Activity for crossmap

crossmap released /v0.7.0/version 0.7.0 source code.zip

crossmap — Fri, 12 Jan 2024 03:11:02 -0000

crossmap released /v0.7.0/version 0.7.0 source code.tar.gz

crossmap — Fri, 12 Jan 2024 03:11:02 -0000

crossmap released /v0.7.0/README.md

crossmap — Fri, 12 Jan 2024 03:11:02 -0000

crossmap released /v0.6.5/v0.6.5.zip

crossmap — Fri, 02 Dec 2022 15:42:02 -0000

crossmap released /v0.6.5/v0.6.5.tar.gz

crossmap — Fri, 02 Dec 2022 15:42:02 -0000

crossmap released /v0.6.5/README.md

crossmap — Fri, 02 Dec 2022 15:42:02 -0000

crossmap released /v0.6.4/version 0.6.4.zip

crossmap — Tue, 12 Jul 2022 14:54:02 -0000

crossmap released /v0.6.4/version 0.6.4.tar.gz

crossmap — Tue, 12 Jul 2022 14:54:02 -0000

crossmap released /v0.6.4/README.md

crossmap — Tue, 12 Jul 2022 14:54:02 -0000

crossmap released /v0.6.3/version 0.6.3.zip

crossmap — Sat, 05 Mar 2022 04:25:03 -0000

crossmap released /v0.6.3/version 0.6.3.tar.gz

crossmap — Sat, 05 Mar 2022 04:25:03 -0000

crossmap released /v0.6.3/README.md

crossmap — Sat, 05 Mar 2022 04:25:03 -0000

crossmap released /v0.6.1/version 0.6.1.zip

crossmap — Tue, 30 Nov 2021 16:32:17 -0000

crossmap released /v0.6.1/version 0.6.1.tar.gz

crossmap — Tue, 30 Nov 2021 16:32:17 -0000

crossmap released /v0.6.1/README.md

crossmap — Tue, 30 Nov 2021 16:32:17 -0000

crossmap released /v0.6.0/CrossMap-0.6.0.tar.gz

crossmap — Tue, 23 Nov 2021 15:50:04 -0000

crossmap released /v0.6.0/version 0.6.0.tar.gz

crossmap — Tue, 23 Nov 2021 15:50:04 -0000

crossmap released /v0.6.0/version 0.6.0.zip

crossmap — Tue, 23 Nov 2021 15:50:04 -0000

crossmap released /v0.6.0/README.md

crossmap — Tue, 23 Nov 2021 15:50:04 -0000

crossmap released /0.5.3/version 0.5.3.zip

crossmap — Sat, 17 Apr 2021 01:15:02 -0000

crossmap released /0.5.3/version 0.5.3.tar.gz

crossmap — Sat, 17 Apr 2021 01:15:02 -0000

crossmap released /0.5.3/README.md

crossmap — Sat, 17 Apr 2021 01:15:02 -0000

crossmap released /CrossMap-0.4.2.tar.gz

crossmap — Thu, 09 Jul 2020 22:58:05 -0000

crossmap released /CrossMap-0.4.0.tar.gz

crossmap — Tue, 24 Mar 2020 16:33:03 -0000

crossmap released /CrossMap-0.4.1.tar.gz

crossmap — Tue, 24 Mar 2020 16:26:04 -0000

crossmap released /v0.3.9/version 0.3.9.zip

crossmap — Thu, 14 Nov 2019 19:47:02 -0000

crossmap released /v0.3.9/version 0.3.9.tar.gz

crossmap — Thu, 14 Nov 2019 19:47:02 -0000

crossmap released /v0.3.9/README.md

crossmap — Thu, 14 Nov 2019 19:47:02 -0000

crossmap released /CrossMap-0.3.8.tar.gz

crossmap — Thu, 14 Nov 2019 19:42:04 -0000

crossmap released /v0.3.9/version 0.3.9.zip

crossmap — Thu, 14 Nov 2019 19:41:53 -0000

crossmap released /v0.3.9/README.md

