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comparison PanExplorer_workflow/Perl/wget.pl @ 1:032f6b3806a3 draft

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author dereeper
date Thu, 30 May 2024 11:16:08 +0000
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0:3cbb01081cde 1:032f6b3806a3
1 #!/usr/bin/perl
2
3 use strict;
4
5 use File::Basename;
6 my $dirname = dirname(__FILE__);
7
8 system("wget https://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt");
9 system("wget https://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/eukaryotes.txt");
10
11 my %continents;
12 open(F,"countries.txt");
13 <F>;
14 while(my $line =<F>){
15 chomp($line);
16 my ($continent,$country) = split(/,/,$line);
17 $continents{$country} = $continent;
18 }
19 close(F);
20
21 my $input = $ARGV[0];
22 my $outdir = $ARGV[1];
23 my $private_genomes = $ARGV[2];
24
25 system("cat $input $private_genomes >$outdir/list.txt");
26
27 my $concat = "";
28 open(O2,">$outdir/genbanks.txt");
29 open(O,">$outdir/strains.txt");
30 open(GENES,">$outdir/genes.txt");
31 open(L,">$outdir/list_genomes.txt");
32 open(L2,">$outdir/list_genomes2.txt");
33 open(L3,">$outdir/genomes.txt");
34 open(L4,">$outdir/genomes2.txt");
35 open(SEQFILE,">$outdir/seqfile");
36 open(PanSN,">$outdir/all_genomes.fa");
37 open(METADATA,">$outdir/metadata_strains.txt");
38
39 open(F,"$outdir/list.txt");
40 #open(TEST,">$outdir/test");
41 while(my $line =<F>){
42 chomp($line);
43 my $genbank = $line;
44 if (!-e "$genbank"){
45 my $grep = `grep '$line' prokaryotes.txt`;
46 #print "$genbank $line aaa $grep\n";exit;
47 my @infos = split(/\t/,$grep);
48 my $status = $infos[15];
49 if ($status !~/Complete Genome/ && $status !~/Chromosome/){
50 #next;
51 }
52 my $ftp_path = $infos[$#infos -2];
53
54 $ftp_path =~s/ftp:/http:/g;
55 my @table = split(/\//,$ftp_path);
56 my $name = $table[$#table];
57 my $prot_file = "$ftp_path/$name"."_protein.faa.gz";
58 my $gbff = "$ftp_path/$name"."_genomic.gbff.gz";
59 my $gff = "$ftp_path/$name"."_genomic.gff.gz";
60 my $genome_fasta = "$ftp_path/$name"."_genomic.fna.gz";
61 my @particules = split(/_/,$name);
62
63 `wget -O $outdir/$genbank.fasta.gz $genome_fasta`;
64 `gunzip $outdir/$genbank.fasta.gz`;
65 `wget -O $outdir/$genbank.gb.gz $gbff`;
66 system("gunzip $outdir/$genbank.gb.gz");
67
68
69 ################################################################
70 # for eukaryotes
71 ################################################################
72 if (!$grep){
73 $grep = `grep '$line' eukaryotes.txt`;
74 my @infos = split(/\t/,$grep);
75 my $gca = $infos[8];
76 if ($gca =~/GCA_(\d\d\d)(\d\d\d)(\d\d\d)/){
77 my $part1 = $1;
78 $ftp_path = "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$1/$2/$3";
79 `wget -O $outdir/$gca.index.html $ftp_path`;
80 my $grep_name = `grep '$gca' $outdir/$gca.index.html`;
81 unlink("$outdir/$gca.index.html");
82 my $name;
83 if ($grep_name =~/href=\"(.*)\"/){
84 $name = $1;
85 $name=~s/\///g;
86 }
87 $ftp_path = $ftp_path."/$name";
88 my $prot_file = "$ftp_path/$name"."_protein.faa.gz";
89 my $gbff = "$ftp_path/$name"."_genomic.gbff.gz";
90 my $gff = "$ftp_path/$name"."_genomic.gff.gz";
