Commit 6342e605765fd2f5b9171c1ced4e92a19438c5e3
1 parent
f03ad4a854
Exists in
master
Added the option to give an input file for the full proteins to locateFragment.pl
Showing 1 changed file with 21 additions and 3 deletions Side-by-side Diff
locateFragment.pl
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6342e60
... | ... | @@ -169,8 +169,13 @@ |
169 | 169 | |
170 | 170 | my ($frag, $acc) = @_; |
171 | 171 | |
172 | + | |
173 | +# print Data::Dumper->Dump([$frag, $acc, $accFile ], [qw(*frag *acc *accFile)]); | |
174 | +# exit; | |
175 | + | |
176 | + | |
172 | 177 | #Sequence for full protein |
173 | - my $accSeq = "$outdir/${acc}.faa"; | |
178 | + my $accSeq = (-f $accFile)? $accFile : "$outdir/${acc}.faa"; | |
174 | 179 | |
175 | 180 | |
176 | 181 | #Save fragment to file |
... | ... | @@ -237,6 +242,14 @@ |
237 | 242 | #Default value for output directory |
238 | 243 | $outdir = "." unless ($outdir); |
239 | 244 | system "mkdir -p $outdir" unless (-d $outdir); |
245 | + | |
246 | + #When accession is not given, take the first part of the input file name as accession | |
247 | + unless ($accession) { | |
248 | + my @pathComp = split(/\//, $accFile); | |
249 | + $accession = $pathComp[-1]; | |
250 | + $accession =~ s/(\.faa|\.fasta)$//g; | |
251 | + } | |
252 | + | |
240 | 253 | } |
241 | 254 | |
242 | 255 | |
... | ... | @@ -327,8 +340,13 @@ |
327 | 340 | |
328 | 341 | Options |
329 | 342 | |
330 | --a, --accession {String} (Mandatory) | |
331 | - NCBI accession of query protein | |
343 | + | |
344 | +-i, --acc-file {PATH} (Mandataory if option -a is not given) | |
345 | + File with the full sequence in fasta format of the proteins where the | |
346 | + fragment will be identified. This opeiont | |
347 | + | |
348 | +-a, --accession {String} (Mandatory if option -i is not given) | |
349 | + NCBI accession of query protein. | |
332 | 350 | |
333 | 351 | -f, --fragment {String} (Mandatory) |
334 | 352 | Sequence fragment to locate within the full protein |