Malformed MAF output?

[subwaystation]

I tried the following:

Download the current public sequence resource GFA from https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca.
Then I did:

~/software/maffer/git/master/bin/maffer -g public_sequence_resource_22042020.gfa -m > public_sequence_resource_22042020.maf

I installed http://compgen.cshl.edu/phast/ which provides an Ubuntu binary.
Then I ran into:

msa_view public_sequence_resource_22042020.maf > public_sequence_resource_22042020.fasta
warning: maf_read: MAF file must be sorted with respect to reference sequence if store_order=TRUE.  Ignoring out-of-order blocks
ERROR maf_read_subset: invalid idx_offset -2

The last post in glennhickey/progressiveCactus#67 might explain our problem.

Currently also taking a look at https://biopython.org/wiki/Multiple_Alignment_Format, but they do not state, if a conversion to FASTA is possible.

[subwaystation]

So I could only get a FASTA output for each alignment:

from Bio import AlignIO

for multiple_alignment in AlignIO.parse("public_sequence_resource_22042020.maf", "maf"):
    print("printing a new multiple alignment")

    for seqrec in multiple_alignment:
    #    print("starts at %s on the %s strand of a sequence %s in length, and runs for %s bp" % \
    #          (seqrec.annotations["start"],
    #           seqrec.annotations["strand"],
    #           seqrec.annotations["srcSize"],
    #           seqrec.annotations["size"]))
        splitty = seqrec.id.split("/")
        splittty = splitty[3].split(":")
        AlignIO.write(multiple_alignment,
                  "%s.fa" % splittty[1],
                  "fasta")

Which is painfully slow of course......

[subwaystation]

from Bio import AlignIO

abc = AlignIO.parse("public_sequence_resource_22042020.maf", "maf")
AlignIO.write(abc,"public_sequence_resource_22042020.maf.fasta", "fasta")

Blindly does the job we want. I guess.

@ekg We should contact people who actually have to work with the data. You got anyone in mind?

[AndreaGuarracino]

Using

H	VN:Z:1.0
S	1	CAAATAAG
S	2	A
S	3	GCT
S	4	T
S	5	C
S	6	TTG
S	7	A
S	8	G
S	9	AAATTTTCTGGA
S	10	GATTACA
S	11	ATATGCATC
S	12	A
S	13	TCA
S	14	CCAACTCTCTG
P	x	1+,3+,5+,6+,8+,9+,10+,11+,13+,14+	*
P	y	1+,5+,6+,8+,9-,10+,11+,13+,11+,14+	*
L	1	+	3	+	0M
L	3	+	5	+	0M
L	5	+	6	+	0M
L	6	+	8	+	0M
L	8	+	9	+	0M
L	8	+	9	-	0M
L	9	+	10	+	0M
L	9	-	10	+	0M
L	10	+	11	+	0M
L	11	+	13	+	0M
L	11	+	14	+	0M
L	13	+	14	+	0M
L	13	+	11	+	0M

and doing

maffer -g t.gfa -m > t.maf
msa_view t.maf

I have a similar problem

ERROR: bad integers or strand in MAF (strand must be + for reference sequence) --
	"s y 13 12 - 64 AAATTTTCTGGA"

that suggests a malformed MAF output.