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Merge pull request #398 from ARTbio/patch_filter_genes
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fix missing header for the first column of filter_genes
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@drosofff
drosofff authored Jun 24, 2019
2 parents ab497ac + d9e43e5 commit 6619541
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Showing 5 changed files with 6 additions and 5 deletions.
3 changes: 2 additions & 1 deletion tools/gsc_filter_genes/filter_genes.R
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@ kept_genes <- rowSums(data.counts != 0) >= (opt$absolute_detection)

# Filter matrix
data.counts <- data.counts[kept_genes,]
data.counts <- cbind(Genes=rownames(data.counts), data.counts)

# Save filtered matrix
write.table(
Expand All @@ -89,5 +90,5 @@ write.table(
sep = "\t",
quote = F,
col.names = T,
row.names = T
row.names = F
)
2 changes: 1 addition & 1 deletion tools/gsc_filter_genes/filter_genes.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="filter_genes" name="Filter genes in single cell data" version="0.9.0">
<tool id="filter_genes" name="Filter genes in single cell data" version="0.9.1">
<description>which are detected in less that a given fraction of the libraries</description>
<requirements>
<requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
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2 changes: 1 addition & 1 deletion tools/gsc_filter_genes/test-data/filtered-0.05.tab
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 1001000173.E5 1001000179.F5 1001000245.G11 1001000185.D5 1001000012.A7 1001000010.B4 1001000265.D11 1001000032.F1 1001000036.H9 1001000245.B3 1001000185.A8 1001000178.C6 1001000037.F10 1001000245.H4 1001000012.B10 1001000245.F2 1001000249.G2 1001000187.E11 1001000266.A4 1001000266.G4 1001000179.E3 1001000178.C11 1001000031.D12 1001000037.D6 1001000250.G2 1001000018.F11 1001000175.F9 1001000254.G1 1001000264.F12 1001000183.B3 1001000241.E6 1001000183.E6 1001000181.F10 1001000176.B1 1001000235.B7 1001000231.D12 1001000230.E7 1001000186.H6 1001000258.H5 1001000237.H10 1001000231.B7 1001000270.H8 1001000240.G1 1001000177.D11 1001000185.D3 1001000238.B5 1001000174.E10
Genes 1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 1001000173.E5 1001000179.F5 1001000245.G11 1001000185.D5 1001000012.A7 1001000010.B4 1001000265.D11 1001000032.F1 1001000036.H9 1001000245.B3 1001000185.A8 1001000178.C6 1001000037.F10 1001000245.H4 1001000012.B10 1001000245.F2 1001000249.G2 1001000187.E11 1001000266.A4 1001000266.G4 1001000179.E3 1001000178.C11 1001000031.D12 1001000037.D6 1001000250.G2 1001000018.F11 1001000175.F9 1001000254.G1 1001000264.F12 1001000183.B3 1001000241.E6 1001000183.E6 1001000181.F10 1001000176.B1 1001000235.B7 1001000231.D12 1001000230.E7 1001000186.H6 1001000258.H5 1001000237.H10 1001000231.B7 1001000270.H8 1001000240.G1 1001000177.D11 1001000185.D3 1001000238.B5 1001000174.E10
BAI3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.97662501806838 0 0 0 0 12.8615775772142 0 0 0 15.9032354384535 0 0 0 0 0 12.2158463533178 9.68026850722175 15.3729581524844 0 0 14.28403727033 0 0 0 0 17.0775051033723 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.86467441602363 0 0 0 0 0 0 14.2185940019444 0 0 0 0 0 9.4604919129408 0 0
