# HG changeset patch
# User cpt
# Date 1656998387 0
# Node ID 21d00cf831372bcc3912ba231605308b9da2c70d
Uploaded
diff -r 000000000000 -r 21d00cf83137 cpt_xmfa_split/cpt-macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_xmfa_split/cpt-macros.xml Tue Jul 05 05:19:47 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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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+ @unpublished{galaxyTools,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 21d00cf83137 cpt_xmfa_split/lcb_split.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_xmfa_split/lcb_split.py Tue Jul 05 05:19:47 2022 +0000
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+import argparse
+import copy
+import logging
+import xmfa
+from itertools import groupby
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+def split_lcb(lcb, window_size=10, threshold=0.7):
+ # Transpose sequence
+ lines = []
+ max_align_num = len(lcb[0]["seq"])
+ for i in range(max_align_num):
+ lines.append([])
+ for j in range(len(lcb)):
+ c = lcb[j]["seq"][i]
+ if c != "-":
+ lines[i].append(j)
+
+ count_groups = []
+ for i in range(0, len(lines), window_size):
+ current_lines = lines[i : i + window_size]
+ flat_list = [a for b in current_lines for a in b]
+ counts = []
+ for i in range(len(lcb)):
+ value = float(flat_list.count(i)) / window_size
+ if value >= threshold:
+ counts.append(i)
+ count_groups.append(counts)
+
+ # groups = [(next(j), len(list(j)) + 1) for i, j in ]
+ # [([4], 2), ([2, 3, 4, 5, 6], 2), ([0, 1, 2, 3, 4, 5, 6], 14), ([0, 3], 1)]
+ # This says for 2 window sizes, we emit a new LCB with just [0:10] and
+ # [10:20] for lcb #4, then one with all but 0/1 for 2, then all for 14.
+ new_lcbs = []
+ position = 0
+ for i, j in groupby(count_groups):
+ tmp = list(j)
+ count = len(tmp)
+ members = tmp[0]
+ local_members = []
+ for member in members:
+ tmp_member = copy.deepcopy(lcb[member])
+ tmp_member["seq"] = tmp_member["seq"][
+ window_size * position : window_size * (position + count)
+ ]
+ tmp_member["start"] = tmp_member["start"] + (3 * window_size * position)
+ tmp_member["end"] = tmp_member["start"] + (3 * window_size * count)
+ local_members.append(tmp_member)
+ if len(local_members) > 0:
+ new_lcbs.append(local_members)
+
+ position += count
+ return new_lcbs
+
+
+def split_lcbs(lcbs, window_size=10, threshold=100):
+ new_lcbs = []
+ for lcb in lcbs:
+ new_lcbs.extend(split_lcb(lcb, window_size=window_size, threshold=threshold))
+ return new_lcbs
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(
+ description="Split XMFA alignments", prog="xmfa2smallerXmfa"
+ )
+ parser.add_argument("xmfa_file", type=argparse.FileType("r"), help="XMFA File")
+
+ parser.add_argument(
+ "--window_size", type=int, help="Window size for analysis", default=10
+ )
+ parser.add_argument(
+ "--threshold",
+ type=float,
+ help="All genomes must meet N percent similarity",
+ default=0.7,
+ )
+
+ args = parser.parse_args()
+
+ # Write
+ xmfa.to_xmfa(
+ # Split
+ split_lcbs(
+ # Parse
+ xmfa.parse_xmfa(args.xmfa_file),
+ window_size=args.window_size,
+ threshold=args.threshold,
+ )
+ )
diff -r 000000000000 -r 21d00cf83137 cpt_xmfa_split/lcb_split.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_xmfa_split/lcb_split.xml Tue Jul 05 05:19:47 2022 +0000
@@ -0,0 +1,36 @@
+
+
+
+
+ macros.xml
+ cpt-macros.xml
+
+
+ $output
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 21d00cf83137 cpt_xmfa_split/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_xmfa_split/macros.xml Tue Jul 05 05:19:47 2022 +0000
@@ -0,0 +1,61 @@
+
+
+
+
+ progressivemauve
+ python
+ biopython
+ cpt_gffparser
+
+
+
+ 2.4.0
+
+ 10.1371/journal.pone.0011147
+
+
+ 10.1093/bioinformatics/btm039
+
+
+
+ "$xmfa"
+
+
+
+
+
+
+ "$sequences"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ "$gff3_data"
+
+
+ genomeref.fa
+
+
+ ln -s $genome_fasta genomeref.fa;
+
+
+ genomeref.fa
+
+
+
+
+