# HG changeset patch
# User cpt
# Date 1652465012 0
# Node ID b4134ad44443ea75f8319537e92599810e78da6a
Uploaded
diff -r 000000000000 -r b4134ad44443 cpt_trnascanse_to_gff/cpt-macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_trnascanse_to_gff/cpt-macros.xml Fri May 13 18:03:32 2022 +0000
@@ -0,0 +1,115 @@
+
+
+
+
+ python
+ biopython
+ requests
+
+
+
+
+
+
+
+ 10.1371/journal.pcbi.1008214
+ @unpublished{galaxyTools,
+ author = {E. Mijalis, H. Rasche},
+ title = {CPT Galaxy Tools},
+ year = {2013-2017},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
+
+ 10.1371/journal.pcbi.1008214
+
+ @unpublished{galaxyTools,
+ author = {E. Mijalis, H. Rasche},
+ title = {CPT Galaxy Tools},
+ year = {2013-2017},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
+
+
+
+ 10.1371/journal.pcbi.1008214
+
+ @unpublished{galaxyTools,
+ author = {C. Ross},
+ title = {CPT Galaxy Tools},
+ year = {2020-},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
+
+
+
+ 10.1371/journal.pcbi.1008214
+
+ @unpublished{galaxyTools,
+ author = {E. Mijalis, H. Rasche},
+ title = {CPT Galaxy Tools},
+ year = {2013-2017},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+ @unpublished{galaxyTools,
+ author = {A. Criscione},
+ title = {CPT Galaxy Tools},
+ year = {2019-2021},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
+
+
+
+ 10.1371/journal.pcbi.1008214
+
+ @unpublished{galaxyTools,
+ author = {A. Criscione},
+ title = {CPT Galaxy Tools},
+ year = {2019-2021},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
+
+
+
+ 10.1371/journal.pcbi.1008214
+
+ @unpublished{galaxyTools,
+ author = {C. Maughmer},
+ title = {CPT Galaxy Tools},
+ year = {2017-2020},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
+
+
+
+ @unpublished{galaxyTools,
+ author = {C. Maughmer},
+ title = {CPT Galaxy Tools},
+ year = {2017-2020},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
+
diff -r 000000000000 -r b4134ad44443 cpt_trnascanse_to_gff/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_trnascanse_to_gff/macros.xml Fri May 13 18:03:32 2022 +0000
@@ -0,0 +1,66 @@
+
+
+
+
+ python
+ biopython
+ cpt_gffparser
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ "$gff3_data"
+
+
+#if str($reference_genome.reference_genome_source) == 'cached':
+ "${reference_genome.fasta_indexes.fields.path}"
+#else if str($reference_genome.reference_genome_source) == 'history':
+ genomeref.fa
+#end if
+
+
+#if $reference_genome.reference_genome_source == 'history':
+ ln -s $reference_genome.genome_fasta genomeref.fa;
+#end if
+
+
+#if str($reference_genome.reference_genome_source) == 'cached':
+ "${reference_genome.fasta_indexes.fields.path}"
+#else if str($reference_genome.reference_genome_source) == 'history':
+ genomeref.fa
+#end if
+
+
+
+
+
+
+ "$sequences"
+
+
+
+
+
diff -r 000000000000 -r b4134ad44443 cpt_trnascanse_to_gff/tRNAscan_to_gff_SE_format.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_trnascanse_to_gff/tRNAscan_to_gff_SE_format.py Fri May 13 18:03:32 2022 +0000
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+import fileinput
+
+print ("##gff-version-3")
+# process each trna in tsv file
+metaLines = 0
+for trna in fileinput.input():
+ if metaLines < 3:
+ metaLines += 1
+ continue
+ cols_tsv = trna.split("\t")
+ if int(cols_tsv[2]) < int(cols_tsv[3]):
+ cols_gff = [
+ cols_tsv[0].strip(),
+ "tRNAscan",
+ "tRNA",
+ cols_tsv[2].strip(),
+ cols_tsv[3].strip(),
+ cols_tsv[8],
+ "+",
+ ".",
+ 'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
+ % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
+ ]
+ else:
+ cols_gff = [
+ cols_tsv[0].strip(),
+ "tRNAscan",
+ "tRNA",
+ cols_tsv[3].strip(),
+ cols_tsv[2].strip(),
+ cols_tsv[8],
+ "-",
+ ".",
+ 'ID=trna.%s;Anticodon=%s;Codon=tRNA-%s'
+ % (cols_tsv[1], cols_tsv[5].lower(), cols_tsv[4]),
+ ]
+ print ("\t".join(cols_gff))
diff -r 000000000000 -r b4134ad44443 cpt_trnascanse_to_gff/tRNAscan_to_gff_SE_format.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_trnascanse_to_gff/tRNAscan_to_gff_SE_format.xml Fri May 13 18:03:32 2022 +0000
@@ -0,0 +1,35 @@
+
+
+
+
+ macros.xml
+ cpt-macros.xml
+
+
+ $output
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r b4134ad44443 cpt_trnascanse_to_gff/test-data/ConvTrnaSe_In.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_trnascanse_to_gff/test-data/ConvTrnaSe_In.tabular Fri May 13 18:03:32 2022 +0000
@@ -0,0 +1,4 @@
+Sequence tRNA Bounds tRNA Anti Intron Bounds Inf
+Name tRNA # Begin End Type Codon Begin End Score Note
+-------- ------ ----- ------ ---- ----- ----- ---- ------ ------
+NC_028755.1 1 49264 49339 Gly TCC 0 0 77.4
diff -r 000000000000 -r b4134ad44443 cpt_trnascanse_to_gff/test-data/ConvTrnaSe_Out.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_trnascanse_to_gff/test-data/ConvTrnaSe_Out.gff3 Fri May 13 18:03:32 2022 +0000
@@ -0,0 +1,2 @@
+##gff-version-3
+NC_028755.1 tRNAscan tRNA 49264 49339 77.4 + . ID=trna.1;Anticodon=tcc;Codon=tRNA-Gly