Commit 7257b4ff authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

Filter empty CDS fields in multiple ways

parent f8d9a07e
...@@ -227,7 +227,6 @@ species_new_id ...@@ -227,7 +227,6 @@ species_new_id
cdsMap = species_cds_map cdsMap = species_cds_map
.reduce([:]) { theMap, newMapping -> theMap[newMapping.name] = newMapping.cds; return theMap } .reduce([:]) { theMap, newMapping -> theMap[newMapping.name] = newMapping.cds; return theMap }
print(cdsMap)
allSpecies allSpecies
.collectSpeciesFile() .collectSpeciesFile()
...@@ -1043,10 +1042,14 @@ process clime { ...@@ -1043,10 +1042,14 @@ process clime {
//only use blast hits where species is of type new //only use blast hits where species is of type new
//also filter out pairs where one of the two does //also filter out pairs where one of the two does
//not supply a CDS file. //not supply a CDS file (filter them real hard).
allVsAllProteomeBlasts_wgd allVsAllProteomeBlasts_wgd
.filter { it[1] == newSpeciesId.value } .filter { it[1] == newSpeciesId.value }
.filter { cdsMap[it[1]] && cdsMap[it[2]] } .filter { cdsMap[it[1]] && cdsMap[it[2]] &&
cdsMap[it[1]]!=null && cdsMap[it[2]]!=null &&
cdsMap[it[1]].value !=null && cdsMap[it[2]].value !=null &&
cdsMap[it[1]]!='' && cdsMap[it[2]]!='' }
.view()
.set { new_species_blasts } .set { new_species_blasts }
......
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