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Changeset 7:d6a7be1b5adb (2018-02-07)

Previous changeset 6:da372a164001 (2018-02-07) Next changeset 8:f733bf4f49ca (2018-04-16)

Commit message:
Uploaded

modified:
Plink.pl
find_indiv.py
plink.xml

added:
test-data/input.vcf
test-data/input_double_id.vcf
test-data/output.vcf
test-data/output_double_id.vcf

diff -r da372a164001 -r d6a7be1b5adb Plink.pl
--- a/Plink.pl Wed Feb 07 00:15:42 2018 -0500
+++ b/Plink.pl Wed Feb 07 00:16:59 2018 -0500

@@ -225,7 +225,7 @@
if (-e "$bed_input.bed"){
system("$PLINK_EXE --bfile $bed_input --out $out $type_cmd $export_cmd $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr 1>$out.plink.stdout 2>$out.plink.stderr");
# for first 1000 SNPs
- system("$PLINK_EXE --bfile $bed_input --out $out.recode $type_cmd --recode vcf-fid $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr --thin-count 800 1>$out.2.plink.stdout 2>$out.2.plink.stderr");
+ system("$PLINK_EXE $bed_input --out $out.recode $type_cmd --recode vcf-fid $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr --thin-count 800 1>$out.2.plink.stdout 2>$out.2.plink.stderr");
}
elsif (-e $bcf_input){
system("$PLINK_EXE --bcf $bcf_input --out $out $type_cmd $export_cmd $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr 1>$out.plink.stdout 2>$out.plink.stderr");

diff -r da372a164001 -r d6a7be1b5adb plink.xml
--- a/plink.xml Wed Feb 07 00:15:42 2018 -0500
+++ b/plink.xml Wed Feb 07 00:16:59 2018 -0500

[

@@ -6,9 +6,11 @@
     
     <requirements>
         <requirement type="binary">perl</requirement>
+        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
<requirement type="package" version="1.90b4">plink</requirement>
     </requirements>

+    <code file="find_indiv.py"/>

     
     <stdio>
@@ -30,7 +32,6 @@
$chromosomes
#end if
     </command>
-    <code file="find_indiv.py"/>
     
     <inputs>
<param name="vcf" type="data" format="vcf" optional="false" label="VCF input" />
@@ -56,6 +57,20 @@
<data name="filelog" format="txt" label="Plink logfile" />
     </outputs>

