Mercurial > repos > nml > srst2
annotate srst2.pl @ 1:599a4dc309aa draft
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
| author | nml |
|---|---|
| date | Wed, 01 Mar 2017 12:39:11 -0500 |
| parents | 6f870ed59b6e |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env perl |
| 2 | |
| 3 | |
| 4 use strict; | |
| 5 use warnings; | |
| 6 use Cwd; | |
| 7 use File::Copy; | |
| 8 | |
|
1
599a4dc309aa
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
nml
parents:
0
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changeset
|
9 #The first 3 arguments should be in this format: |
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599a4dc309aa
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
nml
parents:
0
diff
changeset
|
10 # bam_output scores_output pileup_output ... |
| 0 | 11 |
| 12 | |
| 13 my ($bam_results, $scores, $pileup, $job_type, $txt_results, $genes_results, $fullgenes_results, $name, $databases); | |
| 14 my ($allele_results,$allele_type); | |
| 15 | |
| 16 | |
| 17 $bam_results = $ARGV[0]; | |
| 18 shift(@ARGV); | |
| 19 $scores = $ARGV[0]; | |
| 20 shift(@ARGV); | |
| 21 $pileup = $ARGV[0]; | |
| 22 shift(@ARGV); | |
| 23 | |
| 24 #Now that we shifted the first 4 arguments, get the rest depending on the job type. There are three: | |
| 25 #I pass a letter to tell us which job type was selected. | |
| 26 $job_type = $ARGV[0]; | |
| 27 shift(@ARGV); | |
| 28 | |
| 29 #If m, mlst only: we only have one mlst output file | |
| 30 if($job_type eq "m") | |
| 31 { | |
| 32 $txt_results = $ARGV[0]; | |
| 33 shift(@ARGV); | |
| 34 $allele_results = $ARGV[0]; | |
| 35 shift(@ARGV); | |
| 36 $allele_type = $ARGV[0]; | |
| 37 shift(@ARGV); | |
| 38 } | |
| 39 #If g, genedb only: we have two outputs: genes and fullgenes. We also get the name of the database | |
| 40 elsif($job_type eq "g") | |
| 41 { | |
| 42 $genes_results = $ARGV[0]; | |
| 43 shift(@ARGV); | |
| 44 $fullgenes_results = $ARGV[0]; | |
| 45 shift(@ARGV); | |
| 46 $databases = $ARGV[0]; | |
| 47 shift (@ARGV); | |
| 48 } | |
| 49 #If b, both mlst and genedb: We will have three output files and the database name. | |
| 50 else | |
| 51 { | |
| 52 $txt_results = $ARGV[0]; | |
| 53 shift(@ARGV); | |
| 54 $genes_results = $ARGV[0]; | |
| 55 shift(@ARGV); | |
| 56 $fullgenes_results = $ARGV[0]; | |
| 57 shift(@ARGV); | |
| 58 $databases = $ARGV[0]; | |
| 59 shift(@ARGV); | |
| 60 } | |
| 61 | |
| 62 #After we get the output files/database name, now we get the name of the reads | |
| 63 #This allows SRST2 to give meaningful output instead of just printing 'dataset_xxx' as the sample name | |
| 64 my $filename = $ARGV[0]; | |
| 65 shift(@ARGV); | |
| 66 | |
| 67 #This index offset is used to determine where the 'genedb' option is located. | |
| 68 #If only a single-end input, the genedb will be 3 positions into the arguments: | |
| 69 # -input_se sample.fastq --genedb database.fasta | |
| 70 my $index_offset = 3; | |
| 71 | |
| 72 print @ARGV; | |
| 73 #change the file extensions of the input reads so srst can use them | |
| 74 | |
| 75 #Usually the file name looks like this: sample_S1_L001_R1_001.fastq | |
| 76 #If we use this file name, it confuses srst2 a lot. So we just extract | |
| 77 #the sample name to use as input file name. | |
| 78 my @file_name = split /_/, $filename; | |
| 79 $name = "temp_file_name"; | |
