mapp2g 0.1.1 → 0.1.2
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- checksums.yaml +4 -4
- data/exe/mapp2g +31 -4
- data/lib/mapp2g/version.rb +1 -1
- data/scripts/mapp2g-exonerate_gff2_to_jbgff3.rb +28 -0
- metadata +3 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 2d3b7c217addd7e92a9b0dc4d2af710c216d7dbcf86c2416018ac80bee287e1c
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4
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+
data.tar.gz: 562dbf402617e18af3b2e32cb32fb1e5f157ec783aaa6b61f2f44a5cf3877acc
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 6df38d0b72858bd49d354d0b72eeca57a70cfc80a075444bcffd8ecfcd4b59945395a76a3d38e70caea74254bce0e62f82039f15db6ca23566204444bc9bb5b2
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7
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+
data.tar.gz: 01174fd8de53e2e5f7d6a3021ff8789b242a53af4d8968bc3eaf6c3e1c67795826af82b95e7f0c1290e6c9d888d560d4488de5f1de4774c78d3b793dd52f2dcf
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data/exe/mapp2g
CHANGED
@@ -3,11 +3,38 @@
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3
3
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require "mapp2g"
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4
4
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require 'bio'
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5
5
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require 'tempfile'
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6
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+
require 'optparse'
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6
7
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7
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-
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8
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-
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9
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-
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10
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-
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8
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+
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9
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opt = OptionParser.new
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10
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OPTS = {}
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11
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12
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begin
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13
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#opt.banner = "Usage: #{opt.program_name} [options] QUERY GENOME "
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14
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opt.on_tail("-v", "--version", "show version number") do
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15
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puts Mapp2g::VERSION
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16
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exit
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17
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end
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18
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opt.on("-q QUERY", "--query", "query amino acid sequences in FASTA format"){|v| OPTS[:q] = v}
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19
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opt.on("-g BLASTDB", "--genome", "genome reference as blastdb"){|v| OPTS[:g] = v}
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20
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opt.on("-o [OUTDIR]", "--outdir", "output directory. DEFAULT: mapp2g_out_{process_id}"){|v| OPTS[:o] = v}
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21
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opt.on_tail('-h', '--help', 'show this help message and exit') do
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puts opt
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23
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exit
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24
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end
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25
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opt.parse!(ARGV)
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26
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rescue => e
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27
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puts "ERROR: #{e}\nSee #{opt}"
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28
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exit
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29
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end
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30
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+
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31
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# p OPTS
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32
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33
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query = OPTS[:q]
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34
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genome = OPTS[:g]
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35
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outdir = (OPTS[:o] || "mapp2g_out_#{$$}")
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36
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+
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37
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#p [query, genome, outdir]
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11
38
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12
39
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Dir.mkdir(outdir)
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13
40
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data/lib/mapp2g/version.rb
CHANGED
@@ -0,0 +1,28 @@
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1
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+
name = nil
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2
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target = nil
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3
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ARGF.each do |l|
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4
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+
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5
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if m = /\s+Query:\s/.match(l)
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6
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name = m.post_match.chomp.split[0]
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7
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elsif m = /\s+Target:\s/.match(l)
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8
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target = m.post_match.split[0]
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9
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elsif /^#{target}/.match(l) &&
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10
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(/\texonerate:est2genome\t/.match(l) || /\texonerate:protein2genome:local\t/.match(l)) &&
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11
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(/\tcds\t/.match(l) || /\texon\t/.match(l) || /\tgene\t/.match(l))
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12
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# puts l
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13
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a = l.chomp.split(/\t/)
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14
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b = Array.new(9)
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15
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a.each_with_index{|x, i| b[i] = x}
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16
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if b[2] == "gene"
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b[-1] = "ID=#{name}"
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18
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b[2] = "match"
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19
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elsif (b[2] == "cds" || b[2] == "exon")
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20
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b[-1] = "Parent=#{name}"
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21
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b[2] = "match_part"
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else
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raise
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end
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25
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puts b.join("\t")
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26
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end
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27
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28
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end
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: mapp2g
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version: !ruby/object:Gem::Version
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4
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-
version: 0.1.
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+
version: 0.1.2
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5
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platform: ruby
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authors:
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- Shuji Shigenobu
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autorequire:
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9
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bindir: exe
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cert_chain: []
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11
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-
date: 2023-02-
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+
date: 2023-02-05 00:00:00.000000000 Z
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dependencies: []
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description: mapp2g is a bioinformatics software, which map and align protein sequences
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(amino acid sequences) to genome references in a splicing-aware way. mapp2g alignment
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@@ -30,6 +30,7 @@ files:
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30
30
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- lib/mapp2g/mapper.rb
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31
31
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- lib/mapp2g/version.rb
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32
32
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- mapp2g.gemspec
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33
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+
- scripts/mapp2g-exonerate_gff2_to_jbgff3.rb
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33
34
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- sig/mapp2g.rbs
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34
35
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homepage: https://github.com/shujishigenobu/mapp2g
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35
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licenses:
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