crossmap — Thu, 14 Nov 2019 19:41:53 -0000

crossmap released /v0.3.9/version 0.3.9.tar.gz

crossmap — Thu, 14 Nov 2019 19:41:53 -0000

crossmap released /CrossMap-0.3.9.tar.gz

crossmap — Thu, 14 Nov 2019 19:41:53 -0000

crossmap released /CrossMap-0.3.8.tar.gz

crossmap — Thu, 14 Nov 2019 19:14:02 -0000

crossmap released /CrossMap-0.3.9.tar.gz

crossmap — Thu, 14 Nov 2019 19:13:02 -0000

crossmap released /CrossMap-0.3.7.tar.gz

crossmap — Wed, 21 Aug 2019 14:45:03 -0000

crossmap released /CrossMap-0.3.6.tar.gz

crossmap — Mon, 22 Jul 2019 19:36:02 -0000

Liguo Wang posted a comment on ticket #6

Liguo Wang — Mon, 22 Jul 2019 18:41:16 -0000

This issue is now fixed in CrossMap v0.3.6.

crossmap released /CrossMap-0.3.5.tar.gz

crossmap — Thu, 11 Jul 2019 19:05:05 -0000

Liguo Wang modified ticket #9

Liguo Wang — Tue, 02 Apr 2019 15:55:55 -0000

Possible fix for alt alleles mapped onto the negative strand

Andrew Yates posted a comment on ticket #9

Andrew Yates — Tue, 02 Apr 2019 15:48:15 -0000

Also FYI you can close issue 2 as this bugfix resolves that issue

Andrew Yates posted a comment on ticket #9

Andrew Yates — Tue, 02 Apr 2019 15:47:23 -0000

I've passed 0.3.4 through a flipped position between 37 and 38. The alt allele reverse complements as expected. Thank you!

Liguo Wang modified a comment on ticket #9

Liguo Wang — Tue, 02 Apr 2019 01:13:31 -0000

I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version works as you expected.

Liguo Wang posted a comment on ticket #9

Liguo Wang — Tue, 02 Apr 2019 01:12:54 -0000

I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version work properly.

crossmap released /CrossMap-0.3.4.tar.gz

crossmap — Mon, 01 Apr 2019 18:18:03 -0000

Andrew Yates created ticket #9

Andrew Yates — Thu, 28 Mar 2019 13:17:59 -0000

Possible fix for alt alleles mapped onto the negative strand

Matthieu posted a comment on ticket #3

Matthieu — Sun, 10 Mar 2019 17:47:07 -0000

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...

crossmap released /CrossMap-0.3.3.tar.gz

crossmap — Mon, 07 Jan 2019 17:36:02 -0000

Jules van Laar created ticket #8

Jules van Laar — Mon, 17 Dec 2018 21:49:58 -0000

error converting vcf from hg19 to hg38

crossmap released /CrossMap-0.3.2.tar.gz

crossmap — Fri, 14 Dec 2018 17:17:02 -0000

crossmap released /CrossMap-0.3.1.tar.gz

crossmap — Fri, 16 Nov 2018 21:04:02 -0000

Yi Hsiao posted a comment on ticket #7

Yi Hsiao — Tue, 06 Nov 2018 16:48:43 -0000

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....

Liguo Wang modified a comment on ticket #7

Liguo Wang — Tue, 06 Nov 2018 15:47:27 -0000

Now CrossMap (v0.3.0) supportsPython3. Use "pip3 install CrossMap" to install and test it.

