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TsvSlice: added parameter 'rm'
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@marc-sturm
marc-sturm committed Jan 14, 2025
1 parent 7462907 commit d4535bf
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Showing 3 changed files with 125 additions and 2 deletions.
12 changes: 12 additions & 0 deletions src/TsvSlice/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ class ConcreteTool
addInfile("in", "Input TSV file. If unset, reads from STDIN.", true);
addOutfile("out", "Output file. If unset, writes to STDOUT.", true);
addFlag("numeric", "If set, column names are interpreted as 1-based column numbers.");
addFlag("rm", "If set, the columns given in 'cols' are removed instead of extracted.");
}

virtual void main()
Expand All @@ -40,6 +41,17 @@ class ConcreteTool
//check columns
QVector<int> cols = instream.checkColumns(getString("cols").toUtf8().split(','), getFlag("numeric"));

//remove instead of extract > invert column selection
if (getFlag("rm"))
{
QSet<int> old = cols.toList().toSet();
cols.clear();
for (int c=0; c<instream.columns(); ++c)
{
if (!old.contains(c)) cols << c;
}
}

//write comments
foreach (QByteArray comment, instream.comments())
{
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11 changes: 9 additions & 2 deletions src/tools-TEST/TsvSlice_Test.h
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Original file line number Diff line number Diff line change
Expand Up @@ -6,18 +6,25 @@ Q_OBJECT
private slots:

//test with column names
void test_01()
void test_column_names()
{
EXECUTE("TsvSlice", "-cols chr,start,end,ref,obs,snp_q,variant_frequency,sample -in " + TESTDATA("data_in/TsvSlice_in1.tsv") + " -out out/TsvSlice_out1.tsv");
COMPARE_FILES("out/TsvSlice_out1.tsv", TESTDATA("data_out/TsvSlice_out1.tsv"));
}

//test with column numbers
void test_02()
void test_column_number()
{
EXECUTE("TsvSlice", "-numeric -cols 1,2,3,4,5,7,11,22 -in " + TESTDATA("data_in/TsvSlice_in1.tsv") + " -out out/TsvSlice_out1.tsv");
COMPARE_FILES("out/TsvSlice_out1.tsv", TESTDATA("data_out/TsvSlice_out1.tsv"));
}

//test for rm parameter
void test_rm()
{
EXECUTE("TsvSlice", "-rm -cols snp_q,variant_frequency -in " + TESTDATA("data_in/TsvSlice_in1.tsv") + " -out out/TsvSlice_out2.tsv");
COMPARE_FILES("out/TsvSlice_out2.tsv", TESTDATA("data_out/TsvSlice_out2.tsv"));
}
};


104 changes: 104 additions & 0 deletions src/tools-TEST/data_out/TsvSlice_out2.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
##bli
##bla
##bluff
#chr start end ref obs genotype depth map_q variant region gene variant_details coding snp_1000g2011may_all snp_snp132 phylop repeatmasker omim_ids quality_filter sample
chr5 33733959 33733959 A G hom 20 15 SNV intronic ADAMTS12 . . . . . 417 606184 passed GS120297G5_annotated.tsv
chr15 29524330 29524330 G A hom 12 10 SNV intronic FAM189A1 . . . . . 2476 passed GS120297C11_annotated.tsv
chr16 25560026 25560026 T G hom 10 21 SNV intergenic ZKSCAN2(dist=291171),HS3ST4(dist=143321) . . . . . 2211 passed GS120297C11_annotated.tsv
