# HG changeset patch
# User cpt
# Date 1685932849 0
# Node ID b973bc75693daa195535510bae093d7b61333dbd
# Parent 3f0d07a1040503ef566d5e4ee60f37c23c48ab00
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
diff -r 3f0d07a10405 -r b973bc75693d cpt-macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt-macros.xml Mon Jun 05 02:40:49 2023 +0000
@@ -0,0 +1,115 @@
+
+
+
+ python
+ biopython
+ requests
+ cpt_gffparser
+
+
+
+
+
+
+
+ 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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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 3f0d07a10405 -r b973bc75693d cpt_disruptin_finder/cpt-macros.xml
--- a/cpt_disruptin_finder/cpt-macros.xml Fri Jun 17 12:22:15 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,115 +0,0 @@
-
-
-
-
- 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- @unpublished{galaxyTools,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 3f0d07a10405 -r b973bc75693d cpt_disruptin_finder/disruptin_finder.py
--- a/cpt_disruptin_finder/disruptin_finder.py Fri Jun 17 12:22:15 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-"""
-This program is intended to find gene products that would be acceptable disruptin candidates.
-
-The criteria can be toggled between selecting for proteins with:
- - net charge above a give threshold (default = +4) and length less than given threshold (default = 100 aa)
- OR
- - ratio of number of charged residues to length of the sequence above a given threshold (default = 0.25 residue/aa)
- and length less than given threshold (default = 100 aa)
- OR
- - net charge above a give threshold (default = +4), ratio of number of charged residues to length of the sequence
- above a given threshold (default = 0.25 residue/aa), and length less than given threshold (default = 100 aa)
-
-Net charge of a sequence is calculated so that for every R or K residue the net charge increases by one, and for every
-D or E residue the net charge decreases by one. The ratio of charged residues to length is calculated in a similar manner.
-The residues R, K, D, and E each increase the number of charged residues by one, and total for the sequence is then
-divided by the length to get the ratio.
-
-Input a multi fasta file with all of the predicted protein sequences from the genome as well as a threshold
-sequence length, net charge, and charge residue to length ratio. The program outputs another fasta file.
-The output fasta file includes records for all the sequences meeting the size and charge criteria.
-
-"""
-
-from Bio import SeqIO
-import argparse
-import sys
-
-
-def disruptin_finder(
- fasta_file, thresh_size, thresh_net_charge, thresh_charge_ratio, selection_criteria
-):
- # Iterable variables
- net_charge = 0
- charge_res = 0
-
- # Create record variable to store record information
- total_record = []
-
- # Parse the .fasta file and get the sequence
- for rec in SeqIO.parse(fasta_file, "fasta"):
- sequence = str(rec.seq)
-
- if len(sequence) <= thresh_size:
- for aa in sequence:
- # For R and K residues a positive charge is given
- if aa in "RK":
- net_charge += 1
- charge_res += 1
- # For D and E residues a negative charge is given
- elif aa in "DE":
- net_charge -= 1
- charge_res += 1
-
- # Charge (total charged residues) to size ratio is calculated
- Length = len(sequence)
- charge_ratio = float(charge_res) / float(Length)
-
- # Based on the user-specified selection criteria a list of records is compiled
- if selection_criteria == "net":
- if net_charge >= thresh_net_charge:
- total_record = total_record + [rec]
- elif selection_criteria == "ratio":
- if charge_ratio >= thresh_charge_ratio:
- total_record = total_record + [rec]
- elif selection_criteria == "both":
- if (
- charge_ratio >= thresh_charge_ratio
- and net_charge >= thresh_net_charge
- ):
- total_record = total_record + [rec]
-
- # Reset the iterable variables
- net_charge = 0
- charge_res = 0
-
- # The total list of records is returned by the function
- yield total_record
-
-
-if __name__ == "__main__":
- # Grab all of the filters from our plugin loader
- parser = argparse.ArgumentParser(description="Disruptin Finder")
- parser.add_argument(
- "fasta_file", type=argparse.FileType("r"), help="Multi-FASTA Input"
- )
- parser.add_argument("--thresh_net_charge", type=int, default=4)
- parser.add_argument("--thresh_size", type=int, default=100)
- parser.add_argument("--thresh_charge_ratio", type=float, default=0.25)
- parser.add_argument("--selection_criteria", action="store")
- args = parser.parse_args()
-
- for seq in disruptin_finder(**vars(args)):
- SeqIO.write(seq, sys.stdout, "fasta")
diff -r 3f0d07a10405 -r b973bc75693d cpt_disruptin_finder/disruptin_finder.xml
--- a/cpt_disruptin_finder/disruptin_finder.xml Fri Jun 17 12:22:15 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-
-
- finds proteins with size and charge criteria
-
- macros.xml
- cpt-macros.xml
-
-
- $output]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 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 3f0d07a10405 -r b973bc75693d cpt_disruptin_finder/macros.xml
--- a/cpt_disruptin_finder/macros.xml Fri Jun 17 12:22:15 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-
-
-
-
- python
- biopython
- cpt_gffparser
-
-
-
-
-
-
-
-
-
-
- ln -s $genome_fasta genomeref.fa;
-
-
- genomeref.fa
-
-
diff -r 3f0d07a10405 -r b973bc75693d disruptin_finder.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/disruptin_finder.py Mon Jun 05 02:40:49 2023 +0000
@@ -0,0 +1,93 @@
+"""
+This program is intended to find gene products that would be acceptable disruptin candidates.
