add testing for bean-create-samples

tests/data/var_mini_counts.csv

@@ -0,0 +1,31 @@
+name,rep5_top,rep5_high,rep5_bulk,rep5_low,rep5_bot,rep6_top,rep6_high,rep6_bulk,rep6_low,rep6_bot
+CONTROL_8_g1,368.0,245.0,302.0,798.0,84.0,342.0,1088.0,910.0,670.0,462.0
+CONTROL_8_g2,63.0,54.0,201.0,418.0,20.0,31.0,314.0,100.0,46.0,51.0
+CONTROL_8_g3,253.0,61.0,238.0,221.0,8.0,460.0,1295.0,786.0,1188.0,1019.0
+CONTROL_8_g4,236.0,133.0,324.0,425.0,35.0,338.0,953.0,429.0,864.0,406.0
+CONTROL_8_g5,69.0,55.0,56.0,267.0,16.0,129.0,777.0,140.0,253.0,204.0
+CONTROL_9_g1,259.0,177.0,170.0,514.0,38.0,84.0,234.0,148.0,103.0,79.0
+CONTROL_9_g2,335.0,164.0,225.0,516.0,37.0,654.0,2132.0,1079.0,1188.0,657.0
+CONTROL_9_g3,14.0,57.0,48.0,111.0,20.0,218.0,265.0,228.0,195.0,152.0
+CONTROL_9_g4,302.0,129.0,158.0,423.0,27.0,517.0,1258.0,362.0,935.0,605.0
+CONTROL_9_g5,124.0,67.0,156.0,320.0,21.0,152.0,605.0,321.0,428.0,226.0
+ACAT2_SA_44_g1,558.0,344.0,374.0,1366.0,105.0,512.0,1091.0,570.0,774.0,489.0
+ACAT2_SA_44_g2,1151.0,304.0,867.0,1224.0,144.0,953.0,2993.0,2069.0,1454.0,1038.0
+ACAT2_SA_44_g3,516.0,211.0,535.0,663.0,80.0,976.0,2389.0,1485.0,2520.0,1160.0
+ACAT2_SA_44_g4,432.0,90.0,352.0,459.0,69.0,392.0,1629.0,850.0,1203.0,658.0
+ACAT2_SA_44_g5,602.0,277.0,570.0,637.0,42.0,1024.0,2968.0,1547.0,1020.0,999.0
+ACAT2_SA_45_g1,353.0,146.0,262.0,508.0,54.0,345.0,1355.0,582.0,566.0,399.0
+ACAT2_SA_45_g2,389.0,139.0,280.0,369.0,66.0,446.0,848.0,458.0,584.0,498.0
+ACAT2_SA_45_g3,618.0,240.0,510.0,992.0,60.0,608.0,2514.0,920.0,882.0,773.0
+ACAT2_SA_45_g4,775.0,253.0,559.0,889.0,93.0,860.0,1810.0,991.0,978.0,673.0
+ACAT2_SA_45_g5,1046.0,471.0,830.0,1472.0,164.0,995.0,1966.0,1123.0,1394.0,1192.0
+ACAT2_SA_46_g1,735.0,266.0,496.0,975.0,89.0,2261.0,5981.0,4085.0,5552.0,2804.0
+ACAT2_SA_46_g2,825.0,201.0,444.0,835.0,67.0,394.0,1098.0,731.0,1105.0,723.0
+ACAT2_SA_46_g3,591.0,284.0,414.0,809.0,61.0,241.0,532.0,389.0,425.0,297.0
+ACAT2_SA_46_g4,294.0,147.0,237.0,407.0,50.0,325.0,893.0,642.0,992.0,392.0
+ACAT2_SA_46_g5,342.0,173.0,159.0,438.0,39.0,173.0,425.0,209.0,209.0,27.0
+ACAT2_SA_47_g1,446.0,149.0,90.0,484.0,34.0,164.0,412.0,176.0,227.0,150.0
+ACAT2_SA_47_g2,508.0,274.0,626.0,762.0,106.0,757.0,1840.0,844.0,987.0,903.0
+ACAT2_SA_47_g3,262.0,177.0,203.0,406.0,50.0,325.0,504.0,328.0,189.0,204.0
+ACAT2_SA_47_g4,186.0,115.0,205.0,317.0,13.0,95.0,176.0,161.0,210.0,93.0
+ACAT2_SA_47_g5,401.0,238.0,381.0,599.0,83.0,339.0,985.0,580.0,533.0,376.0

