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cleaned commented code and added STDERR messages for partial alignmen…
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…ts re #54
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@suryasaha
suryasaha committed Oct 7, 2015
1 parent 2c3f786 commit eb49376
Showing 1 changed file with 4 additions and 23 deletions.
27 changes: 4 additions & 23 deletions lib/Bio/GenomeUpdate/TPF.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -1641,7 +1641,6 @@ Returns the length of the accession. Added for use in switchover and trim files
$accession_prefix_last_base = _get_accession_coordinate_5prime ($accession, $bac_ref_start - 1 );
}
elsif($accession_prefix_orientation eq '-'){#count from 3' end
# $accession_prefix_last_base = _get_accession_length ($accession) - _get_accession_coordinate_3prime ($accession, $bac_ref_start - 1 );
$accession_prefix_last_base = _get_accession_coordinate_3prime ($accession, $bac_ref_start - 1 );
}

Expand Down Expand Up @@ -1715,21 +1714,6 @@ Returns the length of the accession. Added for use in switchover and trim files
if ($accession_suffix_orientation eq '-'){
$accession_suffix_first_base = $bac_query_end; #count from 3' if BAC on -ive strand
}
print STDERR "Creating switch point for transition from $accession with length ";
print STDERR _get_accession_length ($accession);
print STDERR "bp to CONTAINED singleton BAC $bac_name\n";
print STDERR "Bac ref start: $bac_ref_start, end: $bac_ref_end\n";
if ($accession_prefix_orientation eq '+'){
print STDERR "Bac WGS start:",_get_accession_coordinate_5prime ($accession, $bac_ref_start);
print STDERR ", end:",_get_accession_coordinate_5prime ($accession, $bac_ref_end );
print STDERR "\n";
}
elsif($accession_prefix_orientation eq '-'){#count from 3' end
print STDERR "Bac WGS start:",_get_accession_coordinate_3prime ($accession, $bac_ref_start);
print STDERR ", end:",_get_accession_coordinate_3prime ($accession, $bac_ref_end);
print STDERR "\n";

}

if ($accession_prefix_last_base != -1){ #singleton BAC
my $sp_prefix_line = Bio::GenomeUpdate::SP::SPLine->new(
Expand Down Expand Up @@ -1759,7 +1743,6 @@ Returns the length of the accession. Added for use in switchover and trim files
$accession_suffix_first_base = _get_accession_coordinate_5prime ($accession, $bac_ref_end + 1 );
}
elsif($accession_suffix_orientation eq '-'){#count from 3' end
# $accession_suffix_first_base = _get_accession_length ($accession) - _get_accession_coordinate_3prime ($accession, $bac_ref_end + 1 );
$accession_suffix_first_base = _get_accession_coordinate_3prime ($accession, $bac_ref_end + 1 );
}

Expand Down Expand Up @@ -1875,7 +1858,6 @@ Returns the length of the accession. Added for use in switchover and trim files
$accession_suffix_first_base = _get_accession_coordinate_5prime ($accession, $bac_ref_end + 1 );
}
elsif($accession_suffix_orientation eq '-'){#count from 3' end
# $accession_suffix_first_base = _get_accession_length ($accession) - _get_accession_coordinate_3prime ($accession, $bac_ref_end + 1 );
$accession_suffix_first_base = _get_accession_coordinate_3prime ($accession, $bac_ref_end + 1 );
}

Expand Down Expand Up @@ -1985,7 +1967,6 @@ Returns the length of the accession. Added for use in switchover and trim files
$accession_prefix_last_base = _get_accession_coordinate_5prime ($accession, $bac_ref_start - 1 );
}
elsif($accession_prefix_orientation eq '-'){#count from 3' end
# $accession_prefix_last_base = _get_accession_length ($accession) - _get_accession_coordinate_3prime ($accession, $bac_ref_start - 1 );
$accession_prefix_last_base = _get_accession_coordinate_3prime ($accession, $bac_ref_start - 1 );
}
$accession_suffix_first_base = $bac_query_start;
Expand Down Expand Up @@ -2084,7 +2065,7 @@ Returns the length of the accession. Added for use in switchover and trim files

#SHRINK gaps when partially spanned by a BAC
#if BAC start is in the middle of a gap
# $bac_ref_start < $agp_sequence_start works as there is a offset of 1 even if mummer does not align at N
#$bac_ref_start < $agp_sequence_start works as there is a offset of 1 even if mummer does not align at N
if ( $prev_line_key
&& $bac_ref_start < $agp_sequence_start
&& $bac_ref_start > $prev_agp_sequence_end
Expand All @@ -2097,7 +2078,7 @@ Returns the length of the accession. Added for use in switchover and trim files
$gaps_to_resize{$gap_location}." bp w.r.t. original TPF\n";
}
elsif( ($bac_query_end - $bac_query_start + 1) < $bac_query_length ){ #partial BAC aligned to ref
print STDERR "Partial alignment for $bac_name query start: $bac_query_start query end: $bac_query_end\n";
print STDERR "Partial alignment for $bac_name query start: $bac_query_start query end: $bac_query_end. CAN CAUSE Segment too short WARNINGS.\n";
if ( $bac_query_start > 1 ){#fix overhang at begininng
my $bac_start_overhang = $bac_query_start - 1;

Expand Down Expand Up @@ -2126,7 +2107,7 @@ Returns the length of the accession. Added for use in switchover and trim files
$gaps_to_resize{$gap_location}." bp w.r.t. original TPF\n";
}
elsif( ($bac_query_end - $bac_query_start + 1) < $bac_query_length ){ #partial BAC aligned to ref
print STDERR "Partial alignment for $bac_name query start: $bac_query_start query end: $bac_query_end\n";
print STDERR "Partial alignment for $bac_name query start: $bac_query_start query end: $bac_query_end. CAN CAUSE Segment too short WARNINGS.\n";
my $bac_end_overhang = $bac_query_length - $bac_query_end + 1;

$gaps_to_resize{ $line_key - 1 } = $agp_sequence_start - $bac_ref_end - $bac_end_overhang ;
Expand Down Expand Up @@ -2182,7 +2163,7 @@ Returns the length of the accession. Added for use in switchover and trim files
my %line_coords = %$agp_line_coords_ref;
$agp_sequence_start = $line_coords{'start'};
$agp_sequence_end = $line_coords{'end'};
if ( $line_key == 1 ) { #deal with first one
if ( $line_key == 1 ) { #deal with first one
if ( $bac_ref_start <= 0 ) {
$insert_before_or_after = 'before';
$insert_line_number = $line_key;
Expand Down

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