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all: incl_blast_n_pfam simplest single_best best_with_homology
simplest:
../util/select_best_ORFs_per_transcript.pl --gff3_file longest_orfs.gff3 --cds_scores longest_orfs.cds.scores > test.simplest
diff test.simplest __test.simplest.expected
single_best:
../util/select_best_ORFs_per_transcript.pl --gff3_file longest_orfs.gff3 --cds_scores longest_orfs.cds.scores --single_best_orf > test.single_best
diff test.single_best __test.single_best.expected
incl_blast_n_pfam:
../util/select_best_ORFs_per_transcript.pl --gff3_file longest_orfs.gff3 --cds_scores longest_orfs.cds.scores --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > test.wBlastNPfam
diff test.wBlastNPfam __test.wBlastNPfam.expected
best_with_homology:
../util/select_best_ORFs_per_transcript.pl --gff3_file longest_orfs.gff3 --cds_scores longest_orfs.cds.scores --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 --single_best_orf > test.best_w_homology
diff test.best_w_homology __test.best_w_homology.expected
clean:
rm -f ./test.*
# for checking the trans count dist:
#
# for file in test.*; do cat $file | perl -lane 'if ($F[2] eq "CDS") { print;}' | print.pl 0 | token_counter.pl > __$file.expected.hist; echo done $file; done
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