4a
update test data
bgruening Oct 18, 2024
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4 changes: 2 additions & 2 deletions tools/varvamp/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">1.2.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@TOOL_VERSION@">1.2.1</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="main_parameters">
<conditional name="main_params">
<param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
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2 changes: 1 addition & 1 deletion tools/varvamp/test-data/ambiguous_consensus.fasta
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@@ -1,2 +1,2 @@
>ambiguous_consensus
>varVAMP_consensus
tatcccgtrtycaractgayatccttattaayytgatgcaaccycgrcagcttgtkttccgrccygaagtyytstggaaycayccgatccagcgrgtyatacataatgagctggagcartactgccgwgcycgygctggycgytgyctkgargtkggsgcycayccaagatcyatyaatgayaacccyaatgtyytgcaccggtgcttyctycgcccggtyggdagagaygtmcagcgytggtaytcygccccsacycgyggyccagcggcyaaytgccgccgytcygcgctacgyggyytgccccctgtcgaycgyacmtaytgcttcgacgggttytcccgctgcgcytttgccgctgagacyggratygctttataytcactrcatgacctytggccytcggaygtygcggaggcya
24 changes: 24 additions & 0 deletions tools/varvamp/test-data/test1.log
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Expand Up @@ -33,3 +33,27 @@ PRIMER_MAX_BASE_PENALTY = 10
PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
PRIMER_PERMUTATION_PENALTY = 0.1

PROGRESS
Job: Checking config.
Result: config file passed
Job: Preprocessing alignment and cleaning gaps.
Result: 0 gaps with 0 nucleotides
Job: Creating consensus sequences.
Result: length of the consensus is 420 nt
Job: Finding primer regions.
Result: 92.6 % of the consensus sequence will be evaluated for primers
Job: Digesting into kmers.
Result: 1245 kmers
Job: Filtering for primers.
Result: 74 fw and 92 rv potential primers
Job: Considering primers with low penalties.
Result: 10 fw and 13 rv primers
Job: Finding potential amplicons.
Result: 17 potential amplicons
Job: Finding amplicons with low penalties.
Result: 1 amplicons.
Job: Finalizing output.
Result: all done

varVAMP 1.2.1 finished in 1.303803 sec!
2024-10-18 11:03:39.364906
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24 changes: 24 additions & 0 deletions tools/varvamp/test-data/test2.log
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Expand Up @@ -35,3 +35,27 @@ PRIMER_MAX_BASE_PENALTY = 10
PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
PRIMER_PERMUTATION_PENALTY = 0.1

PROGRESS
Job: Checking config.
Result: config file passed
Job: Preprocessing alignment and cleaning gaps.
Result: 0 gaps with 0 nucleotides
Job: Creating consensus sequences.
Result: length of the consensus is 420 nt
Job: Finding primer regions.
Result: 100.0 % of the consensus sequence will be evaluated for primers
Job: Digesting into kmers.
Result: 2783 kmers
Job: Filtering for primers.
Result: 265 fw and 310 rv potential primers
Job: Considering primers with low penalties.
Result: 24 fw and 21 rv primers
Job: Finding potential amplicons.
Result: 90 potential amplicons
Job: Creating amplicon scheme.
Result: 99.52 % total coverage with 2 amplicons
Job: Finalizing output.
Result: all done

varVAMP 1.2.1 finished in 2.13504 sec!
2024-10-18 11:04:18.175094
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25 changes: 25 additions & 0 deletions tools/varvamp/test-data/test3.log
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Expand Up @@ -39,7 +39,32 @@ QPROBE_GC_END = (0, 4)
QPRIMER_DIFF = 2
QPROBE_TEMP_DIFF = (5, 10)
QPROBE_DISTANCE = (4, 15)
END_OVERLAP = 5
QAMPLICON_LENGTH = (70, 200)
QAMPLICON_GC = (40, 60)
QAMPLICON_DEL_CUTOFF = 4