FAM63B 0 14.7268225958904 0 0 0 0 0 14.2095873331695 0 0 0 7.05523661711308 0 0 0 0 10.8662524562421 0 0 0 0 0 0 12.5659445674216 0 0 0 0 0 0 17.508917577493 0 15.2092038075611 0 0 16.3552364080959 0 0 0 0 0 0 0 0 0 0 12.833405122753 0 0 0 0 10.631490277574 0 0 0 0 6.49910345713958 0 0 12.6988507765885 0 17.5291982691478 0 0 0 0 0 0 9.72047933810935 0 0 8.00314342388438 0 0 0 0 0 10.5923353166174 0 13.1956852586776 0 0 0 0 14.4254341461373 0 0 0 0 13.2598797712496 0 0 0 0 0 0 0 6.6653716296684 0 0
TMEM132C 0 0 0 0 0 0 0 0 0 15.6304274760255 0 0 0 0 11.3724171014623 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13.7057920287568 0 0 12.4990036192117 0 0 0 0 0 0 0 0 0 0 0 12.3619870470136 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16.6895776681193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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2 changes: 1 addition & 1 deletion tools/gsc_filter_genes/test-data/filtered-5.tab
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 1001000173.E5 1001000179.F5 1001000245.G11 1001000185.D5 1001000012.A7 1001000010.B4 1001000265.D11 1001000032.F1 1001000036.H9 1001000245.B3 1001000185.A8 1001000178.C6 1001000037.F10 1001000245.H4 1001000012.B10 1001000245.F2 1001000249.G2 1001000187.E11 1001000266.A4 1001000266.G4 1001000179.E3 1001000178.C11 1001000031.D12 1001000037.D6 1001000250.G2 1001000018.F11 1001000175.F9 1001000254.G1 1001000264.F12 1001000183.B3 1001000241.E6 1001000183.E6 1001000181.F10 1001000176.B1 1001000235.B7 1001000231.D12 1001000230.E7 1001000186.H6 1001000258.H5 1001000237.H10 1001000231.B7 1001000270.H8 1001000240.G1 1001000177.D11 1001000185.D3 1001000238.B5 1001000174.E10
Genes 1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 1001000173.E5 1001000179.F5 1001000245.G11 1001000185.D5 1001000012.A7 1001000010.B4 1001000265.D11 1001000032.F1 1001000036.H9 1001000245.B3 1001000185.A8 1001000178.C6 1001000037.F10 1001000245.H4 1001000012.B10 1001000245.F2 1001000249.G2 1001000187.E11 1001000266.A4 1001000266.G4 1001000179.E3 1001000178.C11 1001000031.D12 1001000037.D6 1001000250.G2 1001000018.F11 1001000175.F9 1001000254.G1 1001000264.F12 1001000183.B3 1001000241.E6 1001000183.E6 1001000181.F10 1001000176.B1 1001000235.B7 1001000231.D12 1001000230.E7 1001000186.H6 1001000258.H5 1001000237.H10 1001000231.B7 1001000270.H8 1001000240.G1 1001000177.D11 1001000185.D3 1001000238.B5 1001000174.E10
BAI3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.97662501806838 0 0 0 0 12.8615775772142 0 0 0 15.9032354384535 0 0 0 0 0 12.2158463533178 9.68026850722175 15.3729581524844 0 0 14.28403727033 0 0 0 0 17.0775051033723 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.86467441602363 0 0 0 0 0 0 14.2185940019444 0 0 0 0 0 9.4604919129408 0 0
FAM63B 0 14.7268225958904 0 0 0 0 0 14.2095873331695 0 0 0 7.05523661711308 0 0 0 0 10.8662524562421 0 0 0 0 0 0 12.5659445674216 0 0 0 0 0 0 17.508917577493 0 15.2092038075611 0 0 16.3552364080959 0 0 0 0 0 0 0 0 0 0 12.833405122753 0 0 0 0 10.631490277574 0 0 0 0 6.49910345713958 0 0 12.6988507765885 0 17.5291982691478 0 0 0 0 0 0 9.72047933810935 0 0 8.00314342388438 0 0 0 0 0 10.5923353166174 0 13.1956852586776 0 0 0 0 14.4254341461373 0 0 0 0 13.2598797712496 0 0 0 0 0 0 0 6.6653716296684 0 0
