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 |