tests/data/var_mini_guides.csv

@@ -0,0 +1,31 @@
+name,Unnamed: 0,Target gene/variant,Target descriptor,Arbitrary number,gRNA position category,Target base position in gRNA,Target base position in reporter,BE,target_group,sequence,Reporter,barcode,5-nt PAM,offset,target,target_pos,Group2,masked_sequence,masked_barcode,chrom,genomic_pos
+CONTROL_8_g1,90,CONTROL,,8,g1,4,10,ABE,NegCtrl,AAAATTATCGGAAACGGTAG,GCTCGAAAAATTATCGGAAACGGTAGAATCTT,GAAC,AATCT,-10,CONTROL_8,9,NegCtrl,GGGGTTGTCGGGGGCGGTGG,GGGC,,
+CONTROL_8_g2,91,CONTROL,,8,g2,5,11,ABE,NegCtrl,AAAAATTATCGGAAACGGTA,GGCTCGAAAAATTATCGGAAACGGTAGAATCT,CGTG,GAATC,-11,CONTROL_8,10,NegCtrl,GGGGGTTGTCGGGGGCGGTG,CGTG,,
+CONTROL_8_g3,92,CONTROL,,8,g3,5,12,ABE,NegCtrl,AAAAATTATCGGAAACGGT,TGGCTCGAAAAATTATCGGAAACGGTAGAATC,ATCA,AGAAT,-12,CONTROL_8,11,NegCtrl,GGGGGTTGTCGGGGGCGGT,GTCG,,
+CONTROL_8_g4,93,CONTROL,,8,g4,7,13,ABE,NegCtrl,CGAAAAATTATCGGAAACGG,ATGGCTCGAAAAATTATCGGAAACGGTAGAAT,CAAG,TAGAA,-13,CONTROL_8,12,NegCtrl,CGGGGGGTTGTCGGGGGCGG,CGGG,,
+CONTROL_8_g5,94,CONTROL,,8,g5,8,14,ABE,NegCtrl,TCGAAAAATTATCGGAAACG,TATGGCTCGAAAAATTATCGGAAACGGTAGAA,TTCA,GTAGA,-14,CONTROL_8,13,NegCtrl,TCGGGGGGTTGTCGGGGGCG,TTCG,,
+CONTROL_9_g1,95,CONTROL,,9,g1,4,10,ABE,NegCtrl,AGCATTCTCACCAAGACCGA,TAAGATAGCATTCTCACCAAGACCGAATGCCC,TCCC,ATGCC,-10,CONTROL_9,9,NegCtrl,GGCGTTCTCGCCGGGGCCGG,TCCC,,
+CONTROL_9_g2,96,CONTROL,,9,g2,5,11,ABE,NegCtrl,TAGCATTCTCACCAAGACCG,CTAAGATAGCATTCTCACCAAGACCGAATGCC,GGCC,AATGC,-11,CONTROL_9,10,NegCtrl,TGGCGTTCTCGCCGGGGCCG,GGCC,,
+CONTROL_9_g3,97,CONTROL,,9,g3,6,12,ABE,NegCtrl,ATAGCATTCTCACCAAGACC,GCTAAGATAGCATTCTCACCAAGACCGAATGC,GGAC,GAATG,-12,CONTROL_9,11,NegCtrl,GTGGCGTTCTCGCCGGGGCC,GGGC,,
+CONTROL_9_g4,98,CONTROL,,9,g4,6,13,ABE,NegCtrl,ATAGCATTCTCACCAAGAC,CGCTAAGATAGCATTCTCACCAAGACCGAATG,AGCG,CGAAT,-13,CONTROL_9,12,NegCtrl,GTGGCGTTCTCGCCGGGGC,GGCG,,
+CONTROL_9_g5,99,CONTROL,,9,g5,8,14,ABE,NegCtrl,AGATAGCATTCTCACCAAGA,GCGCTAAGATAGCATTCTCACCAAGACCGAAT,CACG,CCGAA,-14,CONTROL_9,13,NegCtrl,GGGTGGCGTTCTCGCCGGGG,CGCG,,
+ACAT2_SA_44_g1,100,ACAT2,SA,44,g1,4,10,ABE,PosCtrl,TGTAGGTTCCTTCAATGGTG,TTCTATTGTAGGTTCCTTCAATGGTGCCTTAG,GGTT,CCTTA,-10,ACAT2_SA_44,9,PosCtrl_inc,TGTGGGTTCCTTCGGTGGTG,GGTT,chr6,160183949.0