PROGRESS
Job: Checking config.
Result: config file passed
Job: Preprocessing alignment and cleaning gaps.
Result: 0 gaps with 0 nucleotides
Job: Creating consensus sequences.
Result: length of the consensus is 420 nt
Job: Finding primer regions.
Result: 71.0 % of the consensus sequence will be evaluated for primers
Job: Digesting into kmers.
Result: 1084 kmers
Job: Filtering for primers.
Result: 67 fw and 82 rv potential primers
Job: Finding qPCR probes.
Result: 100 potential qPCR probes
Job: Finding unique amplicons with probe.
Result: 3 unique amplicons with internal probe
Job: Filtering amplicons for deltaG.
Result: 1 non-overlapping qPCR schemes that passed deltaG cutoff
Job: Finalizing output.
Result: all done

varVAMP 1.2.1 finished in 4.028311 sec!
2024-10-18 11:05:01.961908
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24 changes: 24 additions & 0 deletions tools/varvamp/test-data/test4.log
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Expand Up @@ -33,3 +33,27 @@ PRIMER_MAX_BASE_PENALTY = 10
PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
PRIMER_PERMUTATION_PENALTY = 0.1

PROGRESS
Job: Checking config.
Result: config file passed
Job: Preprocessing alignment and cleaning gaps.
Result: 0 gaps with 0 nucleotides
Job: Creating consensus sequences.
Result: length of the consensus is 420 nt
Job: Finding primer regions.
Result: 92.6 % of the consensus sequence will be evaluated for primers
Job: Digesting into kmers.
Result: 1245 kmers
Job: Filtering for primers.
Result: 88 fw and 107 rv potential primers
Job: Considering primers with low penalties.
Result: 12 fw and 14 rv primers
Job: Finding potential amplicons.
Result: 21 potential amplicons
Job: Finding amplicons with low penalties.
Result: 1 amplicons.
Job: Finalizing output.
Result: all done

varVAMP 1.2.1 finished in 1.407113 sec!
2024-10-18 11:05:42.858771
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20 changes: 10 additions & 10 deletions tools/varvamp/varvamp.xml
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Expand Up @@ -8,7 +8,7 @@
</xrefs>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
<requirement type="package" version="2.0.1">primer3-py</requirement>
<requirement type="package" version="2.0.3">primer3-py</requirement>
<requirement type="package" version="0.7.17">seqfold</requirement>
</requirements>
<version_command>varvamp --version</version_command>
Expand Down Expand Up @@ -53,7 +53,7 @@ results/
#end if
#if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:
## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output
&& cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
&& cp --update=none dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
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this was a warning before

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sorry, what was the warning? Cannot find it.

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everything else looks easy enough to fix :-)

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That -n is deprecated and I should use the long version

#end if
]]></command>
<configfiles>
Expand Down Expand Up @@ -283,7 +283,7 @@ $line]]></configfile>
</output>
<output name="primers_bed" ftype="bed">
<assert_contents>
<has_n_lines n="2" />
<has_n_lines n="3" />
</assert_contents>
</output>
<output name="amplicons_bed" ftype="bed">
Expand All @@ -299,8 +299,8 @@ $line]]></configfile>
</output>
<output name="primer_seqs" ftype="fasta">
<assert_contents>
<has_line line=">AMPLICON_0_LEFT"/>
<has_line line=">AMPLICON_0_RIGHT"/>
<has_line line=">varVAMP_0_LEFT"/>
<has_line line=">varVAMP_0_RIGHT"/>
<has_n_lines n="4"/>
</assert_contents>
</output>
Expand All @@ -321,7 +321,7 @@ $line]]></configfile>
<output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" />
<output name="primers_bed" ftype="bed">
<assert_contents>
<has_n_lines n="4" />
<has_n_lines n="5" />
</assert_contents>
</output>
<output name="amplicons_bed" ftype="bed">
Expand Down Expand Up @@ -371,7 +371,7 @@ $line]]></configfile>
<output name="varvamp_log" ftype="txt" compare="contains" file="test3.log" />
<output name="primers_bed" ftype="bed">
<assert_contents>
<has_n_lines n="3" />
<has_n_lines n="4" />
</assert_contents>
</output>
<output name="amplicons_bed" ftype="bed">
Expand All @@ -381,9 +381,9 @@ $line]]></configfile>
</output>
<output name="primer_seqs" ftype="fasta">
<assert_contents>
<has_line line=">QPCR_SCHEME_0_PROBE"/>
<has_line line=">QPCR_SCHEME_0_LEFT"/>
<has_line line=">QPCR_SCHEME_0_RIGHT"/>
<has_line line=">varVAMP_0_PROBE"/>
<has_line line=">varVAMP_0_LEFT"/>
<has_line line=">varVAMP_0_RIGHT"/>
<has_n_lines n="6"/>
</assert_contents>
</output>
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