From be04faf07894d2b9e4ae94a06be06aa2049a389c Mon Sep 17 00:00:00 2001
From: Haibao Tang <tanghaibao@gmail.com>
Date: Sun, 28 Apr 2024 15:15:21 -0700
Subject: [PATCH] Deprecate alfalfa.py and pistachio.py

---
 jcvi/projects/alfalfa.py   | 62 ----------------------------
 jcvi/projects/misc.py      |  1 -
 jcvi/projects/pistachio.py | 83 --------------------------------------
 3 files changed, 146 deletions(-)
 delete mode 100644 jcvi/projects/alfalfa.py
 delete mode 100644 jcvi/projects/pistachio.py

diff --git a/jcvi/projects/alfalfa.py b/jcvi/projects/alfalfa.py
deleted file mode 100644
index 3a67b7c3..00000000
--- a/jcvi/projects/alfalfa.py
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: UTF-8 -*-
-
-"""
-Random collection of scripts associated with alfalfa assembly.
-"""
-
-import sys
-
-from jcvi.formats.bed import Bed, fastaFromBed
-from jcvi.graphics.mummerplot import main as mummerplot_main
-from jcvi.apps.base import OptionParser, ActionDispatcher, sh
-
-
-def main():
-
-    actions = (("nucmer", "select specific chromosome region based on MTR mapping"),)
-    p = ActionDispatcher(actions)
-    p.dispatch(globals())
-
-
-def nucmer(args):
-    """
-    %prog nucmer mappings.bed MTR.fasta assembly.fasta chr1 3
-
-    Select specific chromosome region based on MTR mapping. The above command
-    will extract chr1:2,000,001-3,000,000.
-    """
-    p = OptionParser(nucmer.__doc__)
-    opts, args = p.parse_args(args)
-
-    if len(args) != 5:
-        sys.exit(not p.print_help())
-
-    mapbed, mtrfasta, asmfasta, chr, idx = args
-    idx = int(idx)
-    m1 = 1000000
-    bedfile = "sample.bed"
-    bed = Bed()
-    bed.add("\t".join(str(x) for x in (chr, (idx - 1) * m1, idx * m1)))
-    bed.print_to_file(bedfile)
-
-    cmd = "intersectBed -a {0} -b {1} -nonamecheck -sorted | cut -f4".format(
-        mapbed, bedfile
-    )
-    idsfile = "query.ids"
-    sh(cmd, outfile=idsfile)
-
-    sfasta = fastaFromBed(bedfile, mtrfasta)
-    qfasta = "query.fasta"
-    cmd = "faSomeRecords {0} {1} {2}".format(asmfasta, idsfile, qfasta)
-    sh(cmd)
-
-    cmd = "nucmer {0} {1}".format(sfasta, qfasta)
-    sh(cmd)
-
-    mummerplot_main(["out.delta", "--refcov=0"])
-    sh("mv out.pdf {0}.{1}.pdf".format(chr, idx))
-
-
-if __name__ == "__main__":
-    main()
diff --git a/jcvi/projects/misc.py b/jcvi/projects/misc.py
index 0a287434..2f4b8114 100644
--- a/jcvi/projects/misc.py
+++ b/jcvi/projects/misc.py
@@ -33,7 +33,6 @@ def main():
         ("oropetium", "plot oropetium micro-synteny (requires data)"),
         # Pomegranate paper (Qin et al., 2017 Plant Journal)
         ("pomegranate", "plot pomegranate macro- and micro-synteny (requires data)"),
-        # Unpublished
         ("birch", "plot birch macro-synteny (requires data)"),
         ("litchi", "plot litchi micro-synteny (requires data)"),
         ("utricularia", "plot utricularia micro-synteny (requires data)"),
diff --git a/jcvi/projects/pistachio.py b/jcvi/projects/pistachio.py
deleted file mode 100644
index 83e1ca93..00000000
--- a/jcvi/projects/pistachio.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: UTF-8 -*-
-
-"""
-Functions related to processing of the pistachio genome.
-"""
-import sys
-
-from jcvi.apps.base import OptionParser, ActionDispatcher
-
-
-def main():
-
-    actions = (("agp", "convert from the table file to agp format"),)
-    p = ActionDispatcher(actions)
-    p.dispatch(globals())
-
-
-def agp(args):
-    """
-    %prog agp Siirt_Female_pistachio_23May2017_table.txt
-
-    The table file, as prepared by Dovetail Genomics, is not immediately useful
-    to convert gene model coordinates, as assumed by formats.chain.fromagp().
-    This is a quick script to do such conversion. The file structure of this
-    table file is described in the .manifest file shipped in the same package::
-
-    pistachio_b_23May2017_MeyIy.table.txt
-        Tab-delimited table describing positions of input assembly scaffolds
-        in the Hirise scaffolds. The table has the following format:
-
-            1. HiRise scaffold name
-            2. Input sequence name
-            3. Starting base (zero-based) of the input sequence
-            4. Ending base of the input sequence
-            5. Strand (- or +) of the input sequence in the scaffold
-            6. Starting base (zero-based) in the HiRise scaffold
-            7. Ending base in the HiRise scaffold
-
-        where '-' in the strand column indicates that the sequence is reverse
-        complemented relative to the input assembly.
-
-    CAUTION: This is NOT a proper AGP format since it does not have gaps in
-    them.
-    """
-    p = OptionParser(agp.__doc__)
-    opts, args = p.parse_args(args)
-
-    if len(args) != 1:
-        sys.exit(not p.print_help())
-
-    (tablefile,) = args
-    fp = open(tablefile)
-    for row in fp:
-        atoms = row.split()
-        hr = atoms[0]
-        scaf = atoms[1]
-        scaf_start = int(atoms[2]) + 1
-        scaf_end = int(atoms[3])
-        strand = atoms[4]
-        hr_start = int(atoms[5]) + 1
-        hr_end = int(atoms[6])
-
-        print(
-            "\t".join(
-                str(x)
-                for x in (
-                    hr,
-                    hr_start,
-                    hr_end,
-                    1,
-                    "W",
-                    scaf,
-                    scaf_start,
-                    scaf_end,
-                    strand,
-                )
-            )
-        )
-
-
-if __name__ == "__main__":
-    main()