91 my $genome_fasta = "$ftp_path/$name"."_genomic.fna.gz";
92 my @particules = split(/_/,$name);
93
94 `wget -O $outdir/$genbank.fasta.gz $genome_fasta`;
95 `gunzip $outdir/$genbank.fasta.gz`;
96 `wget -O $outdir/$genbank.gb.gz $gbff`;
97 `wget -O $outdir/$genbank.faa.gz $prot_file`;
98 system("gunzip $outdir/$genbank.gb.gz");
99 system("gunzip $outdir/$genbank.faa.gz");
100
101 }
102 }
103 }
104 else{
105 my $genbank_file = $genbank;
106 my $grep = `grep 'LOCUS' $genbank_file`;
107 $genbank = "unknown";
108 if ($grep =~/LOCUS\s+([\-\:\w]+)/){$genbank = $1;}
109
110 #$genbank =~s/\:/_/g;
111
112 my $cmd = "cp -rf $genbank_file $outdir/$genbank.gb";
113 system($cmd);
114
115 my %genome_seqs;
116 my $current_chr;
117 my $go = 0;
118 open(G,"$outdir/$genbank.gb");
119 while(<G>){
120 if ($go == 1 && /(\d+) (.*)$/){
121 my $line = $2;
122 $line =~s/ //g;
123 $genome_seqs{$current_chr}.=$line;
124 }
125 if (/LOCUS ([^\s]+)/){
126 $current_chr = $1;
127 }
128 if (/ORIGIN/){$go = 1;}
129 if (/^\/\//){$go = 0;}
130 }
131 close(G);
132
133 open(FASTA,">$outdir/$genbank.fasta");
134 foreach my $ch(keys(%genome_seqs)){
135 print FASTA ">$ch\n";
136 my $seq = $genome_seqs{$ch};
137 print FASTA "$seq\n";
138 }
139 close(FASTA);
140 }
141 #my $get_organism_line = `head -10 $outdir/$genbank.gb | grep DEFINITION `;
142 my $get_organism_line = `head -10 $outdir/$genbank.gb | grep -A 1 DEFINITION `;
143
144 # if several lines for DEFINITION, concatenate the lines
145 my @lines_organism = split(/\n/,$get_organism_line);
146 my $first_line = $lines_organism[0];
147 my $second_line = $lines_organism[1];
148 if ($second_line =~/^ (.*)/){
149 $get_organism_line = $first_line. " ".$1;
150 }
151 else{
152 $get_organism_line = $first_line;
153 }
154
155 my $strain;
156 my $genus;
157 if ($get_organism_line =~/DEFINITION (.*)$/){
158 $strain = $1;
159 ($genus) = split(/\s/,$strain);
160 }
161 my $country = `head -100 $outdir/$genbank.gb | grep country `;
162 $country =~s/^\s+//g;
163 $country =~s/\/country=//g;
164 $country =~s/\"//g;
165 $country =~s/\n//g;$country =~s/\r//g;
166 if ($country =~/:/){
167 my $city;
168 ($country,$city) = split(/:/,$country);
169 }
170 if ($country eq ""){$country = "unresolved";}
171 my $continent = "unresolved";
172 if ($continents{$country}){
173 $continent = $continents{$country};
174 }
175 $strain =~s/\.//g;
176 my ($info1,$info2 ) = split(",",$strain);
177 $strain = $info1;
178 $strain =~s/ /_/g;
179 $strain =~s/strain_//g;
180 $strain =~s/_chromosome//g;
181 $strain =~s/_genome//g;
182 $strain =~s/_str_/_/g;
183 $strain =~s/[^\w\-\_]//g;
184 $strain =~s/\-/_/g;
185
186 print O "$genbank $strain\n";
187 $concat .= "$genbank,";
188 print L "$genbank $outdir/$genbank.gb\n";
189 print L2 "$genbank\n";
190 print L3 "$outdir/$genbank.fasta\n";
191 print L4 "$outdir/$genbank.fasta $strain\n";
192 print SEQFILE "$genbank $outdir/$genbank.fasta\n";
193 print METADATA "$strain\t$genus\t$country\t$continent\n";
194
195
196 my %genome_sequences;
197 my $genome = "";
198 my $seqid = "";
199 open(GENOME,"$outdir/$genbank.fasta");
200 while(<GENOME>){
201 if (!/^>/){
202 my $line = $_;
203 $line =~s/\n//g;$line =~s/\r//g;