| 80 | |
| 81 my ($for_read, $rev_read, $sing_read, $database); | |
| 82 if ($ARGV[0] eq "--input_pe") | |
| 83 { | |
| 84 #Increment index offset if we paired-end inputs | |
| 85 $index_offset++; | |
| 86 | |
| 87 $for_read = $name."_1.dat"; | |
| 88 $rev_read = $name."_2.dat"; | |
| 89 | |
| 90 symlink($ARGV[1], $for_read); | |
| 91 symlink($ARGV[2], $rev_read); | |
| 92 | |
| 93 $ARGV[1] = $for_read; | |
| 94 $ARGV[2] = $rev_read; | |
| 95 } | |
| 96 else | |
| 97 { | |
| 98 $sing_read = $name.".dat"; | |
| 99 | |
| 100 symlink($ARGV[1], $sing_read); | |
| 101 | |
| 102 $ARGV[1] = $sing_read; | |
| 103 | |
| 104 } | |
| 105 #If we are running a job to include genedb, use the database name for input file name | |
| 106 if ($job_type eq 'g' | $job_type eq 'b') | |
| 107 { | |
| 108 my @db_names = split /,/, $databases; | |
| 109 my $num_db = @db_names; | |
| 110 my %names_hash = (); | |
| 111 # loop through dbs to replace spaces with _ and check for duplicates | |
| 112 for (my $i = 0; $i < $num_db; $i++){ | |
| 113 $db_names[$i]=~s/ /_/g; | |
| 114 if( exists($names_hash{$db_names[$i]}) ) { | |
| 115 print STDERR "More than one database with the same name"; | |
| 116 exit(1); | |
| 117 }else{ | |
| 118 $names_hash{$db_names[$i]}=$db_names[$i]; | |
| 119 } | |
| 120 } | |
| 121 | |
| 122 | |
| 123 foreach my $db_name (@db_names){ | |
| 124 (my $base = $db_name) =~ s/\.[^.]+$//; | |
| 125 $database = $base.".dat"; | |
| 126 | |
| 127 symlink($ARGV[$index_offset], $database); | |
| 128 $ARGV[$index_offset] = $database; | |
| 129 | |
| 130 $index_offset++; | |
| 131 } | |
| 132 } | |
| 133 | |
| 134 for (my $i =0; $i< @ARGV; $i++){ | |
| 135 if (index($ARGV[$i], "maxins") != -1){ | |
| 136 my ($maxins, $minins); | |
| 137 my @b2args = split(' ', $ARGV[$i]); | |
| 138 for (my $j = 0; $j < @b2args; $j++){ | |
| 139 if (index($b2args[$j], "maxins") != -1){ | |
| 140 $maxins = $b2args[$j+1]; | |
| 141 } | |
| 142 if (index($b2args[$j], "minins") != -1){ | |
| 143 $minins = $b2args[$j+1]; | |
| 144 } | |
| 145 } | |
| 146 if ($maxins - $minins < 0){ | |
| 147 print STDERR "--minins cannot be greater than --maxins"; | |
| 148 exit(1); | |
| 149 } | |
| 150 } | |
| 151 } | |
| 152 | |
| 153 | |
| 154 | |
|
1
599a4dc309aa
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
nml
parents:
0
diff
changeset
|
155 my $command = "srst2 @ARGV"; |
| 0 | 156 |
| 157 my $exit_code = system($command); | |
| 158 | |
| 159 my $cur_dir = getcwd(); | |
| 160 # make arrays for using multiple custom databases (creates multiple output files - need to be concatenated) | |
| 161 my (@genefiles, @bamfiles, @pileupfiles, @fullgenefiles, @scoresfiles); | |
| 162 | |
| 163 # go through files in the output directory to move/concatenate them as required. | |
| 164 | |
| 165 foreach my $file (<$cur_dir/*>) | |
| 166 { | |
| 167 print $file, "\n"; | |
| 168 #Will cause problems if any files have 'mlst' in them | |
| 169 if ($file =~ /mlst/) | |
| 170 { | |
| 171 move($file, $txt_results); | |
| 172 } | |
| 173 elsif ($file =~ /\.bam$/) | |
| 174 { | |
| 175 push @bamfiles, $file; | |
| 176 } | |
| 177 elsif ($file =~ /\.scores$/) | |
| 178 { | |
| 179 push @scoresfiles, $file; | |
| 180 } | |
| 181 elsif ($file =~ /\.pileup$/) | |
| 182 { | |
| 183 push @pileupfiles, $file; | |
| 184 } | |
| 185 elsif ($file =~ /__fullgenes__/) | |
