# HG changeset patch
# User cpt
# Date 1655470418 0
# Node ID 4c354f12adce1279f5021318485e58f5653cf082
Uploaded
diff -r 000000000000 -r 4c354f12adce cpt_gff_rem_fasta/cpt-macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_gff_rem_fasta/cpt-macros.xml Fri Jun 17 12:53:38 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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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 4c354f12adce cpt_gff_rem_fasta/gff3_remove_fasta_sequences.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_gff_rem_fasta/gff3_remove_fasta_sequences.py Fri Jun 17 12:53:38 2022 +0000
@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+"""
+This program remove the fasta sequences from the end of a .gff3 file
+"""
+
+import argparse
+
+
+def remove_fasta_seq(gff3, ogff3):
+ # iterates line by line through input
+ for line in gff3:
+ # writes lines to output until ##FASTA
+ if line.startswith("##FASTA"):
+ return
+ else:
+ ogff3.write(line)
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(
+ description="Identify lysis gene candidates next to possible endolysin or holin genes",
+ epilog="",
+ )
+ parser.add_argument("gff3", type=argparse.FileType("r"), help="original gff3 file")
+ parser.add_argument("--ogff3", type=argparse.FileType("w"), default="output.gff3")
+ args = parser.parse_args()
+
+ remove_fasta_seq(args.gff3, args.ogff3)
diff -r 000000000000 -r 4c354f12adce cpt_gff_rem_fasta/gff3_remove_fasta_sequences.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_gff_rem_fasta/gff3_remove_fasta_sequences.xml Fri Jun 17 12:53:38 2022 +0000
@@ -0,0 +1,37 @@
+
+
+ Removes FASTA sequences at the end of .gff3 file. All lines after '##FASTA' deleted
+
+ macros.xml
+ cpt-macros.xml
+
+
+
+
+
+
+
+
+
+
+
+ 10.1371/journal.pcbi.1008214
+
+ @unpublished{galaxyTools,
+ author = {A. Holt},
+ title = {CPT Galaxy Tools},
+ year = {2020},
+ note = {https://github.com/tamu-cpt/galaxy-tools/}
+ }
+
+
+
diff -r 000000000000 -r 4c354f12adce cpt_gff_rem_fasta/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_gff_rem_fasta/macros.xml Fri Jun 17 12:53:38 2022 +0000
@@ -0,0 +1,85 @@
+
+
+
+
+ python
+ biopython
+ cpt_gffparser
+
+
+
+
+ "$blast_tsv"
+
+
+
+
+
+
+ "$blast_xml"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ "$gff3_data"
+
+
+#if str($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"
+
+
+
+
+