+
+The criteria can be toggled between selecting for proteins with:
+ - net charge above a give threshold (default = +4) and length less than given threshold (default = 100 aa)
+ OR
+ - ratio of number of charged residues to length of the sequence above a given threshold (default = 0.25 residue/aa)
+ and length less than given threshold (default = 100 aa)
+ OR
+ - net charge above a give threshold (default = +4), ratio of number of charged residues to length of the sequence
+ above a given threshold (default = 0.25 residue/aa), and length less than given threshold (default = 100 aa)
+
+Net charge of a sequence is calculated so that for every R or K residue the net charge increases by one, and for every
+D or E residue the net charge decreases by one. The ratio of charged residues to length is calculated in a similar manner.
+The residues R, K, D, and E each increase the number of charged residues by one, and total for the sequence is then
+divided by the length to get the ratio.
+
+Input a multi fasta file with all of the predicted protein sequences from the genome as well as a threshold
+sequence length, net charge, and charge residue to length ratio. The program outputs another fasta file.
+The output fasta file includes records for all the sequences meeting the size and charge criteria.
+
+"""
+
+from Bio import SeqIO
+import argparse
+import sys
+
+
+def disruptin_finder(
+ fasta_file, thresh_size, thresh_net_charge, thresh_charge_ratio, selection_criteria
+):
+ # Iterable variables
+ net_charge = 0
+ charge_res = 0
+
+ # Create record variable to store record information
+ total_record = []
+
+ # Parse the .fasta file and get the sequence
+ for rec in SeqIO.parse(fasta_file, "fasta"):
+ sequence = str(rec.seq)
+
+ if len(sequence) <= thresh_size:
+ for aa in sequence:
+ # For R and K residues a positive charge is given
+ if aa in "RK":
+ net_charge += 1
+ charge_res += 1
+ # For D and E residues a negative charge is given
+ elif aa in "DE":
+ net_charge -= 1
+ charge_res += 1
+
+ # Charge (total charged residues) to size ratio is calculated
+ Length = len(sequence)
+ charge_ratio = float(charge_res) / float(Length)
+
+ # Based on the user-specified selection criteria a list of records is compiled
+ if selection_criteria == "net":
+ if net_charge >= thresh_net_charge:
+ total_record = total_record + [rec]
+ elif selection_criteria == "ratio":
+ if charge_ratio >= thresh_charge_ratio:
+ total_record = total_record + [rec]
+ elif selection_criteria == "both":
+ if (
+ charge_ratio >= thresh_charge_ratio
+ and net_charge >= thresh_net_charge
+ ):
+ total_record = total_record + [rec]
+
+ # Reset the iterable variables
+ net_charge = 0
+ charge_res = 0
+
+ # The total list of records is returned by the function
+ yield total_record
+
+
+if __name__ == "__main__":
+ # Grab all of the filters from our plugin loader
+ parser = argparse.ArgumentParser(description="Disruptin Finder")
+ parser.add_argument(
+ "fasta_file", type=argparse.FileType("r"), help="Multi-FASTA Input"
+ )
+ parser.add_argument("--thresh_net_charge", type=int, default=4)
+ parser.add_argument("--thresh_size", type=int, default=100)
+ parser.add_argument("--thresh_charge_ratio", type=float, default=0.25)
+ parser.add_argument("--selection_criteria", action="store")
+ args = parser.parse_args()
+
+ for seq in disruptin_finder(**vars(args)):
+ SeqIO.write(seq, sys.stdout, "fasta")
diff -r 3f0d07a10405 -r b973bc75693d disruptin_finder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/disruptin_finder.xml Mon Jun 05 02:40:49 2023 +0000
@@ -0,0 +1,51 @@
+
+ finds proteins with size and charge criteria
+
+ macros.xml
+ cpt-macros.xml
+
+
+ '$output']]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 3f0d07a10405 -r b973bc75693d macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Jun 05 02:40:49 2023 +0000
@@ -0,0 +1,74 @@
+
+
+
+ progressivemauve
+
+ bcbiogff
+
+
+
+ 2.4.0
+
+ 10.1371/journal.pone.0011147
+
+
+ 10.1093/bioinformatics/btm039
+
+
+ '$xmfa'
+
+
+
+
+
+ '$sequences'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ '$gff3_data'
+
+
+ #if str($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
+
+