chr11 92335303 92335303 A G hom 82 21 SNV intronic FAT3 . . . . . 2179 612483 passed GS120297C11_annotated.tsv
chr3 60459604 60459604 T C hom 26 21 SNV intronic FHIT . . . . . 2166 601153 passed GS120297C11_annotated.tsv
chr11 43532248 43532248 C T hom 14 15 SNV intergenic TTC17(dist=15765),MIR670(dist=48958) . . . . . 2211 passed GS120297C11_annotated.tsv
chr9 132586914 132586914 - TAA het 33 46 INDEL upstream TOR1A . . . . . 261 passed GS120297E7_annotated.tsv
chr20 3249206 3249206 T C hom 38 13 SNV intronic C20orf194 . . . . . 2259 614146 passed GS120297C11_annotated.tsv
chr19 42488503 42488503 G A hom 8 28 SNV intronic ATP1A3 . . . . . 2117 182350 failed GS120297C11_annotated.tsv
chr4 127567790 127567790 T C hom 64 34 SNV intergenic MIR2054(dist=1139328),INTU(dist=986297) . . . . . 2703 passed GS120297C11_annotated.tsv
chr9 130941236 130941236 C A het 2710 46 SNV exonic CIZ1 nonsynonymous SNV CIZ1:NM_012127:exon8:c.G1250T:p.R417M,CIZ1:NM_001131016:exon8:c.G1250T:p.R417M, . . -1.12 . passed GS120297B6_annotated.tsv
chr1 242168219 242168219 C T hom 4 10 SNV intergenic MAP1LC3C(dist=5834),PLD5(dist=83470) . . 0.0016 . . 889 failed GS120297C11_annotated.tsv
chr18 20795787 20795787 G C hom 16 32 SNV intronic CABLES1 . . . . . 2491 passed GS120297C11_annotated.tsv
chr9 132322378 132322378 T C hom 21 13 SNV intergenic LOC100506190(dist=46413),C9orf50(dist=52126) . . . . . 2095 passed GS120297C11_annotated.tsv
chr15 64322763 64322763 A C hom 11 19 SNV intronic DAPK2 . . . . . . failed GS120298D7_annotated.tsv
chr19 46947768 46947768 C T hom 13 11 SNV intergenic CCDC8(dist=30849),PNMAL1(dist=21980) . . . . . 1758 failed GS120297C11_annotated.tsv
chr2 10350931 10350931 C T het 15 41 SNV UTR3 C2orf48 . . . . . 1573 passed GS120297G10_annotated.tsv
chr1 176877345 176877345 - CTCC hom 58 48 INDEL intronic ASTN1 . . . . . . 600904 passed GS120297E3_annotated.tsv
chr3 86925756 86925756 - T hom 3 45 INDEL intergenic CADM2(dist=802177),VGLL3(dist=61367) . . . . . 22004 failed GS120297A6_annotated.tsv
chr13 70338821 70338821 A C het 11 57 SNV intronic KLHL1 . . . . . 546 605332 passed GS120297E3_annotated.tsv
chr5 95802169 95802169 C T hom 9 41 SNV intergenic PCSK1(dist=33184),CAST(dist=195572) . . 0.13569 rs79360888 . 4019 failed GS120298G2_annotated.tsv
chr11 132616377 132616377 - AACCACAACTG hom 4 45 INDEL intronic OPCML . . . . . 228 600632 failed GS120297A8_annotated.tsv
chr7 101783192 101783193 TC - hom 4 31 INDEL intronic CUX1 . . . . . 1571 failed GS120297F1_annotated.tsv
chr9 130941121 130941121 T C het 2083 46 SNV exonic CIZ1 synonymous SNV CIZ1:NM_012127:exon8:c.A1365G:p.V455V,CIZ1:NM_001131017:exon9:c.A1182G:p.V394V,CIZ1:NM_001131015:exon9:c.A1197G:p.V399V,CIZ1:NM_001131018:exon8:c.A1125G:p.V375V,CIZ1:NM_001131016:exon8:c.A1365G:p.V455V, 0.0131 rs11549263 . . passed GS120298F5_annotated.tsv
chr11 25824572 25824572 C T hom 4 35 SNV intergenic LUZP2(dist=720386),ANO3(dist=529106) . . . . . 2297 failed GS120297C11_annotated.tsv
chr12 54014430 54014430 C T hom 6 15 SNV intronic ATF7 . . . . . 2100 606371 failed GS120297C11_annotated.tsv
chr12 16079575 16079575 C A het 31 27 SNV intronic DERA . . . . . 2747 failed GS120297C11_annotated.tsv
