> perl -ane 'if(/\>/){$a++;print ">Locus_FPS_$a\n"}else{print;}' FPS_ESTs.fa > FPS_ESTs_renamed.fa
> trformat.pl -output FPS_ESTs.tr -input FPS_ESTs_renamed.fa
> sed -i -e 's/>Locus_FPS_1/>evgLocus_FPS_1/g' FPS_ESTs.tr
In ~/LS_FPS_evigene_Mar31
> tr2aacds.pl -mrnaseq FPS_ESTs.tr \
-NCPU=8 1>tr2aacds_FPS_Mar31.log 2>tr2aacds_FPS_Mar31.err \
-MINCDS=100 -logfile -debug
> cat FPS_ESTs.okalt.aa FPS_ESTs.okay.aa > FPS_ESTs.OA.aa
> awk '/^>/ { p = ($0 ~ /complete/)} p' FPS_ESTs.OA.aa > FPS_ESTs_OA_complete.aa
> awk '/^>/ { p = ($0 ~ /partial3/)} p' FPS_ESTs.OA.aa > FPS_ESTs_OA_partial3.aa
> cat FPS_ESTs_OA_complete.aa FPS_ESTs_OA_partial3.aa > FPS_ESTs_OA_CP3.aa
> cat FPS_ESTs.okalt.cds FPS_ESTs.okay.cds > FPS_ESTs.OA.cds
> awk '/^>/ { p = ($0 ~ /complete/)} p' FPS_ESTs.OA.cds > FPS_ESTs_OA_complete.cds
> awk '/^>/ { p = ($0 ~ /partial3/)} p' FPS_ESTs.OA.cds > FPS_ESTs_OA_partial3.cds
> cat FPS_ESTs_OA_complete.cds FPS_ESTs_OA_partial3.cds > FPS_ESTs_OA_CP3.cds
> perl ~/install/tmp/tmpkplvHF/phobius/phobius.pl -short ~/FPS_ESTs_OA_CP3.aa
> ~/install/signalp-4.1/signalp -f short -l FPS_ESTs_OA_CP3_log.txt -v \
-m ~/mature_signalP_FPS_ESTs_OA_CP3.fa -s best -t euk FPS_ESTs_OA_CP3.aa
[27853606.bc]
> hmmsearch --cut_ga --tblout ~/FPS_ESTs_OA_CP3_Pfam_cutga.txt \
~/database/Pfam-A.hmm ./FPS_ESTs_OA_CP3.aa
1,786 sequences have at least 1 Pfam hit
> cut -f 3 FPS_ESTs_OA_CP3_Pfam_hits.txt | sort | uniq > FPS_ESTs_OA_CP3_Pfam_unique_hits.txt
> grep -Fwf Phobius_FPS_ESTs_OA_CP3_Apr23_hits.txt SignalP_FPS_ESTs_OA_CP3_Apr23_hits.txt \
> SPs_FPS_ESTs_OA_CP3_Apr23.txt
> sed 's/\ .*//' mature_signalP_FPS_ESTs_OA_CP3.fa > mature_signalP_FPS_ESTs_OA_CP3_simplified.fa
> faSomeRecords mature_signalP_FPS_ESTs_OA_CP3_simplified.fa SPs_FPS_ESTs_OA_CP3_Apr23.txt \
SPs_FPS_ESTs_OA_CP3_Apr23.fa
1,946 sequences
> sort -u SPs_FPS_ESTs_OA_CP3_Apr23.txt FPS_ESTs_OA_CP3_Pfam_unique_hits.txt \
> Pfam_or_SP_FPS_Apr23.txt
> faSomeRecords FPS_ESTs_OA_CP3.aa Pfam_or_SP_FPS_Apr23.txt Pfam_or_SP_FPS_Apr23.aa
> faSomeRecords FPS_ESTs_OA_CP3.cds Pfam_or_SP_FPS_Apr23.txt Pfam_or_SP_FPS_Apr23.cds