204 $genome_sequences{$seqid} .= $line;
205 $genome .= $line;
206 print PanSN $_;
207 }
208 elsif (/>([^\s]+)/){
209 $seqid = $1;
210 $seqid =~s/\.\d+$//g;
211 print PanSN ">$strain#$seqid\n";
212 }
213 }
214 close(GENOME);
215
216
217 open(N,">$outdir/$genbank.nuc");
218 open(P,">$outdir/$genbank.pep");
219 open(FUNC,">$outdir/$genbank.func");
220 my $go = 0;
221 my $start;
222 my $end;
223 my $product;
224 my $complement = 0;
225 my $end_gene = "no";
226 my $protein = "";
227
228 #`sed -i "s/'//g" $outdir/$genbank.gb`;
229
230 my $has_translation = `grep -c 'translation=' $outdir/$genbank.gb`;
231 $has_translation =~s/\n//g;$has_translation =~s/\r//g;
232 open(G,"$outdir/$genbank.gb");
233 my $current_gene;
234 my $current_chrom;
235 while(<G>){
236 if (/^\s+ORGANISM\s+(.*)$/){
237 }
238 if (/protein_id=\"(.*)\"/){
239 $current_gene = $1;
240 }
241 if (/LOCUS ([^\s]+)/){
242 $current_chrom = $1;
243 }
244 if (/locus_tag=\"(.*)\"/){
245 $current_gene = $1;
246 }
247 if ($go == 1){
248 my $line = $_;
249 $line =~s/ //g;
250 $line =~s/\n//g;$line =~s/\r//g;
251 $protein .= $line;
252 if (/\"$/){
253 $protein =~s/\"//g;
254 $end_gene = "yes";
255
256 }
257 }
258 if (/\/translation=\"(.*)/ or ($has_translation == 0 && /protein_id=/)){
259 $go = 1;
260 $protein .= $1;
261 print P ">$current_gene\n";
262 print N ">$current_gene\n";
263 print GENES "$current_gene $product [$strain]\n";
264
265 if ($protein =~/\"$/){
266 $end_gene = "yes";
267 }
268 if ($has_translation == 0){$end_gene = "yes";}
269 }
270 if ($end_gene eq "yes"){
271 $protein =~s/\"//g;
272 print P "$protein\n";
273 $protein = "";
274 my $length = $end - $start + 1;
275
276 #print "okkkk $current_chrom\n";
277 #my $geneseq = substr($genome,$start-1,$length);
278 my $geneseq = substr($genome_sequences{$current_chrom},$start-1,$length);
279
280
281 if ($complement){
282 my $revcomp = reverse $geneseq;
283 $revcomp =~ tr/ATGCatgc/TACGtacg/;
284 $geneseq = $revcomp;
285 }
286 print N "$geneseq\n";
287 print FUNC "$current_gene - $product\n";
288 $go = 0;
289 $end_gene = "no";
290 }
291 if (/\/product=\"(.*)\"/){
292 $product = $1;
293 }
294 if (/^\s+CDS\s+(\d+)\.\.(\d+)\s*$/){
295 $start = $1;
296 $end = $2;
297 $complement = 0;
298 }
299 if (/^\s+CDS\s+complement\((\d+)\.\.(\d+)\)\s*$/){
300 $start = $1;
301 $end = $2;
302 $complement = 1;
303 }
304 }
305 close(G);
306 close(P);
307 close(N);
308 close(FUNC);
309
310 if ($has_translation == 0){
311 system("perl $dirname/translate.pl $outdir/$genbank.nuc $outdir/$genbank.pep");
312 }
313
314 my $prot_num = 0;
315 open(PRT,">$outdir/$genbank.prt");
316 open(P,"$outdir/$genbank.pep");
317 while(<P>){
318 if (/>(.*)/){
319 my $prot_id = $1;
320 $prot_num++;
321 my $new_id = "$strain"."_".$prot_num;
322 print PRT ">$new_id\n";
323 }
324 else{
325 print PRT $_;
326 }
327 }
328 close(P);
329 close(PRT);
330 }
331 close(F);
332 close(O);
333 close(METADATA);
334 chop($concat);
335 print O2 $concat;
336 close(O2);
337 close(L);
338 close(L2);
339 close(L3);
340 close(L4);
341 close(GENES);
342 close(SEQFILE);
343 close(PanSN);
344 #close(TEST);
345
346 unlink("prokaryotes.txt");
347 unlink("eukaryotes.txt");