Wednesday, September 24, 2014

perl ~/Scripts/ <DR_004_Arjam_MOE_assembled_v_OR_VR_indices.tblastx >DR_004_Arjam_MOE_assembled_v_OR_VR_indices.tblastx.parsed2
OK, processed 8019 queries, 23298 hits

perl ~/Scripts/ <DR_011_Arjam_VNO_assembled_v_OR_VR_indices.tblastx  >DR_011_Arjam_VNO_assembled_v_OR_VR_indices.tblastx.parsed2
OK, processed 8019 queries, 77307 hits

perl ~/Scripts/ <DR_013_Mored_MOE_assembled_v_OR_VR_indices.tblastx  >DR_013_Arjam_MOE_assembled_v_OR_VR_indices.tblastx.parsed2
OK, processed 8019 queries, 251312 hits

perl ~/Scripts/ <DR_013_Mored_VNO_assembled_v_OR_VR_indices.tblast  >DR_013_Arjam_VNO_assembled_v_OR_VR_indices.tblastx.parsed2
OK, processed 8019 queries, 232694 hits

perl ~/Scripts/ <DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx  >DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx.parsed2
OK, processed 8019 queries, 96314 hits

Tuesday, September 16, 2014

#remove newlines
awk '{if (substr($0,1,1)==">"){print "\n"$0} else printf("%s",$0);p++;}END{print "\n"}' DR_091_Mobl_MOE_assembled.fasta > joined.fasta

If I try running BLASTALL with my transcriptome data as the database, I get this error:

[blastall 2.2.22] ERROR: SeqPortNew: lcl

All the names of the sequences are too similar so I have to rename them--I am just going to rename them by number.
awk '/^>/{print ">" ++i; next}{print}' < DR_091_Mobl_MOE_assembled.fasta > renamed_DR_091_Mobl_MOE_assembled.fasta

#export the path the blast
export PATH=$PATH:/Users/laurelyohe/blast-2.2.22/bin/

#format the database 
#because the transcriptome is bigger than the indices, it will serve as the database
formatdb -i renamed_DR_091_Mobl_MOE_assembled.fasta -o T -p F
#run blast
blastall -p tblastx -d renamed_DR_013_Mored_MOE_assembled.fasta -i OR_VR_indices.fasta -e 1e-06 -v 5 -b 5 -a 2 -o ./DR_013_Mored_MOE_assembled_v_OR_VR_indices.tblastx

#now we need to parse the BLAST script
perl ~/Scripts/ --i DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx > DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx.parsed
#next combine the parsed file with the sequences
~/Scripts/ -i renamed_DR_091_Mobl_MOE_assembled.fasta -t DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx.parsed -s DR_091_Mormoops_blainvelli
Okay, I have finally accepted that my data is not fitting an Ornstein-Uhlenbeck model of evolution and it makes zero sense to be running the tests that I have been running. My alpha value is way too small for all of my traits compared to the height of my tree.

I have run the fitContinuous() function in the "geiger" package on the geometric mean.

Thursday, September 4, 2014