Activity for crossmap
-
crossmap released /v0.7.0/version 0.7.0 source code.zip
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Liguo Wang posted a comment on ticket #6
This issue is now fixed in CrossMap v0.3.6.
-
-
Possible fix for alt alleles mapped onto the negative strand
-
Andrew Yates posted a comment on ticket #9
Also FYI you can close issue 2 as this bugfix resolves that issue
-
I've passed 0.3.4 through a flipped position between 37 and 38. The alt allele reverse complements as expected. Thank you!
-
I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version works as you expected.
-
I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version work properly.
-
-
Possible fix for alt alleles mapped onto the negative strand
-
Matthieu posted a comment on ticket #3
I have a similar issue in v0.3.3, where the ref allele is indeed the reverse complement but not the alt allele. command: CrossMap.py vcf chain/hg19ToHg38.over.chain.gz test.3.vcf genomes/Hsapiens/hg38/seq/hg38.fa test.3.hg38.vcf Input: ##fileformat=VCFv4.2 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ALS 15 23102357 . C A . . . GT 0/1 Output: ##fileformat=VCFv4.2 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ALS 15 22770732 . G A . . . GT 0/1 Expected output: ##fileformat=VCFv4.2 #CHROM POS ID REF...
-
-
Jules van Laar created ticket #8
error converting vcf from hg19 to hg38
-
-
-
Yi Hsiao posted a comment on ticket #7
Thanks, god to know. Does this version break support for Python 2 ? Best regards, Leo (Yi Hsiao) Liguo Wang zbfish@users.sourceforge.net於 2018年11月6日 週二，下午11:46寫道： Now CrossMap (v0.3.0) support Python3. Use "pip3 install CrossMap" to install and test it. [tickets:#7] https://sourceforge.net/p/crossmap/tickets/7/ Python3 support* Status: open Milestone: 1.0 Created: Mon Nov 05, 2018 10:31 AM UTC by Yi Hsiao Last Updated: Mon Nov 05, 2018 10:31 AM UTC Owner: nobody Python3 support. 2020 is approaching....
-
Now CrossMap (v0.3.0) supportsPython3. Use "pip3 install CrossMap" to install and test it.
-
Now CrossMap (v0.3.0) support Python3. Use "pip3 install CrossMap" to install and test it.
-
-
Python3 support
-
-
-
-
Nicola Soranzo posted a comment on ticket #6
Works fine if I downgrade pysam to 0.13.0 (I'm using a Conda environment).
-
`CrossMap.py bam` broken with pysam >=0.14
-
Hi, I can get your region properly mapped using your chain file. Did you use the latest version (0.2.7)? $ cat test.bed 1 64231290 64603895 $CrossMap.py BED ~/Downloads/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain test.bed 1 64231290 64603895 -> 1 71417887 71790492 the attached chain_to_table.py can print a chain file into a table which is more human readable.
-
Dan Bolser modified a comment on ticket #5
To be honest, I don't know how to read the chain file format. It's possible it's incorrectly representing our 1-based database data.
-
Hi Liguo, Thanks for getting back to me . The chain file I'm using is here: ftp://ftp.ensemblgenomes.org/pub/current/plants/assembly_chain/sorghum_bicolor/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain.gz Our internal (1-based) database has the following mapping: V2: 64231291 to 64603896 -> V3: 71417888 to 71790493 When I use our assembly converter tool (backed by crossmap) to 'see' this mapping using BED format, inputting this works: 1 64231291 64603896 but if I 'properly' 0-base the bed file:...
-
To be honest, I don't know how to read the chain file format. It's possible it's incorrectly representing our 1-based data.
-
Hi Liguo, Thanks for getting back to me . The chain file I'm using is here: ftp://ftp.ensemblgenomes.org/pub/current/plants/assembly_chain/sorghum_bicolor/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain.gz Our internal (1-based) database has the following mapping: V2: 64231291 to 64603896 -> V3: 71417888 to 71790493 When I use our assembly converter tool (backed by crossmap) to 'see' this mapping using BED format, inputtign this works: 1 64231291 64603896 but if I 'properly' 0-base the bed file:...
-
This error couldn't happen if your bed and chain files follow the specifications. Could you please provide an example?
-
BED off by one projection error.
-
Limei Chiang created ticket #4
If target and query on different strand might cause incorrect coordinate conversion
-
Sophie S posted a comment on ticket #1
It's not as simple as just installing numpy if you have already tried to install bx-python. This is what you need to do: pip uninstall bx-python pip install numpy pip install --no-chache bx-python If you don't do it this way bx-python will install with a cached version of bx-python which means you still won't get bigwig_file. You can install bx-python 0.7.3.
-
-
David Nix posted a comment on ticket #1
OK, must install numpy to get CrossMap to run. pip install numpy
-
Downloaded bx-python-0.7.3.tar.gz, installed via pip: pip install bx-python-0.7.3.tar.gz --upgrade Still getting ImportError: No module named bigwig_file
-
-
Stephane Plaisance posted a comment on ticket #1
Downloading the latest archive from https://pypi.python.org/pypi/bx-python/0.7.3 and installing from file worked for me too, thanks @hmontenegro
-
hmontenegro posted a comment on ticket #1
Ok, it seems the culprit is bx-python: if installed with pip install bx-python, it does not compile some shared libraries. So one needs to download it from PyPI first, then install with pip install bx-python-0.7.3.tar.gz.
-
Roberto posted a comment on ticket #1
I can't install it by none of the methods described above, so I solved this issue by installing CrossMap with pip and an additional copy/paste of bbi directory from another repository. First of all I install normally: $ pip install CrossMap after that I tried to run: $ python /usr/local/bin/CrossMap.py Traceback (most recent call last): File "bin/CrossMap.py", line 21, in <module> from bx.bbi.bigwig_file import BigWigFile ImportError: No module named bigwig_file So I get bbi directory from https://github.com/mikel-egana-aranguren/SADI-Galaxy-Docker/tree/master/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg/bx/bbi...
-
yun-lung li modified a comment on ticket #1
I had the same issue when I did not install numpy in advance. I think the root cause is bx-python will skip compilation of bigwig_file module when numpy is absent. This is how I solve the issue in fresh docker:14.04 environment: $ apt-get update $ apt-get install -y python-dev libbz2-dev liblzma-dev python-pip zlib1g-dev $ pip install Cython --install-option="--no-cython-compile" pysam numpy CrossMap $ python /usr/local/bin/CrossMap.py
-
I have the same issue when I did install numpy in advance. I think the root cause is bx-python will skip compilation of bigwig_file module when numpy is absent. This is how I solve the issue in fresh docker:14.04 environment: $ apt-get update $ apt-get install -y python-dev libbz2-dev liblzma-dev python-pip zlib1g-dev $ pip install Cython --install-option="--no-cython-compile" pysam numpy CrossMap $ python /usr/local/bin/CrossMap.py
-
jiaxing wang posted a comment on ticket #1
I also have the same issue Is there any solution right now? Thanks JW
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