chr5 133414489 133414489 C A hom 12 13 SNV intergenic VDAC1(dist=73665),TCF7(dist=35913) . . . . . 2345 passed GS120297C11_annotated.tsv
chr12 16079541 16079541 G A het 86 26 SNV intronic DERA . . . . . 2747 passed GS120297C11_annotated.tsv
chr8 142743147 142743147 - GTGACTGCA hom 8 60 INDEL intergenic FLJ43860(dist=225817),MIR4472-1(dist=514553) . . . . . . failed GS120298C6_annotated.tsv
chr4 39430486 39430486 A C hom 7 15 SNV intronic KLB . . . . . 2240 611135 failed GS120297C11_annotated.tsv
chr2 236036140 236036140 A G hom 68 24 SNV intergenic SH3BP4(dist=71782),AGAP1(dist=366593) . . . . . 1625 passed GS120297C11_annotated.tsv
chr6 123526336 123526336 T A hom 23 16 SNV intergenic CLVS2(dist=141273),TRDN(dist=11148) . . . . . 2199 passed GS120297C11_annotated.tsv
chr17 72196887 72196887 G C hom 77 40 SNV intergenic LINC00469(dist=372211),RPL38(dist=2908) . . . . . . passed GS120297A1_annotated.tsv
chr7 14790577 14790577 C G hom 205 25 SNV intronic DGKB . . . . . 2132 604070 failed GS120297C11_annotated.tsv
chr11 123091586 123091586 C T hom 4 32 SNV intergenic CLMP(dist=25579),MIR4493(dist=160562) . . . . . 2511 failed GS120297C11_annotated.tsv
chr17 21824661 21824661 G A hom 19 38 SNV upstream FAM27L . . . . . . passed GS120297B8_annotated.tsv
chr17 19378197 19378197 T G hom 8 15 SNV intergenic RNF112(dist=57608),SLC47A1(dist=58970) . . . . . 2526 failed GS120297C11_annotated.tsv
chr11 66160118 66160118 T C hom 14 21 SNV intergenic SLC29A2(dist=20827),NPAS4(dist=28357) . . . . . 2304 passed GS120297C11_annotated.tsv
chr19 46747638 46747638 G A hom 8 24 SNV intergenic IGFL1(dist=13138),HIF3A(dist=52665) . . . . . 862 failed GS120297C11_annotated.tsv
chr11 73301940 73301940 C G het 38 18 SNV intronic FAM168A . . . . . 2140 passed GS120297C11_annotated.tsv
chr5 33733959 33733959 A G hom 4 15 SNV intronic ADAMTS12 . . . . . 417 606184 failed GS120297G8_annotated.tsv
chr7 148279290 148279290 T G hom 36 31 SNV intergenic CNTNAP2(dist=161202),C7orf33(dist=8367) . . . . . 2227 failed GS120297C11_annotated.tsv
chr12 55389177 55389177 C T hom 4 14 SNV intergenic KIAA0748(dist=10721),NEUROD4(dist=24552) . . . . . 2425 failed GS120297C11_annotated.tsv
chr6 148903981 148903981 G A hom 6 34 SNV intergenic SASH1(dist=30797),UST(dist=164290) . . . . . 2394 failed GS120297C11_annotated.tsv
chr9 87105100 87105100 A G het 6 27 SNV intergenic SLC28A3(dist=121687),NTRK2(dist=178366) . . . . . 2239 failed GS120297C11_annotated.tsv
chr4 110369857 110369857 G A hom 65 26 SNV intronic SEC24B . . . . . 1632 passed GS120297C11_annotated.tsv
chr15 99937578 99937578 T A hom 8 24 SNV intergenic LRRC28(dist=11080),MEF2A(dist=168555) . . . . . 1907 failed GS120297C11_annotated.tsv
chr15 55938654 55938654 A G hom 23 20 SNV intronic PRTG . . 0.0190 rs62017991 . 2557 613261 passed GS120297C11_annotated.tsv
chr9 71730178 71730178 C T hom 43 25 SNV intergenic FXN(dist=15084),TJP2(dist=6002) . . . . . 2501 passed GS120297C11_annotated.tsv
chr9 101750954 101750954 C T hom 5 20 SNV intronic COL15A1 . . . . . 2339 120325 failed GS120297C11_annotated.tsv