+    <tests>
+        <test>
+            <param name="vcf" value="input.vcf"/>
+            <param name="samples" value="AZUCENA,BULUPANDAK,GIZA171,IAC165,KHAODAM,M202,MOROBEREKAN,NIPPONBARE.D,62667,63-104,ARAGUAIA,ARIAS,ARROZCEBADA,BABER,BAGANANASALAO,BAKUNGH,BENGALYVAKARINA,BICOBRANCO,BINULAWAN,CAIAPO,CANAROXA,CANELADEFERRO,CHALOYOE,CHAPHUMA,CICIHBETON,CIRAD358,CIRAD392,CIRAD394,CIRAD403,CIRAD409,CIRAD488,CNA-7.BO.1.1.33-13-6-1,COLOMBIA1,CT13582-15-5-M,CUBA65,CUIABANA,CURINCA,DAM,DANGREY,DAVAO,DAWASANRED,DINORADO,DOURADOAGULHA,DOURADOPRECOCE,ESPERANZA,FOHISOMOTRA,GANIGI,GEMJYAJYANAM,GOGO,GOGOLEMPUK,GOGOLEMPAK,GOMPA2,GRAZI,GUARANI,GUNDILKUNING,HAWMOM,HD1-4,IAC25,IAC47,IDSA77,IGUAPECATETO,INDANE,IR60080-46A,IR63380-16,IR63372-08,IR65907-188-1-B,IR66421-096-2-1-1,IR68704-145-1-1-B,IR71525-19-1-1,IRAT104,IRAT109,IRAT112,IRAT13,IRAT144,IRAT170,IRAT177,IRAT2,IRAT212,IRAT216,IRAT234,IRAT257,IRAT335,IRAT362,IRAT364,IRAT366,IRAT380,JAOHAW,JIMBRUKJOLOWORO,JUMALI,JUMULA2,KAKANI2,KANIRANGA,KARASUKARASURANKASU,KEDAYAN,KENDINGA5H,KETANKONIR,KETANLUMBU,KETANMENAH,KHAOKAPXANG,KINANDANGPATONG,KOMOJAMANITRA,KU115,KUROKA,LAMBAYQUE1,LUDAN,MAHAE,MAINTIMOLOTSY1226,MALAGKITPIRURUTONG,MANANELATRA520,MANDRIRAVINA3512,MARAVILHA,MITSANGANAHIJERY,MOLOK,NABESHI,NEPHOAVANG,NHTA10,NHTA5,NPE253,NPE826,ORYZICASABANA6,OS4,OS6,P5589-1-1-3-P,PACHOLINHA,PADIBOENAR,PADIKASALLE,PALAWAN,PATEBLANCMAN1,PCT11.0.0.2.BO.1.55-1-3-1,PCT4.SA.4.1.1076-2-4-1-5,PEHPINUO,POENOETHITAM,PULULAPA,RATHAL,REKETMAUN,RT1031-69,SENG,SPEAKER,TANDUI,TREMBESE,TRESMESES,TSIPALA89,VARYLAVA90,VARYLAVADEBETAFO,VARYMADINIKA3566,VARYMALADY,VARYSOMOTRASIHANAKA,WAB56-125,WAB56-50,WAB706-3-4-K4-KB-1,YANCAOUSSA,YANGKUMRED,YUNLU7,IR47686-09-01-B-1,IR53236-275-1,IR65261-19-1-B,IR65907-206-4-B,IR66421-105-1-1,IR71524-44-1-1,VIETNAM1,VIETNAM3,IR47684-05-1-B,PRIMAVERA,CHUAN3,CHUAN4,EARLYMUTANTIAC165"/>
+            <param name="frequency" value="0"/>
+            <param name="max_freq" value="0.5"/>
+            <param name="allow_missing" value="1"/>
+            <param name="type_p" value="ALL"/>
+            <param name="chromosomes" value=""/>
+            <param name="bound_start" value="1"/>
+            <param name="bound_end" value="100000000"/>
+            <output name="fileout" file="output.vcf" compare="diff" lines_diff="2"/>
+        </test>
+    </tests>

     
     <help>

diff -r da372a164001 -r d6a7be1b5adb test-data/input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.vcf Wed Feb 07 00:16:59 2018 -0500

[

b'@@ -0,0 +1,6788 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=PQ,Number=1,Type=Float,Description="Read-backed phasing quality">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">\n+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">\n+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">\n+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher\'s exact test to detect strand bias">\n+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">\n+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">\n+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">\n+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">\n+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">\n+##INFO=<ID=PhasingInconsistent,Number=0,Type=Flag,Description="Are the reads significantly haplotype-inconsistent?">\n+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">\n+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">\n+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">\n+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">\n+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">\n+##ReadBackedPhasing="analysis_type=ReadBackedPhasing input_file=[/scratch/hueber-29030/merged_bams_file.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/coffea_cds.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 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diff -r da372a164001 -r d6a7be1b5adb test-data/input_double_id.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_double_id.vcf Wed Feb 07 00:16:59 2018 -0500

[

b'@@ -0,0 +1,16491 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=PQ,Number=1,Type=Float,Description="Read-backed phasing quality">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">\n+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">\n+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">\n+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher\'s exact test to detect strand bias">\n+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">\n+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">\n+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">\n+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">\n+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">\n+##INFO=<ID=PhasingInconsistent,Number=0,Type=Flag,Description="Are the reads significantly haplotype-inconsistent?">\n+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">\n+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">\n+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">\n+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">\n+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">\n+##ReadBackedPhasing="analysis_type=ReadBackedPhasing input_file=[/scratch/hueber-29030/merged_bams_file.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/coffea_cds.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 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diff -r da372a164001 -r d6a7be1b5adb test-data/output.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.vcf Wed Feb 07 00:16:59 2018 -0500

b'@@ -0,0 +1,6764 @@\n+##fileformat=VCFv4.2\n+##fileDate=\n+##source=PLINKv1.90\n+##contig=<ID=1,length=43269459>\n+##contig=<ID=2,length=35890590>\n+##contig=<ID=3,length=36396458>\n+##contig=<ID=4,length=35497660>\n+##contig=<ID=5,length=5476492>\n+##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference 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diff -r da372a164001 -r d6a7be1b5adb test-data/output_double_id.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_double_id.vcf Wed Feb 07 00:16:59 2018 -0500

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