ncbi-hackathons / thehumanpangenome

A Strategy for Building and Using a Human Reference Pangenome

TheHumanPangenome -- Creation of and Toolsets for Human Pangenomic Analysis

The path of GRCh38 through a graph! For details check the DS folder!

https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/DS

A Faster, Better Short-Read Mapper with Hit Chaining. Now with more corn! See the Giraffe folder for details!

https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/Giraffe

Most Genome Annotations can be Imported from gff3 (to ggff!) quite easily! See the annotation folder for details!

https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/annotation

Allele-Specific Expression can be calculated in a lightweight fashion! Grab the workflow in the RNA folder!

https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/RNA

Calculate Mutations In, Outside of, and at Breakpoints of Structural Variants! See the SV folder for Details!

https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/SV/HG002

We Mapped the MHC Region of HG002 to a Graph with Long Reads, Long Reads, 10X and love. Check out the MHC folder!

https://github.com/NCBI-Hackathons/TheHumanPangenome/tree/master/MHC

thehumanpangenome's Issues

Team DS -- where did your images go?

IndexError: string index out of range

Hi,
When I run the maf_to_gfa1.py script to convert alignment.maf to gfa format, but it occurs the following error:

Traceback (most recent call last):
  File "/home/cuixb/tools/biosoft/SibeliaZ-1.2.1/SibeliaZ-LCB/maf_to_gfa1.py", line 177, in <module>
    blocks, sequence = split_maf_blocks(args.maf)
  File "/home/cuixb/tools/biosoft/SibeliaZ-1.2.1/SibeliaZ-LCB/maf_to_gfa1.py", line 102, in split_maf_blocks
    next_profile = profile(maf, next_column)
  File "/home/cuixb/tools/biosoft/SibeliaZ-1.2.1/SibeliaZ-LCB/maf_to_gfa1.py", line 46, in profile
    return [group[i].body[column] == '-' for i in xrange(len(group))]
IndexError: string index out of range

And part of the alignment.maf file:

##maf version=1
# sibeliaz v.1.2.1
# cmd=-f 64 -t 28 -o westar_kale_chrA01 data/westar.fa.split/westar.id_chrA01.fa data/kale.fa.split/kale.id_kale_chrA01.fa

a
s kale_chrA01 19067038 227 + 40689054 GTTTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCCTTTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 18728550 226 + 40689054 >1_1
s kale_chrA01 21852872 224 - 40689054 GTTTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 21847912 224 - 40689054 >1_2
s kale_chrA01 18894209 224 + 40689054 --TTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 18905069 226 + 40689054 >1_3
s kale_chrA01 18937683 224 + 40689054 --TTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 18942636 226 + 40689054 >1_4
s kale_chrA01 21656164 226 - 40689054 --TTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 19062092 225 + 40689054 >1_5
s kale_chrA01 18723593 225 + 40689054 GTTTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 21620759 224 - 40689054 >1_6
s kale_chrA01 21380478 224 - 40689054 --TTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACATGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 21368346 224 - 40689054 >1_7
s kale_chrA01 21317989 224 - 40689054 GTTTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCGGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 21307298 224 - 40689054 >1_8
s kale_chrA01 19477728 226 + 40689054 GTTTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGGTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCCCTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 19488373 226 + 40689054 >1_9
s kale_chrA01 19756575 226 + 40689054 --TTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCCTTTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TT
GCACTAGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s kale_chrA01 20912571 212 - 40689054 >1_10
s chrA01 28065206 226 + 46056803 -TTTACAAGTATTAATAGAGAGAGCACCAAGGAAATTCGAAATGGTTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TTGCACT
AGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCACTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-
s chrA01 27205390 226 + 46056803 >1_11
s chrA01 27210347 200 + 46056803 --TTACAAGTATTAATAGAGAGAGCAACAAGGAAATTCGAAATGGGTAAGCATGTGTAGTCAAAGGACAGGCTGGAACTCC-TTTTGAATCACTTGGCTGTGCTTTCTCACATGC-TTGCACT
AGTAT--AAAGGTAACTTCTCCTTTCCAGCATCATACAGGCTGTC-AAAGTGATCCCTTATCCTTCCTTAACCTCCCTTATCCTCTTTGGTCGAGTTTCCTCTCTTCT-

So, how to solve this error?
Thank you in advance!

Add minimal information, and discussion points to the Haplotype README

@bastienllamas