Liguo Wang posted a comment on ticket #7

Liguo Wang — Tue, 06 Nov 2018 15:46:12 -0000

Now CrossMap (v0.3.0) support Python3. Use "pip3 install CrossMap" to install and test it.

crossmap released /CrossMap-0.3.0.tar.gz

crossmap — Tue, 06 Nov 2018 06:22:03 -0000

Yi Hsiao created ticket #7

Yi Hsiao — Mon, 05 Nov 2018 10:31:09 -0000

Python3 support

crossmap released /CrossMap-0.2.9.tar.gz

crossmap — Thu, 23 Aug 2018 19:49:03 -0000

crossmap released /README.txt

crossmap — Tue, 03 Jul 2018 17:56:05 -0000

crossmap released /CrossMap-0.2.8.tar.gz

crossmap — Tue, 03 Jul 2018 16:19:03 -0000

Nicola Soranzo posted a comment on ticket #6

Nicola Soranzo — Thu, 24 May 2018 21:40:01 -0000

Works fine if I downgrade pysam to 0.13.0 (I'm using a Conda environment).

Nicola Soranzo created ticket #6

Nicola Soranzo — Thu, 24 May 2018 21:38:19 -0000

`CrossMap.py bam` broken with pysam >=0.14

Liguo Wang posted a comment on ticket #5

Liguo Wang — Mon, 26 Mar 2018 14:16:15 -0000

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

Dan Bolser — Fri, 23 Mar 2018 09:05:12 -0000

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.

Dan Bolser modified a comment on ticket #5

Dan Bolser — Fri, 23 Mar 2018 09:03:36 -0000

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:...

Dan Bolser posted a comment on ticket #5

Dan Bolser — Fri, 23 Mar 2018 08:59:58 -0000

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.

Dan Bolser posted a comment on ticket #5

Dan Bolser — Fri, 23 Mar 2018 08:58:08 -0000

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:...

Liguo Wang posted a comment on ticket #5

Liguo Wang — Thu, 22 Mar 2018 14:43:03 -0000

This error couldn't happen if your bed and chain files follow the specifications. Could you please provide an example?

Dan Bolser created ticket #5

Dan Bolser — Thu, 22 Mar 2018 13:13:30 -0000

BED off by one projection error.

Limei Chiang created ticket #4

Limei Chiang — Thu, 15 Mar 2018 16:10:10 -0000

If target and query on different strand might cause incorrect coordinate conversion

Sophie S posted a comment on ticket #1

Sophie S — Wed, 31 Jan 2018 18:34:17 -0000

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.

crossmap released /chain_files/GRCh37ToHg19.over.chain.gz

crossmap — Fri, 15 Dec 2017 17:23:04 -0000

David Nix posted a comment on ticket #1

David Nix — Fri, 06 Oct 2017 15:22:25 -0000

OK, must install numpy to get CrossMap to run. pip install numpy

David Nix posted a comment on ticket #1

David Nix — Fri, 06 Oct 2017 15:04:22 -0000

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

crossmap released /CrossMap-0.2.7.tar.gz

crossmap — Thu, 07 Sep 2017 04:03:02 -0000

Stephane Plaisance posted a comment on ticket #1

Stephane Plaisance — Mon, 03 Jul 2017 10:09:15 -0000

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

hmontenegro — Tue, 13 Jun 2017 22:22:25 -0000

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

Roberto — Tue, 13 Jun 2017 20:30:38 -0000

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 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

yun-lung li — Fri, 02 Jun 2017 03:17:53 -0000

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

yun-lung li posted a comment on ticket #1

yun-lung li — Fri, 02 Jun 2017 03:17:08 -0000

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

jiaxing wang — Fri, 26 May 2017 13:17:56 -0000

I also have the same issue Is there any solution right now? Thanks JW

crossmap released /CrossMap-0.2.6.tar.gz

crossmap — Wed, 10 May 2017 17:32:05 -0000

crossmap released /Ensembl_chain_files/homo_sapiens(human)/README.txt

crossmap — Tue, 09 May 2017 20:09:22 -0000

crossmap released /Ensembl_chain_files/homo_sapiens(human)/GRCh38_to_NCBI34.chain.gz