chr3 99969008 99969008 T C hom 4 20 SNV intergenic TMEM30C(dist=55978),TBC1D23(dist=10678) . . . . . 2325 failed GS120297C11_annotated.tsv
chr9 130932398 130932399 CA - het 1918 49 INDEL intronic CIZ1 . . . rs59232258 . . passed GS120297F8_annotated.tsv
chr2 133012716 133012716 A G hom 14 23 SNV ncRNA_intronic ANKRD30BL . . . rs5002053 . 14662 passed GS120297C11_annotated.tsv
chr19 35597152 35597152 G C hom 6 10 SNV ncRNA_exonic LOC100128675 . . . . . . failed GS120298E8_annotated.tsv
chr6 13651789 13651789 G A hom 8 12 SNV intronic RANBP9 . . . . . 2544 603854 failed GS120297C11_annotated.tsv
chrY 8979472 8979472 T G hom 20 28 SNV intergenic TTTY11(dist=294049),RBMY1A3P(dist=175198) . . . . . 846 failed GS120297G10_annotated.tsv
chr5 79947134 79947134 T C hom 156 27 SNV intronic DHFR . . . . . . 126060 failed GS120297G10_annotated.tsv
chr5 95228102 95228102 T C hom 4 15 SNV intronic ELL2 . . . . . 2375 601874 failed GS120297C11_annotated.tsv
chr8 71382092 71382092 T C hom 5 15 SNV intergenic NCOA2(dist=66072),TRAM1(dist=103361) . . . . . 2376 failed GS120297C11_annotated.tsv
chr3 49401748 49401748 G A hom 4 13 SNV intronic RHOA . . . . . 2342 failed GS120297C11_annotated.tsv
chr8 124974386 124974386 T C hom 3 27 SNV intronic FER1L6 . . . . . 2238 failed GS120297C11_annotated.tsv
chrX 96694399 96694399 A T hom 6 23 SNV intronic DIAPH2 . . . . . 2529 300108 failed GS120297C11_annotated.tsv
chr17 55548777 55548777 G A hom 3 28 SNV intronic MSI2 . . . . . 1790 failed GS120297C11_annotated.tsv
chr10 72584846 72584846 A T het 12 20 SNV intronic SGPL1 . . . . . 1221 603729 failed GS120297C11_annotated.tsv
chr19 13571311 13571311 C A hom 5 45 SNV intronic CACNA1A . . 0.4436 rs10422148 . . 601011 failed GS120297C11_annotated.tsv
chr14 20444588 20444588 T C het 6118 40 SNV exonic OR4K15 nonsynonymous SNV OR4K15:NM_001005486:exon1:c.T911C:p.L304P, 0.5184 rs2153466 1.03 . passed GS120297C11_annotated.tsv
chr1 182178672 182178672 T G hom 14 37 SNV intergenic ZNF648(dist=147825),GLUL(dist=172167) . . . . . . passed GS120297E2_annotated.tsv
chr15 41670820 41670820 T C hom 33 24 SNV intronic NUSAP1 . . . . . 2104 612818 passed GS120297C11_annotated.tsv
chr5 99382244 99382244 G A hom 1055 39 SNV intergenic LOC100289230(dist=1115531),LOC100133050(dist=332965) . . 0.0084 rs77299228 . . passed GS120297G10_annotated.tsv
chrX 96694445 96694445 G A hom 11 22 SNV intronic DIAPH2 . . . . . 2529 300108 passed GS120297C11_annotated.tsv
chr17 72196892 72196892 - GTC hom 41 45 INDEL intergenic LINC00469(dist=372216),RPL38(dist=2903) . . . . . . failed GS120297A4_annotated.tsv
chr11 14144010 14144010 T C hom 14 18 SNV intronic SPON1 . . . . . 2447 604989 passed GS120297C11_annotated.tsv
chr2 123976454 123976454 C T het 9 46 SNV intergenic TSN(dist=1451026),CNTNAP5(dist=806410) . . . . . 17496 failed GS120297F3_annotated.tsv
chr19 14466501 14466501 - GTCAAAGTTC het 77 49 INDEL intergenic LPHN1(dist=149504),CD97(dist=25455) . . . . . 1521 passed GS120297B5_annotated.tsv
chr1 157696563 157696563 C T hom 6 21 SNV intergenic FCRL3(dist=25916),FCRL2(dist=18960) . . . . . 1900 failed GS120297C11_annotated.tsv