TMEM132C 0 0 0 0 0 0 0 0 0 15.6304274760255 0 0 0 0 11.3724171014623 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13.7057920287568 0 0 12.4990036192117 0 0 0 0 0 0 0 0 0 0 0 12.3619870470136 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16.6895776681193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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2 changes: 1 addition & 1 deletion tools/gsc_filter_genes/test-data/filtered-null.tab
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 1001000173.E5 1001000179.F5 1001000245.G11 1001000185.D5 1001000012.A7 1001000010.B4 1001000265.D11 1001000032.F1 1001000036.H9 1001000245.B3 1001000185.A8 1001000178.C6 1001000037.F10 1001000245.H4 1001000012.B10 1001000245.F2 1001000249.G2 1001000187.E11 1001000266.A4 1001000266.G4 1001000179.E3 1001000178.C11 1001000031.D12 1001000037.D6 1001000250.G2 1001000018.F11 1001000175.F9 1001000254.G1 1001000264.F12 1001000183.B3 1001000241.E6 1001000183.E6 1001000181.F10 1001000176.B1 1001000235.B7 1001000231.D12 1001000230.E7 1001000186.H6 1001000258.H5 1001000237.H10 1001000231.B7 1001000270.H8 1001000240.G1 1001000177.D11 1001000185.D3 1001000238.B5 1001000174.E10
Genes 1001000235.G10 1001000174.B1 1001000177.C5 1001000182.H4 1001000175.A2 1001000230.B11 1001000237.E9 1001000173.E10 1001000241.E7 1001000249.A3 1001000179.A7 1001000247.F11 1001000240.D9 1001000178.G5 1001000249.E3 1001000174.H6 1001000181.F8 1001000177.A10 1001000235.D2 1001000240.G10 1001000248.E7 1001000012.B6 1001000179.H4 1001000230.C1 1001000175.H9 1001000241.G11 1001000174.G2 1001000252.C6 1001000186.D11 1001000239.G7 1001000258.G11 1001000264.A1 1001000174.A10 1001000255.E9 1001000242.B5 1001000179.F3 1001000185.F9 1001000267.F8 1001000183.G10 1001000247.E7 1001000031.A2 1001000271.B1 1001000187.G6 1001000236.C6 1001000238.C12 1001000187.D6 1001000235.E10 1001000036.C1 1001000253.H2 1001000231.C2 1001000178.C10 1001000267.C1 1001000180.E4 1001000173.E5 1001000179.F5 1001000245.G11 1001000185.D5 1001000012.A7 1001000010.B4 1001000265.D11 1001000032.F1 1001000036.H9 1001000245.B3 1001000185.A8 1001000178.C6 1001000037.F10 1001000245.H4 1001000012.B10 1001000245.F2 1001000249.G2 1001000187.E11 1001000266.A4 1001000266.G4 1001000179.E3 1001000178.C11 1001000031.D12 1001000037.D6 1001000250.G2 1001000018.F11 1001000175.F9 1001000254.G1 1001000264.F12 1001000183.B3 1001000241.E6 1001000183.E6 1001000181.F10 1001000176.B1 1001000235.B7 1001000231.D12 1001000230.E7 1001000186.H6 1001000258.H5 1001000237.H10 1001000231.B7 1001000270.H8 1001000240.G1 1001000177.D11 1001000185.D3 1001000238.B5 1001000174.E10
BAI3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.97662501806838 0 0 0 0 12.8615775772142 0 0 0 15.9032354384535 0 0 0 0 0 12.2158463533178 9.68026850722175 15.3729581524844 0 0 14.28403727033 0 0 0 0 17.0775051033723 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9.86467441602363 0 0 0 0 0 0 14.2185940019444 0 0 0 0 0 9.4604919129408 0 0
JPH1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10.9442475033749 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7.03963574788986 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10.3969315865349
GSTA5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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