| 186 { | |
| 187 push @fullgenefiles, $file; | |
| 188 } | |
| 189 elsif ($file =~ /__genes__/) | |
| 190 { | |
| 191 push @genefiles, $file; | |
| 192 } | |
| 193 elsif ($file =~ /all_consensus_alleles.fasta$/ && $allele_type eq 'all') { | |
| 194 move($file,$allele_results); | |
| 195 } | |
| 196 elsif ($file =~ /new_consensus_alleles.fasta$/ && $allele_type eq 'new'){ | |
| 197 move($file,$allele_results); | |
| 198 } | |
| 199 } | |
| 200 | |
| 201 | |
| 202 my ($cmd, $temp_head, $temp_full, $cat_header, $final_bam, @headers ); | |
| 203 | |
| 204 # create new concatenated bam file with all bam files. | |
| 205 if (@bamfiles > 1){ | |
| 206 my $counter = 0; | |
| 207 $cat_header = "cat_header"; | |
| 208 while ($counter < @bamfiles) { | |
| 209 $headers[$counter] = "bam_header".$counter; | |
| 210 # make a header file for each bam results file | |
| 211 my $cmd = "samtools view -H $bamfiles[$counter] > $headers[$counter]"; | |
| 212 system($cmd); | |
| 213 if ($counter >= 1){ | |
| 214 # only keep the @hd and @pg from first file because the final concatenated file can only have one of each (doesn't matter location) | |
| 215 $temp_head="cut_head".$counter; | |
| 216 # cut off first row and last row of each file (the @HD and @PG) | |
| 217 $cmd = "tail -n +2 $headers[$counter] | head -n -1 > $temp_head"; | |
| 218 system($cmd); | |
| 219 unlink $headers[$counter]; | |
| 220 # replace the old header with the new cut header in the array | |
| 221 $headers[$counter] = $temp_head; | |
| 222 } | |
| 223 $counter++; | |
| 224 } | |
| 225 # combine all header files | |
| 226 $cmd = "cat ".join(" ",@headers)." > $cat_header"; | |
| 227 system($cmd); | |
| 228 | |
| 229 $final_bam = "final_bam"; | |
| 230 # concatenate all the bam files *must include the concatenated header file created above | |
| 231 $cmd = "samtools cat -h $cat_header -o $final_bam ".join(" ",@bamfiles)." "; | |
| 232 system($cmd); | |
| 233 | |
| 234 # sort the bam file so it can be indexed | |
| 235 $cmd = "samtools sort $final_bam 'last_bam'"; | |
| 236 system($cmd); | |
| 237 | |
| 238 # move bam file to where Galaxy expects it. | |
| 239 $cmd = "mv 'last_bam.bam' $bam_results"; | |
| 240 system($cmd); | |
| 241 } else { | |
| 242 # only one bam file, don't need to concatenate | |
| 243 move($bamfiles[0], $bam_results); | |
| 244 } | |
| 245 | |
| 246 # concatenate all pileup files | |
| 247 if (@pileupfiles > 1){ | |
| 248 $cmd = "cat ".join(" ",@pileupfiles)." > $pileup"; | |
| 249 system($cmd); | |
| 250 } else { | |
| 251 move($pileupfiles[0], $pileup); | |
| 252 } | |
| 253 | |
| 254 # perform find-replace to restore original user-specified file names | |
| 255 foreach my $gene (@genefiles){ | |
| 256 my $data = read_file($gene); | |
| 257 $data =~ s/temp_file_name/$file_name[0]/g; | |
| 258 write_file($gene, $data); | |
| 259 } | |
| 260 | |
| 261 foreach my $gene (@fullgenefiles){ | |
| 262 my $data = read_file($gene); | |
| 263 $data =~ s/temp_file_name/$file_name[0]/g; | |
| 264 write_file($gene, $data); | |
| 265 } | |
| 266 | |
| 267 # concatenate gene files with a space separating each file | |
| 268 if (@genefiles > 1){ | |
| 269 my $join = join(" <(echo) ", @genefiles); | |
| 270 my @args = ("bash", "-c", "cat $join > $genes_results"); | |
| 271 system(@args); | |
| 272 } else { | |
| 273 # only one gene results file | |