+ACAT2_SA_44_g2,101,ACAT2,SA,44,g2,5,11,ABE,PosCtrl,TTGTAGGTTCCTTCAATGGT,TTTCTATTGTAGGTTCCTTCAATGGTGCCTTA,CATA,GCCTT,-11,ACAT2_SA_44,10,PosCtrl_inc,TTGTGGGTTCCTTCGGTGGT,CGTG,chr6,160183949.0
+ACAT2_SA_44_g3,102,ACAT2,SA,44,g3,6,12,ABE,PosCtrl,ATTGTAGGTTCCTTCAATGG,CTTTCTATTGTAGGTTCCTTCAATGGTGCCTT,GACG,TGCCT,-12,ACAT2_SA_44,11,PosCtrl_inc,GTTGTGGGTTCCTTCGGTGG,GGCG,chr6,160183949.0
+ACAT2_SA_44_g4,103,ACAT2,SA,44,g4,7,13,ABE,PosCtrl,TATTGTAGGTTCCTTCAATG,CCTTTCTATTGTAGGTTCCTTCAATGGTGCCT,AGTG,GTGCC,-13,ACAT2_SA_44,12,PosCtrl_inc,TGTTGTGGGTTCCTTCGGTG,GGTG,chr6,160183949.0
+ACAT2_SA_44_g5,104,ACAT2,SA,44,g5,8,14,ABE,PosCtrl,CTATTGTAGGTTCCTTCAAT,GCCTTTCTATTGTAGGTTCCTTCAATGGTGCC,AAGC,GGTGC,-14,ACAT2_SA_44,13,PosCtrl_inc,CTGTTGTGGGTTCCTTCGGT,GGGC,chr6,160183949.0
+ACAT2_SA_45_g1,105,ACAT2,SA,45,g1,4,10,ABE,PosCtrl,TCTAGGCTGTGGGCAGAATC,CCTCTTTCTAGGCTGTGGGCAGAATCCTGTTA,GATT,CTGTT,-10,ACAT2_SA_45,9,PosCtrl_inc,TCTGGGCTGTGGGCGGGGTC,GGTT,chr6,160188035.0
+ACAT2_SA_45_g2,106,ACAT2,SA,45,g2,5,11,ABE,PosCtrl,TTCTAGGCTGTGGGCAGAAT,TCCTCTTTCTAGGCTGTGGGCAGAATCCTGTT,TCAC,CCTGT,-11,ACAT2_SA_45,10,PosCtrl_inc,TTCTGGGCTGTGGGCGGGGT,TCGC,chr6,160188035.0
+ACAT2_SA_45_g3,107,ACAT2,SA,45,g3,6,12,ABE,PosCtrl,TTTCTAGGCTGTGGGCAGAA,TTCCTCTTTCTAGGCTGTGGGCAGAATCCTGT,TGTC,TCCTG,-12,ACAT2_SA_45,11,PosCtrl_inc,TTTCTGGGCTGTGGGCGGGG,TGTC,chr6,160188035.0
+ACAT2_SA_45_g4,108,ACAT2,SA,45,g4,7,13,ABE,PosCtrl,CTTTCTAGGCTGTGGGCAGA,GTTCCTCTTTCTAGGCTGTGGGCAGAATCCTG,TTCT,ATCCT,-13,ACAT2_SA_45,12,PosCtrl_inc,CTTTCTGGGCTGTGGGCGGG,TTCT,chr6,160188035.0
+ACAT2_SA_45_g5,109,ACAT2,SA,45,g5,8,14,ABE,PosCtrl,TCTTTCTAGGCTGTGGGCAG,TGTTCCTCTTTCTAGGCTGTGGGCAGAATCCT,TAGG,AATCC,-14,ACAT2_SA_45,13,PosCtrl_inc,TCTTTCTGGGCTGTGGGCGG,TGGG,chr6,160188035.0
+ACAT2_SA_46_g1,110,ACAT2,SA,46,g1,4,10,ABE,PosCtrl,TCTAGGCTCCTCACTTGGCT,CTGACTTCTAGGCTCCTCACTTGGCTTACTTG,CGAC,TACTT,-10,ACAT2_SA_46,9,PosCtrl_inc,TCTGGGCTCCTCGCTTGGCT,CGGC,chr6,160189541.0
+ACAT2_SA_46_g2,111,ACAT2,SA,46,g2,5,11,ABE,PosCtrl,TTCTAGGCTCCTCACTTGGC,TCTGACTTCTAGGCTCCTCACTTGGCTTACTT,AGAC,TTACT,-11,ACAT2_SA_46,10,PosCtrl_inc,TTCTGGGCTCCTCGCTTGGC,GGGC,chr6,160189541.0
