> perl -ane 'if(/\>/){$a++;print ">Locus_stringtie_AE_$a\n"}else{print;}' \
stringtie_Nov14_AE_gtf.fa > stringtie_Nov14_AE_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_stringtie_AF_$a\n"}else{print;}' \
stringtie_Nov14_AF_gtf.fa > stringtie_Nov14_AF_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_stringtie_AG_$a\n"}else{print;}' \
stringtie_Nov14_AG_gtf.fa > stringtie_Nov14_AG_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_stringtie_AH_$a\n"}else{print;}' \
stringtie_Nov14_AH_gtf.fa > stringtie_Nov14_AH_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_Scallop_AE_$a\n"}else{print;}' \
scallop_Dec30_AE_gtf.fa > scallop_Dec30_AE_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_scallop_AF_$a\n"}else{print;}' \
scallop_Dec30_AF_gtf.fa > scallop_Dec30_AF_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_scallop_AG_$a\n"}else{print;}' \
scallop_Dec30_AG_gtf.fa > scallop_Dec30_AG_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_scallop_AH_$a\n"}else{print;}' \
scallop_Dec30_AH_gtf.fa > scallop_Dec30_AH_gtf_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_strawberry_AE_$a\n"}else{print;}' \
strawberry_AE_Dec30_assembled_transcripts.fa > strawberry_AE_Dec30_assembled_transcripts_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_strawberry_AF_$a\n"}else{print;}' \
strawberry_AF_Dec30_assembled_transcripts.fa > strawberry_AF_Dec30_assembled_transcripts_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_strawberry_AG_$a\n"}else{print;}' \
strawberry_AG_Dec30_assembled_transcripts.fa > strawberry_AG_Dec30_assembled_transcripts_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_strawberry_AH_$a\n"}else{print;}' \
strawberry_AH_Dec30_assembled_transcripts.fa > strawberry_AH_Dec30_assembled_transcripts_renamed.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_Trinity_AE_$a\n"}else{print;}' \
Trinity_AE_genome_guided_Dec30.fasta > Trinity_AE_genome_guided_Dec30_renamed.fasta
> perl -ane 'if(/\>/){$a++;print ">Locus_Trinity_AF_$a\n"}else{print;}' \
Trinity_AF_genome_guided_Dec30.fasta > Trinity_AF_genome_guided_Dec30_renamed.fasta
> perl -ane 'if(/\>/){$a++;print ">Locus_Trinity_AG_$a\n"}else{print;}' \
Trinity_AG_genome_guided_Dec30.fasta > Trinity_AG_genome_guided_Dec30_renamed.fasta
> perl -ane 'if(/\>/){$a++;print ">Locus_Trinity_AH_$a\n"}else{print;}' \
Trinity_AH_genome_guided_Dec30.fasta > Trinity_AH_genome_guided_Dec30_renamed.fasta
> perl -ane 'if(/\>/){$a++;print ">Locus_Trinity_RF_Nov18_$a\n"}else{print;}' \
Trinity_RF_Nov18.fasta > Trinity_RF_Nov18_renamed.fasta
> cp ~/Mar28_DRR_ST_transcripts.fa ~/LS_evigene_Mar30/Stringtie_DRR_Mar28.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_Stringtie_DRR_$a\n"}else{print;}' \
Stringtie_DRR_Mar28.fa > Stringtie_DRR_Mar28_renamed.fa
> cp ~/Mar28_DRR_scallop_transcripts.fa ~/LS_evigene_Mar30/Scallop_DRR_Mar28.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_Scallop_DRR_$a\n"}else{print;}' \
Scallop_DRR_Mar28.fa > Scallop_DRR_Mar28_renamed.fa
> cp ~/LS_strawberry_DRR_transcripts_Mar28.fa ~/LS_evigene_Mar30/Strawberry_DRR_Mar28.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_Strawberry_DRR_$a\n"}else{print;}' \
Strawberry_DRR_Mar28.fa > Strawberry_DRR_Mar28_renamed.fa
> cp ~/Trinity_GG_LS_DRR_Mar28/Trinity-GG.fasta ~/LS_evigene_Mar30/Trinity_GG_DRR_Mar28.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_Trinity_GG_DRR_$a\n"}else{print;}' \
Trinity_GG_DRR_Mar28.fa > Trinity_GG_DRR_Mar28_renamed.fa
> cp ~/Trinity_DRR_unmapped_Mar30_renamed/Trinity.fasta ~/LS_evigene_Mar30/Trinity_unmapped_DRR_Mar30.fa
> perl -ane 'if(/\>/){$a++;print ">Locus_Trinity_UM_DRR_$a\n"}else{print;}' \
Trinity_unmapped_DRR_Mar30.fa > Trinity_unmapped_DRR_Mar30_renamed.fa
cat *_renamed.fa > LS_GS_DRR_renamed_Mar30.fa
## Normalize IDs
trformat.pl -output LS_GS_DRR_renamed_Mar30.tr -input LS_GS_DRR_renamed_Mar30.fa
## Manually change first ID
sed -i -e 's/>Locus_Scallop_AE_1/>evgLocus_Scallop_AE_1/g' LS_GS_DRR_renamed_Mar30.tr
echo export PATH=$PATH$( find ~/evigene18jan01/scripts/ -type d -printf ":%p" ) >> ~/.bashrc
## Evigene pipeline, collapses 100% identical transcripts
tr2aacds.pl -mrnaseq LS_GS_DRR_renamed_Mar30.tr \
-NCPU=8 1>tr2aacds_Mar30.log 2>tr2aacds_Mar30.err \
-MINCDS=100 -logfile -debug
Files are in the ./okayset
folder.
## CDS
cat LS_GS_DRR_renamed_Mar30.okalt.cds LS_GS_DRR_renamed_Mar30.okay.cds > LS_GS_DRR_renamed_Mar30_ok_okalt.cds
## Amino acid sequences
cat LS_GS_DRR_renamed_Mar30.okalt.aa LS_GS_DRR_renamed_Mar30.okay.aa > LS_GS_DRR_renamed_Mar30_ok_okalt.aa
Files are in the ./okayset
folder.
awk '/^>/ { p = ($0 ~ /complete/)} p' LS_GS_DRR_renamed_Mar30_ok_okalt.cds > LS_GS_DRR_renamed_Mar30_ok_okalt_complete.cds
awk '/^>/ { p = ($0 ~ /partial3/)} p' LS_GS_DRR_renamed_Mar30_ok_okalt.cds > LS_GS_DRR_renamed_Mar30_ok_okalt_partial3.cds
cat LS_GS_DRR_renamed_Mar30_ok_okalt_complete.cds LS_GS_DRR_renamed_Mar30_ok_okalt_partial3.cds > LS_evigene_Mar30_OA_CP3.cds
awk '/^>/ { p = ($0 ~ /complete/)} p' LS_GS_DRR_renamed_Mar30_ok_okalt.aa > LS_GS_DRR_renamed_Mar30_ok_okalt_complete.aa
awk '/^>/ { p = ($0 ~ /partial3/)} p' LS_GS_DRR_renamed_Mar30_ok_okalt.aa > LS_GS_DRR_renamed_Mar30_ok_okalt_partial3.aa
cat LS_GS_DRR_renamed_Mar30_ok_okalt_complete.aa LS_GS_DRR_renamed_Mar30_ok_okalt_partial3.aa > LS_evigene_Mar30_OA_CP3.aa