Print fasta of query seqs that did not align

find way to include paths of lib modules in scripts that call them without hardcoding them.

Columns for Trim curation file:

• Taxid (value (Solanum lycopersicum)=4081)
• AssmGrp (value=TGP)
• AssmUnit (value=Primary)
• Chr (values=1-12, Un)
• TPFType (values=chromosome, contig)
• Acc.ver
• TrimPos (1-based; first or last base used in AGP)
• FromEnd (values = L, H; L: trim bases with values lt TrimPos; H: trim bases with values gt TrimPos)
• Comment

Create new classes

Check AlignCoordGroup.pm

sample nucmer output

18361542 18377740 1 16206 16199 16206 99.94 70787664 203766 0.02 7.95 1 1 SL2.50ch03 Contig90
53614018 53614614 17944 17348 597 597 99.66 70787664 203766 0.00 0.29 1 -1 SL2.50ch03 Contig90

500bp.mixedoutoforder.agp.group_coords.stdout

Contig90 SL2.50ch03 18361542 18564072 202530 1 203766 203766 154944 1 1 0 Contains 0 0 48822 0 596 SL2.50ch03:597:53614018:53614614

The location is relative to the original TPF line but multiple insertions are done with respect to the original line number, not the new location. Need to maintain a separate offset counter for 'before' and 'after' insertions for each original TPF line.

See Jeremy's controller code

Maybe move .PL /scripts into scripts dir. Only if history is preserved.

Print filtered delta output file without the BACs that are aligned out of order.

nof components
nof gaps
avg, std dev
% covered by components and gaps

Add methods AlignmentCoordsGroup.pm. Removing BAC alignments that align in non co-linear order to ref chr.

get_tpf_with_bacs_inserted

The problem is that mummer does not report alignments to N's so BAC regions that extend beyond the WGS contig are not considered. Need to compute "overhangs" from BAC length and seq_in_clusters.

Needed for BAC alignments to all chrs.
Fix get_gap_overlap()
Then remove err msg from align_BACends_group_coords.pl and test

query BAC aligns to both + and - strand of ref chr

Align BACs to all chrs and validate if they align to only the chr they belong to. If not, add them to the no_chr set.

File: query_bacends.fasta

-r Fasta file of reference (required)
-q Fasta file of query (assembled and singleton BACs, required)
-c Contig or component AGP file for reference (includes scaffold gaps)
-s Chromosome AGP file for reference (with only scaffolds and gaps)

Modify copy_updated_coordinates_to_vcf to sort -V its output file so that features end up in correct order and are ready for compression and display in jbrowse.

Attribute (accession_prefix_last_base) does not pass the type constraint because: The string, -1, was not a positive coordinate at /usr/local/lib/x86_64-linux-gnu/perl/5.20.2/Moose/Object.pm line 24
Moose::Object::new('Bio::GenomeUpdate::SP::SPLine', 'chromosome', 10, 'accession_prefix', 'AEKE02007654', 'accession_suffix', 'AC239654', 'accession_prefix_orientation', '-', 'accession_suffix_orientation', '+', 'accession_prefix_last_base', -1, 'accession_suffix_first_base', 1, 'comment', 'BAC AC239654 is contained within WGS contig AEKE02007654 from previous version. Designates switch point from WGS contig to BAC.') called at /home/surya/work/Eclipse/Bio-GenomeUpdate/lib/Bio/GenomeUpdate/TPF.pm line 1628

Columns for switch point curation file:

• Taxid (value (Solanum lycopersicum)=4081)
• AssmGrp (value=TGP)
• AssmUnit (value=Primary)
• Chr (values=1-12, Un)
• TPFType (values=chromosome, contig (latter used for unlocalized or unplaced scaffolds, see TPF spec))
• Acc.ver1
• Acc.ver2
• Orient1 (orientation of acc.ver1 in AGP)
• Orient2 (orientation of acc.ver2 in AGP)
• Point1 (1-based, last base of acc.ver1 to be used in AGP)
• Point2 (1-based, first base of acc.ver2 to be used in AGP)
• Comment (req’d, min 25 char)

Contig 469 for Chr 10 represented by the following TPF lines
AC244937 ? SL2.50sc05925 MINUS
AC244803 ? SL2.50sc05925 PLUS
AC244944 ? SL2.50sc05925 PLUS
AC254768 ? SL2.50sc05925 MINUS

Can be
AC244937 ? SL2.50sc05925 MINUS
AC244944 ? SL2.50sc05925 PLUS
AC254768 ? SL2.50sc05925 MINUS

Check using GRC tpf_solo pipeline.

AEKE02023669 ? SL2.50sc05925 MINUS
AC244870 ? SL2.50sc05925 PLUS
AC244937 ? SL2.50sc05925 MINUS contig469
AC244803 ? SL2.50sc05925 PLUS contig469
AC244944 ? SL2.50sc05925 PLUS contig469
AC254768 ? SL2.50sc05925 MINUS contig469
AEKE02023661 ? SL2.50sc05925 MINUS

Contig469_right_1000 aligns to -ive AEKE02023661.1
Contig469_right_1000 aligns to -ive end of AC244937
Contig469_left_1000 aligns to -ive end of AC254768
Contig469_left_1000 aligns to middle of AC244870

Correct order
AEKE02023669 ? SL2.50sc05925 MINUS
AC244870 ? SL2.50sc05925 PLUS
AC254768 ? SL2.50sc05925 MINUS contig469
AC244944 ? SL2.50sc05925 PLUS contig469
AC244803 ? SL2.50sc05925 PLUS contig469
AC244937 ? SL2.50sc05925 MINUS contig469
AEKE02023661 ? SL2.50sc05925 MINUS

68kb 99% identical alignment between AC244870 and AC254768
9.2kb 99% identical alignment between AC244937 and AEKE02023661

Is it required???

TPF spec v1.8 added biological feature in a non-sequence line (centromere or heterochromatin).

Should be able to read in set of AGP/TPF files and produce tabular report

Will be substituted in for "ContigX" placeholder from the group_coords sdtout.

uniq in mixed, outoforder
common in both_errors

add #,length of gaps covered for components/contigs and scaffolds to groupcoords report

Use 500 1 convention of nucmer

-t <TPF_file> Original TPF file (mandatory)
-s scaffold AGP file (mandatory)
-c chromosome AGP file (mandatory)

Should include switch over cases. For testing GFF -> TPF pipeline for bld 3.0