+ACAT2_SA_46_g3,112,ACAT2,SA,46,g3,6,12,ABE,PosCtrl,CTTCTAGGCTCCTCACTTGG,TTCTGACTTCTAGGCTCCTCACTTGGCTTACT,GAGA,CTTAC,-12,ACAT2_SA_46,11,PosCtrl_inc,CTTCTGGGCTCCTCGCTTGG,GGGG,chr6,160189541.0
+ACAT2_SA_46_g4,113,ACAT2,SA,46,g4,7,13,ABE,PosCtrl,ACTTCTAGGCTCCTCACTTG,TTTCTGACTTCTAGGCTCCTCACTTGGCTTAC,GCGT,GCTTA,-13,ACAT2_SA_46,12,PosCtrl_inc,GCTTCTGGGCTCCTCGCTTG,GCGT,chr6,160189541.0
+ACAT2_SA_46_g5,114,ACAT2,SA,46,g5,7,14,ABE,PosCtrl,ACTTCTAGGCTCCTCACTT,ATTTCTGACTTCTAGGCTCCTCACTTGGCTTA,GATG,GGCTT,-14,ACAT2_SA_46,13,PosCtrl_inc,GCTTCTGGGCTCCTCGCTT,GGTG,chr6,160189541.0
+ACAT2_SA_47_g1,115,ACAT2,SA,47,g1,4,10,ABE,PosCtrl,CCCAGCTGAAAATGTAGCCA,TCCTTTCCCAGCTGAAAATGTAGCCAAAAAAT,CATC,AAAAA,-10,ACAT2_SA_47,9,PosCtrl_inc,CCCGGCTGGGGGTGTGGCCG,CGTC,chr6,160196200.0
+ACAT2_SA_47_g2,116,ACAT2,SA,47,g2,5,11,ABE,PosCtrl,TCCCAGCTGAAAATGTAGCC,CTCCTTTCCCAGCTGAAAATGTAGCCAAAAAA,CTTC,AAAAA,-11,ACAT2_SA_47,10,PosCtrl_inc,TCCCGGCTGGGGGTGTGGCC,CTTC,chr6,160196200.0
+ACAT2_SA_47_g3,117,ACAT2,SA,47,g3,6,12,ABE,PosCtrl,TTCCCAGCTGAAAATGTAGC,TCTCCTTTCCCAGCTGAAAATGTAGCCAAAAA,ACCG,CAAAA,-12,ACAT2_SA_47,11,PosCtrl_inc,TTCCCGGCTGGGGGTGTGGC,GCCG,chr6,160196200.0
+ACAT2_SA_47_g4,118,ACAT2,SA,47,g4,7,13,ABE,PosCtrl,TTTCCCAGCTGAAAATGTAG,TTCTCCTTTCCCAGCTGAAAATGTAGCCAAAA,GGTG,CCAAA,-13,ACAT2_SA_47,12,PosCtrl_inc,TTTCCCGGCTGGGGGTGTGG,GGTG,chr6,160196200.0
+ACAT2_SA_47_g5,119,ACAT2,SA,47,g5,8,14,ABE,PosCtrl,CTTTCCCAGCTGAAAATGTA,TTTCTCCTTTCCCAGCTGAAAATGTAGCCAAA,TTTC,GCCAA,-14,ACAT2_SA_47,13,PosCtrl_inc,CTTTCCCGGCTGGGGGTGTG,TTTC,chr6,160196200.0

tests/data/var_mini_samples.csv

@@ -0,0 +1,11 @@
+,condition,rep,lower_quantile,upper_quantile
+rep5_top,top,rep5,0.8,1.0
+rep5_high,high,rep5,0.6,0.8
+rep5_bulk,bulk,rep5,0.0,1.0
+rep5_low,low,rep5,0.2,0.4
+rep5_bot,bot,rep5,0.0,0.2
+rep6_top,top,rep6,0.8,1.0
+rep6_high,high,rep6,0.6,0.8
+rep6_bulk,bulk,rep6,0.0,1.0
+rep6_low,low,rep6,0.2,0.4
+rep6_bot,bot,rep6,0.0,0.2

tests/data/var_mini_screen_annotated.translation_ref_mismatches.csv

@@ -0,0 +1 @@
+,gene,rel_pos,ref,edit