chr3 52596133 52596133 T C hom 5 18 SNV intronic PBRM1 . . . . . 2486 606083 failed GS120297C11_annotated.tsv
chr14 59921750 59921750 G A het 17 21 SNV intergenic DAAM1(dist=85279),GPR135(dist=8490) . . . . . 2460 failed GS120297C11_annotated.tsv
chrX 153580214 153580214 G T hom 502 44 SNV intronic FLNA . . . . . . 300017 passed GS120297G10_annotated.tsv
chr17 72196817 72196817 - A hom 118 39 INDEL intergenic LINC00469(dist=372141),RPL38(dist=2978) . . . . . . passed GS120298E8_annotated.tsv
chr19 12541229 12541229 T A hom 215 30 SNV exonic ZNF443 nonsynonymous SNV ZNF443:NM_005815:exon4:c.A1757T:p.K586I, . . -0.43 . passed GS120297G10_annotated.tsv
chr1 120270301 120270301 A C hom 12 13 SNV intronic PHGDH . . . . . 2461 606879 failed GS120297C11_annotated.tsv
chr17 29754040 29754040 A C hom 19 29 SNV intronic RAB11FIP4 . . . . . 2306 611999 passed GS120297C11_annotated.tsv
chr4 114612679 114612679 T C hom 4 18 SNV intronic CAMK2D . . . . . 2220 607708 failed GS120297C11_annotated.tsv
chr2 27435800 27435800 G T het 924 47 SNV intronic C2orf28 . . . . . . passed GS120297G10_annotated.tsv
chr5 33733959 33733959 A G hom 4 15 SNV intronic ADAMTS12 . . . . . 417 606184 failed GS120297D10_annotated.tsv
chr12 77084097 77084097 G A hom 65 31 SNV intergenic OSBPL8(dist=130508),ZDHHC17(dist=73757) . . . . . 2130 passed GS120297C11_annotated.tsv
chr2 96888657 96888657 - GCCTTGTA hom 16 42 INDEL intergenic STARD7(dist=14084),LOC285033(dist=17320) . . . . . 3558 passed GS120297G12_annotated.tsv
chr6 14890845 14890845 A C hom 9 10 SNV intergenic CD83(dist=753697),JARID2(dist=355682) . . . . . 2040 failed GS120297C11_annotated.tsv
chr21 40456589 40456589 C T hom 45 40 SNV intergenic ETS2(dist=259711),PSMG1(dist=90795) . . . . . 2466 passed GS120297C11_annotated.tsv
chr10 76604746 76604746 G A hom 8 24 SNV intronic KAT6B . . . . . 1912 605880 failed GS120297C11_annotated.tsv
chr7 151234386 151234386 C T hom 19 19 SNV intergenic RHEB(dist=17376),PRKAG2(dist=18815) . . . . . 1839 passed GS120297C11_annotated.tsv
chr2 233152351 233152351 T C hom 6 53 SNV intronic DIS3L2 . . . . . 1689 614184 failed GS120297H12_annotated.tsv
chr15 48512198 48512198 C T hom 17 22 SNV intronic SLC12A1 . . . . . 1907 600839 passed GS120297C11_annotated.tsv
chr2 233152135 233152135 - ACCCCTT hom 4 47 INDEL intronic DIS3L2 . . . . . 1689 614184 failed GS120297E7_annotated.tsv
chr17 27258725 27258725 G T hom 4 31 SNV intronic PHF12 . . . . . 2283 failed GS120297C11_annotated.tsv
chr20 47953366 47953366 T A hom 53 14 SNV intergenic ZNFX1-AS1(dist=47571),KCNB1(dist=35139) . . . . . 2107 passed GS120297C11_annotated.tsv
chr3 180390245 180390245 - TCCTCAA hom 4 32 INDEL intronic CCDC39 . . . . . 2111 613798 failed GS120297E2_annotated.tsv
chr1 176877440 176877440 C T hom 37 38 SNV intronic ASTN1 . . . . . . 600904 passed GS120298E5_annotated.tsv
chr13 114579076 114579076 G T hom 8 10 SNV intergenic LOC100506394(dist=9271),FLJ44054(dist=7534) . . . rs72670634 . . failed GS120297A8_annotated.tsv

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