full_lengther_next 0.9.9 → 1.0.0
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- checksums.yaml +4 -4
- data/bin/download_fln_dbs.rb +5 -5
- data/lib/full_lengther_next/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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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: 7800e4b0a50889d7b627ea4a01dc87629e30338e
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4
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+
data.tar.gz: 1dc9f576f8ebbc28e0e53ed822183ca40db94b6a
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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: c0898c6a4e46d5ac7d35baf1484e6aa45420f5b77412b3070a46fceded8803a49fc39b92a2dec94135a0dfa7d2060d34b3ea44da768a41849c9bd8734b3f3f1a
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7
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+
data.tar.gz: 0b11a85a7e6fb17647cffadbfbc0b6e8d9ba4105adb4edb624663dda47a13d983efa2932aa73abc08e024511b643d44b1e7bf38913cedca2778825f76e69ae84
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data/bin/download_fln_dbs.rb
CHANGED
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@@ -79,7 +79,7 @@ def compare_list(string, list)
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79
79
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return res
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80
80
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end
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81
81
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82
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-
def conecta_uniprot(my_array, formatted_db_path)
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82
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+
def conecta_uniprot(my_array, formatted_db_path, no_trembl)
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83
83
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84
84
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Dir.mkdir(formatted_db_path) if !File.exists?(formatted_db_path)
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85
85
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varsplic_out=File.join(formatted_db_path,'uniprot_sprot_varsplic.fasta.gz')
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@@ -91,7 +91,7 @@ def conecta_uniprot(my_array, formatted_db_path)
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91
91
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puts "connected to UniProt"
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92
92
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my_array.each do |db_group|
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93
93
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puts "Downloading #{db_group}"
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94
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-
download_uniprot(db_group, formatted_db_path)
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94
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+
download_uniprot(db_group, formatted_db_path, no_trembl)
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95
95
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end
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96
96
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97
97
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#archivo de variantes de splicing. POR QUE?
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@@ -102,13 +102,13 @@ def conecta_uniprot(my_array, formatted_db_path)
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102
102
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puts "isoform files downloaded"
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103
103
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end
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104
104
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105
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-
def download_uniprot(uniprot_group, formatted_db_path)
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105
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+
def download_uniprot(uniprot_group, formatted_db_path, no_trembl)
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106
106
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107
107
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sp_out=File.join(formatted_db_path,"uniprot_sprot_#{uniprot_group}.dat.gz")
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108
108
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tr_out=File.join(formatted_db_path,"uniprot_trembl_#{uniprot_group}.dat.gz")
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109
109
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$ftp.chdir("/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions")
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110
110
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$ftp.getbinaryfile("uniprot_sprot_#{uniprot_group}.dat.gz", sp_out)
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111
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-
$ftp.getbinaryfile("uniprot_trembl_#{uniprot_group}.dat.gz", tr_out)
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111
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+
$ftp.getbinaryfile("uniprot_trembl_#{uniprot_group}.dat.gz", tr_out) if !no_trembl
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112
112
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113
113
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puts "#{uniprot_group} files downloaded"
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114
114
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@@ -375,7 +375,7 @@ puts "\nTo set the path for storing databases, execute next line in your termina
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375
375
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download_ncrna(formatted_db_path, options[:no_download]) if !options[:no_ncrna]
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376
376
|
|
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377
377
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if !options[:no_download]
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378
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-
conecta_uniprot(options[:uniprot_div], formatted_db_path)
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378
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+
conecta_uniprot(options[:uniprot_div], formatted_db_path, options[:no_trembl])
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379
379
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end
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380
380
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381
381
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if !options[:no_uniprot]
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