| 274 move($genefiles[0], $genes_results); | |
| 275 } | |
| 276 | |
| 277 # concatenate full gene results files but only keep header in first file. | |
| 278 if (@fullgenefiles >1){ | |
| 279 for (my $i= 1; $i < @fullgenefiles; $i++){ | |
| 280 # go through all files but the first one to remove headers | |
| 281 # create a temp file to save the file after header is removed | |
| 282 $temp_full = "temp_full".$i; | |
| 283 $cmd = "tail -n +2 $fullgenefiles[$i] > $temp_full"; | |
| 284 system($cmd); | |
| 285 unlink $fullgenefiles[$i]; | |
| 286 $fullgenefiles[$i] = $temp_full; | |
| 287 } | |
| 288 $cmd = "cat ". join(" ",@fullgenefiles)." > $fullgenes_results"; | |
| 289 system($cmd); | |
| 290 } else{ | |
| 291 # only one full gene results file | |
| 292 move($fullgenefiles[0], $fullgenes_results); | |
| 293 } | |
| 294 | |
| 295 # concatenate full gene results files but only keep header in first file. | |
| 296 if (@scoresfiles >1){ | |
| 297 for (my $i= 1; $i < @scoresfiles; $i++){ | |
| 298 # go through all files but the first one to remove headers | |
| 299 # create a temp file to save the file after header is removed | |
| 300 $temp_full = "temp_full".$i; | |
| 301 $cmd = "tail -n +2 $scoresfiles[$i] > $temp_full"; | |
| 302 system($cmd); | |
| 303 unlink $scoresfiles[$i]; | |
| 304 $scoresfiles[$i] = $temp_full; | |
| 305 } | |
| 306 $cmd = "cat ". join(" ",@scoresfiles)." > $scores"; | |
| 307 system($cmd); | |
| 308 } else{ | |
| 309 # only one scores file | |
| 310 move($scoresfiles[0], $scores); | |
| 311 } | |
| 312 | |
| 313 # cleanup srst2 output and temp files | |
| 314 foreach my $file (@fullgenefiles){ | |
| 315 unlink $file; | |
| 316 } | |
| 317 foreach my $file (@genefiles){ | |
| 318 unlink $file; | |
| 319 } | |
| 320 foreach my $file (@pileupfiles){ | |
| 321 unlink $file; | |
| 322 } | |
| 323 foreach my $file (@bamfiles){ | |
| 324 unlink $file; | |
| 325 } | |
| 326 foreach my $file (@headers){ | |
| 327 unlink $file; | |
| 328 } | |
| 329 foreach my $file (@scoresfiles){ | |
| 330 unlink $file; | |
| 331 } | |
| 332 unlink $temp_head; | |
| 333 unlink $temp_full; | |
| 334 unlink $cat_header; | |
| 335 unlink $final_bam; | |
| 336 | |
| 337 #get rid of symlinks | |
| 338 if ($for_read) | |
| 339 { | |
| 340 unlink $for_read; | |
| 341 } | |
| 342 if ($rev_read) | |
| 343 { | |
| 344 unlink $rev_read; | |
| 345 } | |
| 346 if ($sing_read) | |
| 347 { | |
| 348 unlink $sing_read; | |
| 349 } | |
| 350 if ($database) | |
| 351 { | |
| 352 unlink $database; | |
| 353 } | |
| 354 $exit_code = $exit_code >> 8; | |
| 355 exit $exit_code; | |
| 356 | |
| 357 sub read_file { | |
| 358 my ($filename) = @_; | |
| 359 | |
| 360 open my $in, '<:encoding(UTF-8)', $filename or die "Could not open '$filename' for reading $!"; | |
| 361 local $/ = undef; | |
| 362 my $all = <$in>; | |
| 363 close $in; | |
| 364 | |
| 365 return $all; | |
| 366 } | |
| 367 | |
| 368 sub write_file { | |
| 369 my ($filename, $content) = @_; | |
| 370 | |
| 371 open my $out, '>:encoding(UTF-8)', $filename or die "Could not open '$filename' for writing $!";; | |
| 372 print $out $content; | |
| 373 close $out; | |
| 374 | |
| 375 return; | |
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1
599a4dc309aa
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
nml
parents:
0
diff
changeset
|
376 } |